Diego P Morgavi

Milka Popova

David Yáñez-Ruiz

Colonization and establishment of the rumen microbiota -opportunities to influence productivity and methane emissions

come   L'archive ouverte pluridisciplinaire

development of the GIT microbiota starts in earnest at birth and it is characterized by a succession of dynamic communities in the early stages of life [START_REF] Savage | Microbial ecology of the gastrointestinal tract[END_REF][START_REF] Jami | Exploring the bovine rumen bacterial community from birth to adulthood[END_REF][START_REF] Rey | Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential[END_REF]. This process of acquisition of various microbial populations and their evolution within the ecosystem is essential for the correct functioning and interaction of the microbiota with the host [START_REF] Costello | The application of ecological theory toward an understanding of the human microbiome[END_REF].

Determinism is a strong driver dictating the microbial community structure of the GIT of animals as there is a strong selection by the diet, anatomy and gut physico-chemical conditions [START_REF] Ley | Worlds within worlds: evolution of the vertebrate gut microbiota[END_REF]). Yet, stochastic and historical events also influence the assemblage of the GIT microbiota that may have lasting effects in ruminants [START_REF] Yáñez-Ruiz | The persistence of bacterial and methanogenic archaeal communities residing in the rumen of young lambs[END_REF][START_REF] Morgavi | Rumen microbial communities influence metabolic phenotypes in lambs[END_REF][START_REF] Moraïs | The road not taken: the rumen microbiome, functional groups, and community states[END_REF]. Here, we review current information in the establishment of the microbiota in the rumen and posterior intestinal tract in young ruminants and its modulation for promoting health and favouring desirable phenotypes.

Establishment of the rumen microbiota

As the composition of the rumen microbiota directly influences the digestive and metabolic performance of the host animal, many studies have explored the microbial colonization of the rumen from birth to adulthood. These include early work using cultural methods [START_REF] Fonty | Ecological factors determining establishment of cellulolytic bacteria and protozoa in the rumens of meroxenic lambs[END_REF][START_REF] Fonty | Establishment of ciliate protozoa in the rumen of conventional and conventionalized lambs: influence of diet and management conditions[END_REF] to more recent studies using high throughput sequencing methods in calves, lambs and goats [START_REF] Jami | Exploring the bovine rumen bacterial community from birth to adulthood[END_REF][START_REF] Rey | Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential[END_REF][START_REF] Guzman | Presence of selected methanogens, fibrolytic bacteria, and proteobacteria in the gastrointestinal tract of neonatal dairy calves from birth to 72 hours[END_REF], Wang et al., 2017b[START_REF] Abecia | Analysis of the rumen microbiome and metabolome to study the effect of an antimethanogenic treatment applied in early life of kid goats[END_REF][START_REF] Dias | Bacterial community dynamics across the gastrointestinal tracts of dairy calves during preweaning development[END_REF]. The developing rumen in the newborn ruminant may provide a unique opportunity to manipulate the symbiotic microbiota for a long-lasting impact in the adult ruminant [START_REF] Yanez-Ruiz | Manipulating rumen microbiome and fermentation through interventions during early life: a review[END_REF].

Colonisation: from birth (preruminant) to a fully functional rumen Recent reviews describe the microbial community successions that occur in the rumen from birth to weaning and after, when animals feed exclusively on solid feeds [START_REF] Malmuthuge | The gut microbiome and its potential role in the development and function of newborn calf gastrointestinal tract[END_REF][START_REF] Yanez-Ruiz | Manipulating rumen microbiome and fermentation through interventions during early life: a review[END_REF], Meale et al., 2017a). Functional populations, as well as taxa present in adult rumens, appear very early after birth, in a progressive way and a defined sequence. Several studies monitored the establishment of the rumen bacterial community in calves from birth to weaning using high throughput sequencing and qPCR approaches [START_REF] Jami | Exploring the bovine rumen bacterial community from birth to adulthood[END_REF][START_REF] Rey | Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential[END_REF][START_REF] Guzman | Presence of selected methanogens, fibrolytic bacteria, and proteobacteria in the gastrointestinal tract of neonatal dairy calves from birth to 72 hours[END_REF]. They show that rapid changes occur in the composition of the rumen bacterial community during the first days of life. Proteobacteria and Streptococcus-related sequences are proportionally abundant in 1 to 3-day old calves and are rapidly replaced by strictly anaerobic bacterial taxa [START_REF] Jami | Exploring the bovine rumen bacterial community from birth to adulthood[END_REF]. Proteobacteria are then gradually replaced by Bacteroidetes as the animal grows, Firmicutes being present from early age to adulthood (Table 1). These results are in accordance with early studies using culture techniques reporting that aerobic and facultative anaerobic bacteria establish first [START_REF] Fonty | Establishment of the microflora and anaerobic fungi in the rumen of lambs[END_REF]. Notwithstanding, strict anaerobes that are important for function in the mature rumen, such as cellulolytic bacteria and methanogenic archaea are already present in the rumen 1 or 2 days after birth [START_REF] Fonty | Establishment of the microflora and anaerobic fungi in the rumen of lambs[END_REF][START_REF] Gagen | Methanogen colonisation does not significantly alter acetogen diversity in lambs isolated 17 h after birth and raised aseptically[END_REF][START_REF] Jami | Exploring the bovine rumen bacterial community from birth to adulthood[END_REF][START_REF] Guzman | Presence of selected methanogens, fibrolytic bacteria, and proteobacteria in the gastrointestinal tract of neonatal dairy calves from birth to 72 hours[END_REF]. Methanogenic archaea can be enumerated in the immature rumen of lambs at 2-4 days, well before the consumption of solid feeds, and after two weeks, their concentration is equivalent to that found in adult animals [START_REF] Fonty | Establishment of the microflora and anaerobic fungi in the rumen of lambs[END_REF][START_REF] Morvan | Establishment of hydrogen-utilizing bacteria in the rumen of the newborn lamb[END_REF].

Although not detected by culture, a low-abundant but diverse population of methanogens (predominantly Methanobrevibacter spp.) was identified using molecular methods in lambs placed into sterile isolators 17 h after birth [START_REF] Gagen | Methanogen colonisation does not significantly alter acetogen diversity in lambs isolated 17 h after birth and raised aseptically[END_REF]. A recent study in goat kids also indicated that active methanogens colonized the rumen at one day of life, Methanobrevibacter, Methanosphaera (both Methanobacteriales order) and Candidatus Methanomethylophilus (Methanomassiliicoccales order) being the top three genera (Wang et al., 2017b). There are four major methanogenic orders usually found in the rumen: Methanobacteriales, Methanomicrobiales, Methanosarcinales and Methanomassiliicoccales [START_REF] Janssen | Structure of the archaeal community of the rumen[END_REF]. All these are abundantly present in calves from day 1 to 2 weeks of age, whereas only Methanobacteriales and Methanomassiliicoccales could be qPCR-detected in the mature rumen [START_REF] Friedman | Compositional and functional dynamics of the bovine rumen methanogenic community across different developmental stages[END_REF].

Based on substrate utilisation for methanogenesis, the authors suggest that the early methanogenic community may be characterized by a high activity of methylotrophic methanogenesis, likely performed by members of the order Methanosarcinales. Eukaryotic microorganisms also establish sequentially. Anaerobic fungi can be enumerated in the rumen of lambs by 8-10 days after birth [START_REF] Fonty | Establishment of the microflora and anaerobic fungi in the rumen of lambs[END_REF]. Anaerobic fungi, which are cellulolytic, are thus present in the rumen long before the animal ingests solid feeds regularly. Ciliates are detected from 2 to 3 weeks of age, with Entodinium establishing first (15-20 days), then Polyplastron,Eudiplodinium,, and finally Isotricha (50 days) [START_REF] Fonty | Establishment of ciliate protozoa in the rumen of conventional and conventionalized lambs: influence of diet and management conditions[END_REF]. In contrast to bacteria and archaea, protozoa do not establish when newborns are isolated from their dams shortly after birth [START_REF] Fonty | Establishment of ciliate protozoa in the rumen of conventional and conventionalized lambs: influence of diet and management conditions[END_REF]Chaucheyras-Durand et al, personal communication). In addition, ciliate protozoa require the presence of a complex microbiota to establish [START_REF] Fonty | Ecological factors determining establishment of cellulolytic bacteria and protozoa in the rumens of meroxenic lambs[END_REF][START_REF] Fonty | Establishment of ciliate protozoa in the rumen of conventional and conventionalized lambs: influence of diet and management conditions[END_REF]. Figure 1 shows the main colonization events by groups of microbes in lamb's rumen throughout the suckling period and up to the end of weaning.

Colonization of the rumen wall by epimural bacteria is also age-related, with sequential diversification of bacterial morphotypes [START_REF] Rieu | Electron microscopy study of the bacteria adherent to the rumen wall in young conventional lambs[END_REF]. The phylum Proteobacteria is dominant on the rumen epithelium with an important contribution of the genus Escherichia [START_REF] Jiao | Rumen development process in goats as affected by supplemental feeding v. grazing: age-related anatomic development, functional achievement and microbial colonisation[END_REF], Wang et al., 2017a). As for the lumen, the abundance of Proteobacteria associated with rumen epithelium decreases, and that of Firmicutes and Bacteroidetes increases with age [START_REF] Jiao | Rumen development process in goats as affected by supplemental feeding v. grazing: age-related anatomic development, functional achievement and microbial colonisation[END_REF].

Large differences between digesta and epimural bacterial communities have been observed in the rumen of pre-weaned calves, with higher abundances of Prevotella and lower abundances of Bacteroidetes in digesta compared with epimural bacteria [START_REF] Malmuthuge | Taxonomic identification of commensal bacteria associated with the mucosa and digesta throughout the gastrointestinal tracts of preweaned calves[END_REF].

Although the focus of this review is on the rumen compartment, we will mention some aspects of the microbiota of other GIT sections when relevant and/or available. Whilst the rumen microbial community evolution with age has been well studied, information on the other pre-gastric compartments (reticulum and omasum) is scarce. Recent studies analysed fluid samples from these organs in goats from 3 to 56 days after birth [START_REF] Lei | Exploring the Spatial-Temporal Microbiota of Compound Stomachs in a Pre-weaned Goat Model[END_REF] or in calves from birth to 21 days [START_REF] Yeoman | Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract[END_REF]. As for the rumen, Proteobacteria gradually decrease with age while the relative abundance of Bacteroidetes increases.

For the post-gastric compartments, a surprisingly diverse microbiota is also described in the first hours post-delivery [START_REF] Alipour | The composition of the perinatal intestinal microbiota in cattle[END_REF]. Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes dominate the newborn's rectal microbiota but composition rapidly changes in the early postnatal life. Pioneer studies reported E. coli and Streptococcus to be the firsts to colonise all GIT regions in calves and lambs few hours after birth [START_REF] Smith | The development of the flora of the alimentary tract in young animals[END_REF] and culture-independent studies confirmed their high abundance in rectal microbiota one day after birth [START_REF] Alipour | The composition of the perinatal intestinal microbiota in cattle[END_REF]. As for the rumen [START_REF] Jami | Exploring the bovine rumen bacterial community from birth to adulthood[END_REF], it is assumed that these facultative anaerobes scavenge oxygen and render the environment suitable for strictly anaerobic gut microbes. Lactobacilli take advantage of these conditions and colonise all intestinal sections of one-day-old ruminants [START_REF] Smith | The development of the flora of the alimentary tract in young animals[END_REF].

Proteobacteria, Firmicutes and Bacteroidetes are the prevalent phyla in all anatomical locations within the first 3 weeks of life [START_REF] Malmuthuge | Taxonomic identification of commensal bacteria associated with the mucosa and digesta throughout the gastrointestinal tracts of preweaned calves[END_REF][START_REF] Alipour | The composition of the perinatal intestinal microbiota in cattle[END_REF][START_REF] Yeoman | Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract[END_REF].

Firmicutes dominate distal parts of the GIT in young ruminants (colon and faeces), whereas Bacteroidetes abundance is higher in the reticulum, rumen, omasum and abomasum [START_REF] Malmuthuge | Taxonomic identification of commensal bacteria associated with the mucosa and digesta throughout the gastrointestinal tracts of preweaned calves[END_REF][START_REF] Yeoman | Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract[END_REF]. It should be noted that while Firmicutes and Bacteroidetes are more abundant in luminal contents, Proteobacteria dominate mucosal samples [START_REF] Yeoman | Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract[END_REF]. This niche specialisation for mucosa-associated populations is certainly driven by environmental conditions (presence of trace oxygen) and available substrates such as mucins.

Interestingly, richness and α-diversity in luminal samples increase with age in most anatomical sections, whereas no such trend is observed for mucosa-associated populations. Nevertheless, mucosa-associated bacterial communities in the small and large intestine are more diverse than digesta-associated communities [START_REF] Malmuthuge | Taxonomic identification of commensal bacteria associated with the mucosa and digesta throughout the gastrointestinal tracts of preweaned calves[END_REF]. Though the post-gastric intestinal tract has not received much attention this far, there is evidence that its microbiota plays a crucial role in older animals' health and performance. For instance, lactic acid bacteria increase IgA production by stimulating host's adaptive immune system, boosting calves' active immunity by the time when passive immunity from colostrum decline [START_REF] Corthésy | Cross-talk between probiotic bacteria and the host immune system[END_REF].

Interaction host-microbiota

The gastrointestinal tract of mammals has a diverse array of non-specific and specific protective mechanisms to allow it to coexist with resident microbiota [START_REF] Hooper | Interactions between the microbiota and the immune system[END_REF]. The functions of nutrients absorption, symbiotic microbial tolerance and pathogenic microbial barrier, create a conflict in function which requires a complex system of physical, biochemical and cellular mechanisms for protecting the gastro-intestinal epithelium and the host against invading agents [START_REF] Kuhn | Peripheral education of the immune system by the colonic microbiota[END_REF]. Several studies have shown the education process that the immune system needs to go through to deal with microbial loads and this is of particular relevance during early life stages (Collado et al., 2012, Wu and[START_REF] Wu | The role of gut microbiota in immune homeostasis and autoimmunity[END_REF]. However, the mechanisms involved in the 'tolerance' to the first colonizers of the rumen are largely unknown, partly because the rumen epithelial structure has its own peculiarities as compared to the lower intestinal tract. The rumen has a multi-strated, keratinized epithelium with up to 15 cells layer and no organized lymphoid tissue [START_REF] Sharpe | The immune response of the host animal to bacteria in the rumen and caecum[END_REF], which limits the permeability of large molecules such as immunoglobulins. The immunological equilibrium in the rumen is thought to be achieved by a combination of two main mechanisms: i) the signalling of Toll-like receptors (TLRs) [START_REF] Malmuthuge | Regional and age dependent changes in gene expression of Toll-like receptors and key antimicrobial defence molecules throughout the gastrointestinal tract of dairy calves[END_REF] and ii) provision of immunoglobulins (mainly secretory IgA) via saliva [START_REF] Williams | A vaccine against rumen methanogens can alter the composition of archaeal populations[END_REF]. i) TLRs are a family of pattern recognition receptors (PRRs) that play a key role at mucosal surfaces by acting as sensors to detect molecular patterns expressed by both pathogenic and commensal microbiota alike. Cattle express a similar repertoire of TLRs compared with other mammalian species, as TLR1-10 have been identified and characterized [START_REF] Mcguire | Radiation hybrid mapping of all 10 characterized bovine Toll-like receptors[END_REF] and several studies have shown the relationship between nutritional disturbances (i.e. acidosis) and TLR expression levels. [START_REF] Chen | Variation of bacterial communities and expression of Toll-like receptor genes in the rumen of steers differing in susceptibility to subacute ruminal acidosis[END_REF]. However, little is known in relation to early-life colonization.

The expression of TLR in the GIT of newborn calves is greater than at 6 months of age with the exception of TLR-1 and TLR-3 [START_REF] Malmuthuge | Regional and age dependent changes in gene expression of Toll-like receptors and key antimicrobial defence molecules throughout the gastrointestinal tract of dairy calves[END_REF]. More recently, [START_REF] Abecia | Natural and artificial feeding management before weaning promote different rumen microbial colonization but not differences in gene expression levels at the rumen epithelium of newborn goats[END_REF] evaluated the impact of two different management practices in the early life of goat kids (maternal vs. artificial milk feeding) on the immune response of the rumen. They observed that TLRs 1, 2, 5, 8 and 10 displayed an age-dependent expression, consisting of increased gene expression between days 5 and 7 of life and then a subsequent decrease and stabilization. The increase in expression coincided with a rise in VFA concentration and microbial biomass colonization. However, although colonization continued in the following days, this did not trigger higher expression levels. This is in agreement with reports showing down regulation of TLR expression levels in the blood of newborns with increasing age, whereas memory T cells increased in number [START_REF] Teran | Immune system development during early childhood in tropical Latin America: Evidence for the age-dependent down regulation of the innate immune response[END_REF][START_REF] Malmuthuge | Regional and age dependent changes in gene expression of Toll-like receptors and key antimicrobial defence molecules throughout the gastrointestinal tract of dairy calves[END_REF]. The down-regulation of TLR activity might also be promoted by the production of butyrate that enhanced barrier function through stable tight junctions signalling [START_REF] Jiao | Shifts in host mucosal innate immune function are associated with ruminal microbial succession in supplemental feeding and grazing goats at different ages[END_REF]. Therefore, the few available published studies suggest that down-regulation with increasing age might be one mechanism by which the host avoids unnecessary inflammatory responses to commensal microbiota.

In suckling calves fed raw milk, the expression of IL-8, IL-10 and claudin-4 in the mucosa of the colon was low compared to calves of the same age fed heat-treated milk [START_REF] Bach | Influence of milk processing temperature on growth performance, nitrogen retention, and hindgut's inflammatory status and bacterial populations in a calf model[END_REF]. These calves fed raw milk had a higher Lactobacilli population suggesting that the down-regulation observed with increasing age mentioned above is associated with a more developed microbiota.

ii) Immunoglobulins find their way into the rumen mainly through saliva, particularly IgA that is the major Ig secreted in saliva and also the dominant type in the rumen [START_REF] Subharat | Vaccination of cattle with a methanogen protein produces specific antibodies in the saliva which are stable in the rumen[END_REF][START_REF] Abecia | Natural and artificial feeding management before weaning promote different rumen microbial colonization but not differences in gene expression levels at the rumen epithelium of newborn goats[END_REF]. IgA is apparently more resistant to degradation in the rumen compared to IgG, possibly because the secretory component of IgA makes the immunoglobulin more resistant to proteases [START_REF] Snoeck | The IgA system: a comparison of structure and function in different species[END_REF]. Secretory IgA coats commensal bacteria in the GIT of calves [START_REF] Tsuruta | Commensal bacteria coated by secretory immunoglobulin A and immunoglobulin G in the gastrointestinal tract of pigs and calves[END_REF][START_REF] Fouhse | Host immune selection of rumen bacteria through salivary secretory IgA[END_REF] and the oral microbiota coated with IgA had a greater resemblance to whole rumen microbiota than non-coated oral microbiota, suggesting salivary IgA-coating may be a host-derived mechanism impacting commensal colonization [START_REF] Fouhse | Host immune selection of rumen bacteria through salivary secretory IgA[END_REF]. This contrasts somehow with earlier works conducted on specific rumen microbes for the development of vaccines, which suggest that salivary IgA inhibit certain microbes. However, a recent work supports the hypothesis of [START_REF] Fouhse | Host immune selection of rumen bacteria through salivary secretory IgA[END_REF] by showing that specific immune recognition by IgA facilitated bacterial adherence to intestinal epithelial cells that mediates stable colonization [START_REF] Donaldson | Gut microbiota utilize immunoglobulin A for mucosal colonization[END_REF]. This suggests that in addition to its role in pathogen clearance, IgA can drive commensal microbes acceptance for colonization. This, however, remains to be demonstrated in early life colonization of the rumen.

Colonization of the rumen induces also a liver response with transcription of genes that can be associated with the development of tolerance to symbiotic microbes [START_REF] Li | Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow[END_REF]. Following the transfer of rumen fluid from an adult cow into lactating calves, the main up-regulated genes in the host's liver were linked to immune response, anti-inflammatory response and cell signalling [START_REF] Li | Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow[END_REF].

Weaning and stabilization of the rumen microbiota

Important questions addressed in studies on the developing rumen are what are the main driving factors for a healthy and functional microbiota at weaning (age, pre-weaning diet, late weaning) and at what age the rumen microbiota stabilize and can be considered mature? The weaning transition under standard farm management practices could be a stressful period that reduces intake and growth. The developing rumen of a preweaned calf contains the same dominant phyla, Bacteroidetes, Firmicutes, and Proteobacteria, as the postweaned rumen, although the relative abundances of these phyla vary with age and stage of development [START_REF] Li | Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools[END_REF][START_REF] Jami | Exploring the bovine rumen bacterial community from birth to adulthood[END_REF][START_REF] Meale | Development of ruminal and fecal microbiomes are affected by weaning but not weaning strategy in dairy calves[END_REF][START_REF] Dias | Bacterial community dynamics across the gastrointestinal tracts of dairy calves during preweaning development[END_REF]. Generally, the relative abundance of Firmicutes increases after weaning, while that of Bacteroidetes declines [START_REF] Jami | Exploring the bovine rumen bacterial community from birth to adulthood[END_REF][START_REF] Meale | Development of ruminal and fecal microbiomes are affected by weaning but not weaning strategy in dairy calves[END_REF], Meale et al., 2017b). However, the precise evolution with time of these phyla as well as the successions of bacterial families or genera may be different depending on the type of ruminant and there are even differences between studies. The microbial successions also fluctuate depending on management practices, age at weaning or the nature of the feed [START_REF] Meale | Development of ruminal and fecal microbiomes are affected by weaning but not weaning strategy in dairy calves[END_REF](Meale et al., , 2017a(Meale et al., , 2017b)). For example, β-diversity of ruminal microbiota shifted rapidly in early-weaned calves (6 weeks), whereas, a more gradual shift was observed in late-weaned calves (8 weeks) (Meale et al., 2017b). The authors concluded that the gradual increase in solid feed consumption of late-weaned calves resulted probably in lesser physiological stress during the weaning transition than that observed in earlyweaned calves. Also, feeding starter concentrate in addition to milk to pre-weaned calves promoted greater diversity of bacterial taxa known to degrade readily fermentable carbohydrates in the rumen (e.g., Megasphaera, Sharpea, and Succinivribrio) and favoured Methanosphaera instead of Methanobrevibacter [START_REF] Dias | Bacterial community dynamics across the gastrointestinal tracts of dairy calves during preweaning development[END_REF]. In this last study, the relative abundance of fungi did not change significantly with diet or age, maybe due to high inter-animal variation and low fibre content of the diet. In goats, recent work showed that the rumen microbial community and the metabolome before and after weaning are clearly different, illustrating the impact of the diet [START_REF] Abecia | Analysis of the rumen microbiome and metabolome to study the effect of an antimethanogenic treatment applied in early life of kid goats[END_REF]. Also in goats, variability and instability in the composition of the methanogen community were observed according to the change of diet and age, and stabilization appears to occur at weaning (Wang et al., 2017b). Weaning seems to be a turning point for the rumen with a microbiota structure that resembles that of adult ruminants. Notwithstanding, at lower taxonomical level many microbial taxa differed [START_REF] Dill-Mcfarland | Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation[END_REF]. The transition from weaning to an adult-like microbiota between weaning can take several months and up to one year of age [START_REF] Fonty | Establishment of ciliate protozoa in the rumen of conventional and conventionalized lambs: influence of diet and management conditions[END_REF][START_REF] Dill-Mcfarland | Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation[END_REF].

Microbial activities and functions

Most studies to date have used 16S (18S/ITS) rDNA amplicon sequencing for monitoring the rumen microbial colonization. It is important to complete these studies by measuring microbial activities or enumerating functional microbial species to ascertain the establishment of feeddegrading and other functional activities. As already mentioned, cellulolytic bacteria and methanogens are present in the rumen of 1 to 2-day old ruminants [START_REF] Fonty | Establishment of the microflora and anaerobic fungi in the rumen of lambs[END_REF][START_REF] Guzman | Presence of selected methanogens, fibrolytic bacteria, and proteobacteria in the gastrointestinal tract of neonatal dairy calves from birth to 72 hours[END_REF]. Enzymatic activities critical for utilisation of feed nutrients such as plant fibre, proteins and starch are detected in the rumen from the first days of life [START_REF] Rey | Establishment of ruminal enzyme activities and fermentation capacity in dairy calves from birth through weaning[END_REF][START_REF] Jiao | Rumen development process in goats as affected by supplemental feeding v. grazing: age-related anatomic development, functional achievement and microbial colonisation[END_REF]. These activities increase throughout the first weeks showing maximal specific activity at around one month of age, which is after the initial stage of microbial colonization is achieved [START_REF] Jiao | Rumen development process in goats as affected by supplemental feeding v. grazing: age-related anatomic development, functional achievement and microbial colonisation[END_REF]. These changes may partially reflect dietary transitions from colostrum to milk or milk replacer, and then to a progressive consumption of solid feeds. As indicated above, methanogenic activity can be measured as early as 2-3 days of life [START_REF] Morvan | Establishment of hydrogen-utilizing bacteria in the rumen of the newborn lamb[END_REF][START_REF] Friedman | Compositional and functional dynamics of the bovine rumen methanogenic community across different developmental stages[END_REF]. The establishment of hydrogenotrophic activity in the rumen of lambs, investigated by culture and isotope-labelling experiments, appeared also to be sequential. Hydrogen-dependent acetogenesis was present in the rumen of 20-h-old lambs while hydrogenotrophic methanogenesis was detected from 30-h of life.

Hydrogen-utilizing sulphate-reducing bacteria established by the third day after birth [START_REF] Morvan | Establishment of hydrogen-utilizing bacteria in the rumen of the newborn lamb[END_REF]. The colonization of reductive acetogens after birth was also explored analysing the presence of genes acetyl-CoA synthase and formyltetrahydrofolate synthetase in the immature lamb rumen.

Potential acetogens identified were affiliated with the Blautia genus and the Lachnospiraceae family, whereas establishment of methanogenic activity did not substantially affect acetogen diversity in these lambs [START_REF] Gagen | Methanogen colonisation does not significantly alter acetogen diversity in lambs isolated 17 h after birth and raised aseptically[END_REF]. The functional diversity of the rumen microbiome of the preruminant calf was also explored through metagenomics [START_REF] Li | Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools[END_REF]. More than 8000 putative Pfam protein families were detected in the rumen of 14-day old calves with up to sixty glycosyl hydrolase families identified, indicating a high metabolic potential for carbohydrate processing long before weaning [START_REF] Li | Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools[END_REF]. An increase in carbohydrate metabolism from 5 to 9 weeks of age in calves inferred from 16S rRNA gene sequences was also suggested (Meale et al., 2017b), although the use of functional metabolic predictions based on taxonomic information should be interpreted with prudence [START_REF] Vieira-Silva | Species-function relationships shape ecological properties of the human gut microbiome[END_REF].

Modes of transmission

It has been conventionally considered that the uterus is a sterile environment and microbial inoculation of the newborn's gut starts immediately after birth, through the vaginal canal, faecal material, colostrum, skin and saliva of the dam as well as from the environment. However, bacterial and archaeal DNA has been detected in the rumen, intestines and meconium of calves as early as 20 min after birth [START_REF] Guzman | Presence of selected methanogens, fibrolytic bacteria, and proteobacteria in the gastrointestinal tract of neonatal dairy calves from birth to 72 hours[END_REF], which led the authors to suggest that inoculation of the rumen may occur before birth. Studies on human and on mice newborns suggest that colonization of the intestine in these species starts in utero [START_REF] Ihekweazu | Development of the pediatric gut microbiome: impact on health and disease[END_REF]. This has led to investigations in ruminants with contrasting results. Some studies suggest that the colonization of the ruminant intestine may begin before birth [START_REF] Alipour | The composition of the perinatal intestinal microbiota in cattle[END_REF] but negative results were reported by others [START_REF] Malmuthuge | Fetal environment and fetal intestine are sterile during the third trimester of pregnancy[END_REF]. Caution should be exerted when interpreting results from humans or other animals as the structure of the placenta and the maternal-fetal interaction differ greatly among mammals, with ruminants having the most complete type of placental barrier [START_REF] Benirschke | Pathology of the Human Placenta[END_REF]. Another caveat is contamination when analysing this kind of samples with low microbial numbers [START_REF] Malmuthuge | Fetal environment and fetal intestine are sterile during the third trimester of pregnancy[END_REF]. The information available is not enough to confirm or disprove the in utero transfer of microbes into the gut in ruminants.

Whether or not the bacterial colonization of the digestive tract begins before birth, the relative contribution of all the other sources of inoculation is not well known. It is well established that the dam is an important source of microbial inoculation of the newborn rumen. Indeed, in newborns lambs separated from their dams and reared individually, no cellulolytic bacteria, fungi and protozoa established in the rumen [START_REF] Fonty | Establishment of ciliate protozoa in the rumen of conventional and conventionalized lambs: influence of diet and management conditions[END_REF]. Also, similarities between rumen methanogen populations found in newborn twin lambs suggested that the dam was the most important source of inoculation [START_REF] Skillman | 16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs[END_REF]. The dam's oral microbiota may be particularly important because of rumination, which would facilitate the oral transfer of rumen microorganisms to the newborn as a result of the natural instinct to lick them after birth. Colostrum and milk are also a source of bacterial colonization of the newborn gut. As for monogastric animals, liquid feeds in suckling ruminants go directly to the true stomach, the abomasum, through the oesophageal groove.

However, the groove is not completely hermetic and small amounts of milk are also found in the rumen where taxa able to utilize milk nutrients such as Bacteroides and Lactobacillus are dominant in suckling calves fed milk only [START_REF] Dias | Bacterial community dynamics across the gastrointestinal tracts of dairy calves during preweaning development[END_REF]. The ability to grow on milk lactose by F. succinogenes can explain the active presence of this cellulolytic bacterium in pre-weaning calves [START_REF] Ghali | Diauxic growth of Fibrobacter succinogenes S85 on cellobiose and lactose[END_REF]. The importance of the microbiota from different body sites of the dam to seed the newborn's gastrointestinal tract was explored recently [START_REF] Alipour | The composition of the perinatal intestinal microbiota in cattle[END_REF][START_REF] Yeoman | Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract[END_REF].

The oral microbiota of the dam most closely resembled the rectal microbiota of the newborn calf in the study of [START_REF] Alipour | The composition of the perinatal intestinal microbiota in cattle[END_REF]. Whereas, in the study of [START_REF] Yeoman | Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract[END_REF] the udder skin microbiota of the dam shared the largest number of OTUs with both luminal and mucosal microbiota of the calves from day 1-21 as compared with colostrum or vaginal samples. Surprisingly, fibrolytic bacteria and methanogenic archaea sequences were identified in the cow vaginal samples, suggesting a colonization role during birth [START_REF] Yeoman | Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract[END_REF]. This is in addition to the important role that the dam vaginal microbiota has in colonizing the upper respiratory tract of the offspring [START_REF] Lima | The Bos taurus maternal microbiome: Role in determining the progeny early-life upper respiratory tract microbiome and health[END_REF].

Impact of management practices

Assuming that a key turning point in rumen microbial colonization is the introduction of solid feed in the diet (see above), an important issue to address is whether the feeding management of the newborn alters the colonization pattern. Few studies have compared the microbial colonization of the undeveloped rumen in the context of the factors that facilitate (or prevent) the colonization of some microbial groups (i.e. maternal influence, offspring reared in isolation, use of microbial modulators, etc).

As presented above, the dam has an important influence in early colonization. The maternal influence in relation to management systems has been further addressed in recent studies (Abecia et al., 2014b[START_REF] Belanche | Effect of progressive inoculation of fauna-free sheep with holotrich protozoa and total-fauna on rumen fermentation, microbial diversity and methane emissions[END_REF][START_REF] Abecia | Natural and artificial feeding management before weaning promote different rumen microbial colonization but not differences in gene expression levels at the rumen epithelium of newborn goats[END_REF], 2018[START_REF] Yeoman | Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract[END_REF]. Two main systems exist for rearing offspring in ruminant production. In commercial dairy systems, newborns are typically separated from the dam after birth and fed either milk replacer or whole milk. In contrast, in beef and extensive production systems, the offspring remains with the dam until weaning. These two systems, therefore, imply differences in regards to milk type (whole milk vs. milk replacer) and contact or not with adult conspecifics that in many cases are confounded. Protozoa in artificially reared animals showed a different colonization pattern as compared to those raised by the dams (Abecia et al., 2014a[START_REF] Belanche | Effect of progressive inoculation of fauna-free sheep with holotrich protozoa and total-fauna on rumen fermentation, microbial diversity and methane emissions[END_REF]. Natural milk feeding via the dam vs. artificial feeding with milk replacer resulted in consistently lower pH in the developing rumen of goat kids that stayed with the mothers (Abecia et al., 2014a). The authors hypothesised that naturally raised kids would have consumed more concentrate at an earlier stage as a result of social feeding learning as also shown by [START_REF] De | Presence of an older weaned companion influences feeding behavior and improves performance of dairy calves before and after weaning from milk[END_REF], who observed that the presence of an older companion with preweaned calves stimulated feeding behaviour and growth before and after weaning. In addition to learning behaviour, the presence of older conspecifics influences the rumen microbiota as damreared goat kits showed substantially greater bacterial diversity throughout the colonization process than those artificially reared [START_REF] Abecia | Natural and artificial feeding management before weaning promote different rumen microbial colonization but not differences in gene expression levels at the rumen epithelium of newborn goats[END_REF]. Fibrobacteres (one of the main cellulolytic phyla in the rumen) was present in naturally raised kids from day seven after birth; however, it did not colonize the rumen of kids kept in isolation from dams until day 28, similarly to Succiniclasticum which ferment succinate to propionate. Also, greater VFA concentration was observed in the rumen of kids with dams, which may suggest a quicker establishment of microbial fermentation in these animals (Abecia et al., 2014a). However, it remains unknown whether this distinct microbial colonization between animals, reared naturally or artificially, may have effects on the animal digestive performance later in life. The effect of the dam in the colonisation after birth deserves further research as it could help to develop new inoculation strategies in livestock farming.

Modulating the gastrointestinal microbiota in young ruminants for health and production

As stated in previous sections, a number of factors influence the GIT microbial colonization in young ruminants. Among them, the type of production system, farm management and diet are the most important. Good management practices normally recommended to reduce the onset of diseases and promote a vigorous growth in the first weeks of life have an obvious impact on the GIT microbiota. For instance, feeding high-quality colostrum allows establishing a beneficial, mucosaassociated bacterial barrier and thus provides protection against enteric infections in young ruminants [START_REF] Malmuthuge | The gut microbiome and its potential role in the development and function of newborn calf gastrointestinal tract[END_REF]. Colostrum favours the development of beneficial Bifidobacterium whereas it reduces potential pathogens and members of Escherichia and Shigella genera in the colon [START_REF] Song | Colostrum feeding shapes the hindgut microbiota of dairy calves during the first 12 h of life[END_REF]. Suckling from the dam and contact with conspecific adults is the best way to ensure the natural acquisition of a functional GIT microbiota in early life. However, this otherwise natural practice is not always applicable under current production systems and nutritional interventions in early-life may be considered to facilitate (or prevent) the colonization of some microbial groups. In some particular cases, contact with the dam might not be recommended if there is a risk of transmission of non-desirable microbial populations. The risk of transmission of Mycobacterium avium subsp. paratuberculosis, the causative agent of Johne's disease, increased with the number of days that newborns remained with affected adults, particularly in the first week of life [START_REF] Burgess | Early-life exposures and Johne's disease risk in zoo ruminants[END_REF]. Inversely, it is reasonable to hypothesize that the contact with some animals should be promoted for facilitating the transmission of microbiotas associated to desired phenotypes such as reduced enteric methane emission or improved feed efficiency [START_REF] Shabat | Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants[END_REF][START_REF] Difford | Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows[END_REF].

Diet is a well-known modulator of the GIT microbiota at all ages but it seems to have a particular influencing role in the development of the microbiota and the microbiota-host dialogue in young ruminants (i.e.: [START_REF] Bach | Influence of milk processing temperature on growth performance, nitrogen retention, and hindgut's inflammatory status and bacterial populations in a calf model[END_REF][START_REF] Dill-Mcfarland | Diet influences early microbiota development in dairy calves without long-term impacts on milk production[END_REF][START_REF] Dong | Weaning methods affect ruminal methanogenic archaea composition and diversity in Holstein calves[END_REF]. Differences in milk processing that can be considered minor from a macronutrient standpoint had large consequences on some gut microbial populations and inflammation parameters. As opposed to heat-treated milk (pasteurised and UHT), raw milk increased Lactobacillus numbers, decreased the expression of proinflammatory interleukins, and improved growth in dairy calves [START_REF] Bach | Influence of milk processing temperature on growth performance, nitrogen retention, and hindgut's inflammatory status and bacterial populations in a calf model[END_REF].

In addition to the management and diet factors cited, two main nutritional interventions in earlylife may be considered to modulate the GIT microbiota. These are the direct inoculation of specific microorganisms and the use of compounds (i.e. additives) that prevent or facilitate the colonization of some microbial groups. These two strategies are mainly tested for improving phenotypes of interest.

4. Early-life strategies for improving health and production (case studies)

Feeding live microorganisms to ruminants is not a novel concept and extensive work has been published on the use of direct-fed microbials (DFM) (Martin andNisbet, 1992, Jeyanathan et al., 2014). [START_REF] Theodorou | The effect of a fungal probiotic on intake and performance of early weaned calves[END_REF] reported that the addition of an anaerobic rumen fungus, Neocallimastix spp., increased intake and live weight gain in calves at weaning, whilst [START_REF] Ziolecka | The effect of Stabilized Rumen Extract on growth and development of calves. 1. Liveweight gain and efficiency of feed utilization[END_REF], Ziolecki et al., 1984) reported that a stabilized rumen extract enhanced live weight gain and stimulated rumen development in calves during weaning. The use of fresh rumen fluid inoculated in early life has gained new attention. Most recent studies showed that inoculation of fresh rumen fluid from adults into the rumen of newborns has a positive effect on productive parameters [START_REF] Zhong | Effects of inoculation with rumen fluid on nutrient digestibility, growth performance and rumen fermentation of early weaned lambs[END_REF], De Barbieri et al., 2015b). After weaning, average daily gain, intake, digestibility and rumen development improved in treated animals (lambs and kits) as compared to non-treated.

Some of these effects may not last, although the composition of ruminal bacterial communities still differed up to 5 months of age, well after the initial inoculation (De Barbieri et al., 2015a, 2015b).

For specific DFM preparations, the administration of lactic acid bacteria to suckling calves was shown to stimulate rumination and ruminal development [START_REF] Nakanishi | Effects of feeding Lactobacillus acidophilus yogurt on performance and behavior of dairy calves[END_REF] and the use of lactic acid bacteria or Bifidobacterium increased feed conversion efficiency and body weight gain [START_REF] Abe | Effect of Administration of Bifidobacteria and Lactic Acid Bacteria to Newborn Calves and Piglets[END_REF]. In this latter work, the DFMs decreased diarrhoea. The effect of lactic acid bacteria DFM on the prevalence of diarrhoea was confirmed in a meta-analysis [START_REF] Signorini | Impact of probiotic administration on the health and fecal microbiota of young calves: A meta-analysis of randomized controlled trials of lactic acid bacteria[END_REF]. Interestingly, the protection was only observed with multi-strains DFM and for calves fed raw milk. All these effects of lactic acid bacteria can be partially ascribed to the positive modulating activities of these bacterial groups on host immunology as described in the subsection Interaction host-microbiota (see above). The rumen bacterium Megasphaera elsdenii uses lactate to produce butyrate, a beneficial energy compound used by the GIT epithelial mucosa. This bacterium was also used as DFM in young ruminant with contrasting results. [START_REF] Muya | Effect of Megasphaera elsdenii NCIMB 41125 dosing on rumen development, volatile fatty acid production and blood beta-hydroxybutyrate in neonatal dairy calves[END_REF] showed improved feed intake and rumen development, suggesting increased epithelium metabolism and improved absorption of digestive end products. Whereas, no effect was observed in another study using the same strain and a similar protocol [START_REF] Yohe | Short communication: Does early-life administration of a Megasphaera elsdenii probiotic affect long-term establishment of the organism in the rumen and alter rumen metabolism in the dairy calf?[END_REF].

Diarrhoea is one of the main health issues in preweaned ruminants, particularly in dairy (USDA, 2018). A low faecal microbial diversity, notably a low relative abundance of Faecalibacterium spp., a symbiotic bacterium with known anti-inflammatory activity, was associated with an increased incidence of diarrhoea [START_REF] Oikonomou | Fecal Microbial Diversity in Pre-Weaned Dairy Calves as Described by Pyrosequencing of Metagenomic 16S rDNA. Associations of Faecalibacterium Species with Health and Growth[END_REF]. Inversely, Faecalibacterium spp. is positively associated with weight gain. Substantiating these effects, the use of Faecalibacterium prausnitzii as DFM in dairy calves decreased the incidence of severe diarrhoea by half and mortality by two thirds as compared to untreated controls [START_REF] Foditsch | Oral administration of Faecalibacterium prausnitzii decreased the incidence of severe diarrhea and related mortality rate and increased weight gain in preweaned dairy heifers[END_REF].

Another strategy gaining attention is the use of life yeasts in early life. Although yeasts are widely used in ruminant nutrition [START_REF] Chaucheyras-Durand | Use of Yeast Probiotics in Ruminants: Effects and Mechanisms of Action on Rumen pH, Fibre Degradation, and Microbiota According to the Diet[END_REF], the concept of applying them in the diet of pre-ruminants to alter microbial colonization is more novel. It has been showed that yeasts, particularly as DFM, have positive effects on growth, rumen and small intestine development, immunity and general health of the calf [START_REF] Kim | The stress of weaning influences serum levels of acute-phase proteins, iron-binding proteins, inflammatory cytokines, cortisol, and leukocyte subsets in Holstein calves[END_REF][START_REF] Alugongo | Review: Utilization of yeast of Saccharomyces cerevisiae origin in artificially raised calves[END_REF]. Specifically, Saccharomyces cerevisiae yeast (SCY) can improve DMI, growth, feed efficiency [START_REF] Lesmeister | Effects of corn processing on growth characteristics, rumen development, and rumen parameters in neonatal dairy calves[END_REF]Heinrichs, 2004, Alugongo et al., 2017) and reduce diarrhoea in calves [START_REF] Galvao | Effect of feeding live yeast products to calves with failure of passive transfer on performance and patterns of antibiotic resistance in fecal Escherichia coli[END_REF][START_REF] Brewer | Amelioration of salmonellosis in pre-weaned dairy calves fed Saccharomyces cerevisiae fermentation products in feed and milk replacer[END_REF]. Furthermore, subtle improvements were seen in rumen fermentation (increased butyrate production) and rumen papillae growth [START_REF] Lesmeister | Effects of corn processing on growth characteristics, rumen development, and rumen parameters in neonatal dairy calves[END_REF]. These positive results, however, are more pronounced in calves stressed or exposed to significant levels of disease-causing agents. Despite the increasing number of published works studying the use of SCY in early-life of ruminants, there is a lack of knowledge about its impact on the microbial colonization. Recently, [START_REF] Terré | Effect of Saccharomyces cerevisiae CNCM I-1077 supplementation on performance and rumen microbiota of dairy calves[END_REF] reported that supplementing young male calves with live SCY increased the presence of the fibrolytic bacterium R. albus in the rumen and it also increased rumen pH but no effect was observed on other bacteria and protozoa. Supplementation of newborn lambs fed milk replacer by live yeasts was also shown to increase the colonization of the rumen by F. succinogenes, fungi and protozoa (Chaucheyras-Durand et al, personal communication). Other reported effects of SCY are an increase in Lactobacillus in faeces [START_REF] Fomenky | Impact of Saccharomyces cerevisiae boulardii CNCMI-1079 and Lactobacillus acidophilus BT1386 on total lactobacilli population in the gastrointestinal tract and colon histomorphology of Holstein dairy calves[END_REF] and greater oxidative burst and phagocytosis activity during weaning stress indicating a stronger innate immune response [START_REF] Fomenky | Saccharomyces cerevisiae var. boulardii CNCM I-1079 and Lactobacillus acidophilus BT1386 influence innate immune response and serum levels of acute-phase proteins during weaning in Holstein calves[END_REF]. Generally, for all DFM and the engraftment of adult rumen microbiota, there is still a need for further research in whole microbiome analysis and areas such as gut immunity and the persistence of effects later in life, especially in dairy systems due to their management of newborns.

This information is necessary to draw consistent conclusions on their potential in early life.

5. Early-life strategies for reducing enteric methane emissions (case studies)

Modulating the microbial colonization in the developing rumen towards communities that produce less methane is also gaining attention. For this objective, compounds used as feed additives or feed supplements have been tested with two different approaches: one that specifically targets methanogens and the other uses general inhibitors that were described as having various mechanisms of action. For the specific approach, the application of bromochloromethane to young goat kids modified archaeal colonisation of the rumen, which was linked to a reduction in methane emission of around 50 %. The effects persisted for 3 months after weaning and cessation of treatment in kids raised by does that received the same treatment as the kids [START_REF] Abecia | Nutritional intervention in early life to manipulate rumen microbial colonization and methane output by kid goats postweaning[END_REF](Abecia et al., , 2014a)). For the generalist modulation approach, different types of lipids and plant extracts with proven efficacy to alter microbial metabolism and methane emissions in adult animals were tested. [START_REF] Debruyne | Supplementing goat kids with coconut medium chain fatty acids in early life influences growth and rumen papillae development until 4 months after supplementation but effects on in vitro methane emissions and the rumen microbiota are transient[END_REF] tested in goats prenatal and postnatal supplementation with coconut oil medium chain fatty acids. The treatment reduced in vitro methane emissions in four-week-old kids by reducing methanogen abundance and activity but at the expense of rumen fermentation and eubacterial abundance. Unfortunately, the treatment also suppressed daily gain of treated kids.

Some rumen papillae characteristics differed at 28 weeks old due to postnatal treatment which ended at week 11 of life, indicating rumen papillary development can be affected by the early-life nutritional management. [START_REF] Saro | Effectiveness of interventions to modulate the rumen microbiota composition and function in pre-ruminant and ruminant lambs[END_REF] tested a combination of garlic oil and linseed oil in earlylife of lambs and the potential impact of re-treating the animals later in life. The archaeal methanogenic community was modified during the treatment but, in accordance with methane emissions, disappeared afterwards. In contrast, bacterial community structure differed between treated and non-treated lambs during and after the intervention. Rumen and urine metabolomics profiles conducted after the intervention ceased, highlighted interactions between microbes and metabolites, notably that of methylated compounds and Methanomassiliicocceae methanogens.

They demonstrated that a long-term early-life intervention induced modifications in the composition of the rumen bacterial community that persisted after the intervention ceased with little or no effect on archaeal and protozoal communities. However, there was no persistence of the early-life intervention on methanogenesis suggesting a notable resilience for this function. Similarly, Lyons et al. ( 2017) treated lambs with linseed oil and found persistence of differences in the bacterial community structure but not associated changes in phenotypic response.

Methanogens occupy a specific niche in the rumen ecosystem. When methanogens are inhibited, there is a shift in hydrogen flow and other electron-donor metabolites towards alternative electron acceptors such as propionate. This implies the rearrangement of trophic networks and changes in microbial populations that are mainly observed for the bacterial communities in all studies cited above. The abundance of methanogens was not always affected but their diversity was commonly altered although the changes were different probably due to the type of inhibitor used.

Linseed and garlic oil decreased the Methanomassiliicoccales relative abundance in lambs [START_REF] Saro | Effectiveness of interventions to modulate the rumen microbiota composition and function in pre-ruminant and ruminant lambs[END_REF]. Bromochloromethane increased the relative abundance of Methanobrevibacter and decreased that of Methanosphaera in kids (Abecia et al., 2014b). Whereas, linseed increased Methanosphaera relative abundance in lambs [START_REF] Lyons | Linseed oil supplementation of lambs' diet in early life leads to persistent changes in rumen microbiome structure[END_REF].

6. Summary and outstanding questions/future trends From birth, ruminants are constantly exposed to different sources of microbes. The establishment of stable communities depends on the creation of suitable conditions with a close interplay between diet and maturation of the GIT. The sequential evolution of the gut microbiota that is followed by the expansion of metabolic functions is a coordinated process that matches the anatomical and physiological development of the GIT. In the non-ruminant phase (0-3 weeks), the establishment of a diverse microbial community, particularly bacteria in the post-gastric section, is important for health and grow [START_REF] Oikonomou | Fecal Microbial Diversity in Pre-Weaned Dairy Calves as Described by Pyrosequencing of Metagenomic 16S rDNA. Associations of Faecalibacterium Species with Health and Growth[END_REF][START_REF] Bach | Influence of milk processing temperature on growth performance, nitrogen retention, and hindgut's inflammatory status and bacterial populations in a calf model[END_REF], whereas changes in the rumen are predominant during the transition (3-8 weeks) and rumination phases (+8 weeks of age) [START_REF] Jiao | Rumen development process in goats as affected by supplemental feeding v. grazing: age-related anatomic development, functional achievement and microbial colonisation[END_REF]. The periods when these alimentary, anatomical and physiological modifications occur seem to be the more suitable for interventions for long-term modifications of the GIT microbiota [START_REF] Dill-Mcfarland | Diet influences early microbiota development in dairy calves without long-term impacts on milk production[END_REF].

The GIT microbiota at an early age is influenced and can be modulated by various strategies (Figure 2). Nevertheless, for the application of these strategies in farms there are still some outstanding questions that need to be addressed. Ongoing research on the role of GIT microbiota on animal phenotypes will bring information on the type of microbial communities that should be favoured in young ruminants. The effect of the prenatal period, including whether there is a prenatal colonisation of the GIT and its role in the establishment of the mature microbiota have to be assessed. Similarly, the best window(s) of age when the microbiota could be modulated have to be refined. Establishment of different populations might not be a single isolated event and a continuous exposure seems to be necessary for acquiring adult-like communities [START_REF] Morgavi | Rumen microbial communities influence metabolic phenotypes in lambs[END_REF] or successfully engraft specific microbes [START_REF] Yohe | Short communication: Does early-life administration of a Megasphaera elsdenii probiotic affect long-term establishment of the organism in the rumen and alter rumen metabolism in the dairy calf?[END_REF]. A better definition of the role of early microbial communities on the host-microbiota dialogue and the regulation of the immune system is also important for this subject. Expected advances in all these topics in the coming years have the potential to improve the sustainability of ruminant production through better health in young animals and enhanced efficiency. Major international research projects and networks -Rumen Microbial Genomics Network, Global Research Alliance-Livestock Group. A large international network fostering collaborations and exchanges between microbiologists working with ruminants

7.

  Where to look for further information Key conferences -Gut Microbiology Symposium; jointly organized by INRA France and the Rowett Institute -Aberdeen University, every two years -Congress on Gastrointestinal Function; in Chicago (USA) every two years -Annual meetings from animal science societies such as Annual Meeting of the European Federation of Animal Science and American Dairy Science Association -Smart Calve rearing Conference (https://smart-calf-rearing.com)

Figure 1 .

 1 Figure 1. Microbial colonisation of the lamb rumen. Colonisation of the rumen by microbial groups detected by cultural and molecular methods. Lambs were kept with their dams. Arrows indicate the start of the colonization period.

Figure 2 .

 2 Figure 2. Acquisition of gastrointestinal microbiota in early life could be modulated (blue arrows) through management and targeted interventions to favour health and phenotypes of interest such as increased feed efficiency and decreased methane emissions.Modulating options are: allowing contact with dams or mature conspecific harbouring a desirable microbiota, inoculation with gastrointestinal contents (engraftment) obtained from mature conspecific, diet and supplementation with direct-fed microbials (DFM), prebiotics and feed additives.

Table 1. Time line for colonisation of the major bacteria phyla from birth to adulthood (values expressed as range of mean percentages) Age 3-days 7-days 14-days 28-days 42-days 6-months 2-years Phyla Bacteroidetes 13.9-42.6 56. 3-56.9 46.0-61.3 49.9-56.3 56.3-74 38.5-55.2 38.5-50.2 Firmicutes 5.1-13.9 13.9-17.5 13.9-34.0 13.9-42.1 10-43.9 36.8-48.9 34.5-56.7

Actinobacteria 0.05-4.9 0.6-4.9 0.9-4.9 0.3-4.9 0.


Philippe Maugis

Damien + Connétable

Paul Eyméoud

Stability of Zener order in martensite: an atomistic evidence

Steels

Long-range ordering Elastic behaviour

Martensite is a supersaturated solid solution of carbon in body-centered iron wherein interstitial carbon atoms preferentially occupy a single octahedral sublattice. Despite a centwy of rese.arch, the mechanism of this long-range ordering is still a subject of debate. Recently, Zener's theory of ordering was chal lenged both experimentally and theoretically. ln an attempt to settle the controversy, we investigated by density functional theory the ground states of Fe-C configurations having various degrees of order. We conclude that the fully Zener-ordered configurations are always the most stable energetically, thus confirming Zener's theory. Comparison with mean-field elasticity and Ising-type modelling supports the elastic origin of Zener ordering.

Densicy functional theory (DFf) Mean-field modelling

Fink and Campbell in 1926 (1] established that a'-martensite is a supersaturated solid solution of carbon in body-centered iron. The carbon atoms preferentially occupy the octahedral interstitial positions between nearest iron atoms in one of the three (001} crystal directions. This preferential occupation causes a tetragonal distortion of the matrix, quantified by the lattice parameter ra tio c/a > 1. Based on Bain's transformation, Kurdjumov and Sachs [2] suggested that carbon distribution in martensite lattice inher its from the diffusionless face-centered to body-centered structural transformation of the parent austenite phase. Assuming that long range carbon-carbon interactions are predominantly elastic, Zener [3] stated that the ordered distribution of carbon atoms is en ergetically more favorable than disorder. He predicted an order disorder transition between cubic ferrite and tetragonal martensite (Fig. 1 ). Zener's mean-field theory has been challenged ever since, partly because the so-called Zener ordering transition was never evidenced directly.

Kurdjumov et al. (4] provided indirect proof of Zener ordering: they measured an increase in tetragonality of quenched marten site during ageing at room temperature, interpreted as progressive ordering via carbon jumps into the favoured octahedral sites. Re cently, an in situ X-ray diffraction study of martensite formation during quench evidenced the set up of tetragonality as soon as martensite forms , confirming Bain's scheme [5]. In another study, in situ neutron diffraction revealed a decrease in axial ratio to-

• Corresponding author.

E-mail addresses: philippe.maugis@im2np.fr, philippe.maugis@univ-amu.fr (P.

Maugis).

URL: hrrp:/Jwww.im2np.fr (P. Maugis) hrcps:// doi.org/10.1016/j .scriptamat2020.l l 3632 wards c/a = 1 during ageing after quench [6], i.e. a case of Zener disordering. Finally, cases were reported of high-carbon austenite isothermally transformed into cubic martensite, thus challenging Zener's model (7,8]. On the other hand, room-temperature mea surements of the lattice parameters of Fe-C steels of various car bon contents ail show an abrupt transition between low-carbon cubic ferrite and high-carbon tetragonal martensite (9)(10)(11), which is coherent with Zener's theory. On the theoretical side, investigations of carbon ordering in iron involved various techniques: thermodynamic mean-field modelling (12)(13)(14)(15)(16), the microscopie elasticity theory (4,10,(17)(18)(19), the CAL PHAD formalism [20.21], molecular dynamics (14,(22)(23)(24) and com bined ab initio-Monte Carlo (16,(25)(26)(27). Most of these approaches, although based on ditferent hypotheses and approximations, pro vide results in favour of Zener ordering. One exception is the work of Ruban (25,26], which predicts an "anti-Zener" ordering consist ing of carbon atoms occupying specific sites on two preferred oc tahedral sublattices, associated with a ratio c/a < 1. The relative stability of this configuration, as compared to Zener order, is ex plained by the asserted dominating effect of carbon-carbon short range interactions.

It is worth noting that mechanical external conditions affect the phase stabilities (see e.g. [28,291) and modify the equilibrium or der. In particular, coherency stress or applied stress can turn the first-order Zener transition into a continuous transition (12,30]. When compressive, a uniaxial stress may also stabilise "beyond Zener" order, i.e. an orthorhombic structure where the three octa hedral sublattices are unevenly occupied by carbon atoms (30)(31)(32)(33).

This literature survey leads to the conclusion that Zener or dering may or may not occur, depending on yet unclear reasons. Moreover, there is no theoretical consensus on whether Zener order is the most stable state of order in supersaturated iron or not. The subject needs further prospection, given its importance in understanding and predicting the mechanisms of martensite transformation and the resulting martensitic microstructures.

In this study, we investigated from first principles the energetic stability of various states of carbon order. Special quasirandom structures (SQS) were used to simulate random distributions of carbon atoms over each sublattice. Density functional theory (DFT) computations were performed under prescribed applied stress. The results were compared to the mean-field elastochemical model [33] supplemented by short-range carbon-carbon interactions. The most stable structures were identified as function of the applied stress.

In a crystal of body-centered iron, interstitial carbon atoms are distributed over the 3 sublattices of octahedral sites. Carbon fraction on sublattice i is noted c i and total carbon fraction is c = c i .

To study the effect of carbon distribution over the sublattices at constant carbon fraction c, it is convenient to introduce two long- [001], i.e. all carbon atoms sitting on sublattice 3. This configuration will be referred to as the Z3 orientational variant. The combinations (-0 . 5 , -1) and (-0 . 5 , 1) describe the Z1 and Z2 fully ordered variants along directions [100] and [010], respectively. Intermediate values of (η, ζ ) represent partially ordered structures. Among them, (-0 . 5 , 0) is the inverse-Zener order: it has empty sublattice 3 and equal occupancy of sublattices 1 and 2. Finally, (0,0) is the fully disordered structure with equal occupancy of the three sublattices.

The thermodynamical stability of a given state of order under applied stress tensor σ is characterised by the enthalpy of ordering H(η, ζ ) , where symbol expresses that the disordered state is taken as reference. H can be calculated from the energy of ordering U and the strain of ordering ε via the relationship

H = U -V σ • ε , ( 1
)
where V is the volume of the stress-free carbon-free crystal. DFT calculations are known to render correctly the short-range interactions between solute atoms, irrespective of their origin, "chemical" or "elastic". In this study, by allowing the supercell to relax, we also captured the long-range carbon-strain interaction and the resulting homogeneous strain.

In order to represent carbon-vacancy disorder on octahedral interstitial sublattices, we used the SQS approach. Supercells were built with mcsqs [34] modulus of ATAT code [35] , following the procedure described in [36] : computation of the correlations functions on clusters containing C-C pairs equal to or shorter than √ 3 a 0 ( a 0 is the lattice parameter of iron). The computed tetragonality and energy somewhat depend on the relative positions of the carbon atoms in the supercell [37,38] ), this is why we averaged each case over a set 13 SQS structures. To extract energetic and structural properties from these structures using DFT, we employed an in-house version of VASP code [39,40] allowing to impose stresses on cells. We used the following parameters: generalized gradient approximation [41] with projector augmented wave method [42] and Perdew-Burke-Ernzerhof exchangecorrelation functional [43,44] , 400 eV energy cut-off (as used in Refs. [36,45,46] ), spin-polarized approximation, 10 -5 eV energy convergence criterion of the electronic self-consistency, 4 × 4 × 4 Monkhorst-Pack k-points grid [47] for 128 iron atom supercells and Methfessel-Paxton smearing [48] for reciprocal space integration. To relax the supercells we used a conjugate-gradient algorithm with ionic relaxation criterion of 10 -4 eV in energy for zero-stress calculations and 0.01 eV/ Å in force for stress-imposed calculations. Calculations were performed on Fe 128 C 12 supercells of composition Fe-8.6at%C and varying states of order.

In a first series of calculations, the degree of Zener order along A second series of calculations aimed at investigating the effect of tension ( +2 GPa) and compression ( -2 GPa) along axis 3 on the relative stability of selected states of order, namely (1,0), (-0 . 5 , 0) and (-0 . 5 , 1) . The comparative plotting of Fig. 3 gives the following results: (i) tension stabilises tetragonal Zener order along the stress axis (variant Z3); (ii) compression stabilises orthorhombic Zener order in a direction transverse to the stress axis (variant Z1 or Z2); and (iii) disorder and inverse-Zener order are disfavoured in all cases.

Additional calculations on variants (0,0) and (1,0) revealed that carbon distribution and applied stress have negligible impact on the magnetic moments (less than 0.02 μ B /atomic species). This negligible role of Zener order on magnetism suggests that an empirical potential without magnetism would be able to capture the discussed effects on Zener ordering.

Here, the main advantages of our first-principles approach are: (i) it correctly represents interstitial disorder thanks to the use of SQS; (ii) it does not raise an issue of empirical potential representativeness, as it is the case for the embedded-atom method [50] and pairwise interactions models; and (iii) it considers both homogeneous elasticity by lattice deformation and C-C chemical interactions. However, this approach does not easily allow discriminating the long-range elastic contribution from the short-range interaction contribution. To investigate this point, we used the meanfield elastochemical model of Maugis [16,33] together with pairwise C-C interactions. The theory is summarised below.

In the framework of the continuum elasticity theory of point defects, long-range carbon-strain interactions are accounted for via the dipole moment tensor P of interstitial carbon [51,[START_REF] Balluffi | Introduction to elasticity theory for crystal defects[END_REF] . Carbon atoms and axial stress σ induce a relaxed strain tensor ε , whose normal components write as functions of η and ζ :

⎧ ⎪ ⎪ ⎪ ⎪ ⎪ ⎪ ⎨ ⎪ ⎪ ⎪ ⎪ ⎪ ⎪ ⎩ ε 11 = V C 3 V 0 c + V 3 V 0 c -η - 3 2 ζ + S 12 σ ε 22 = V C 3 V 0 c + V 3 V 0 c -η + 3 2 ζ + S 12 σ ε 33 = V C 3 V 0 c + 2 V 3 V 0 cη + S 11 σ (2)
Constants V 0 , V C and V are respectively the atomic volume of the lattice, the relaxation volume and the tetragonal distortion due to an interstitial carbon. The latter are related to the elastic properties of the defect and the host matrix [16] :

V C = (S 11 + 2 S 12 )(P c + 2 P a ) , V = (S 11 -S 12 )(P c -P a ) .
(

) 3
P a and P c are the two independent components of the dipole moment tensor and S i j are the components of the elastic compliance tensor of the host matrix. It is clear from Eqs. 2 that crystal symmetry is governed by both applied stress and order parameters.

Indeed, the Bravais lattice may be either cubic ( η = ζ = 0 , σ = 0 ; full disorder), tetragonal prolate (e.g. η > 0 , ζ = 0 , σ > 0 ; Zener order), tetragonal oblate (e.g. η < 0 , ζ = 0 , σ < 0 ; inverse-Zener order [26,27] ) or orthorhombic (e.g. η = 0 , ζ = 0 ; beyond-Zener order [4,30] ).

The homogeneous strain contributes to the enthalpy of ordering by the amount H el written as

H el = -h c 2 η 2 + 3 4 ζ 2 - 2 3 V σ cη (4)
where h is the strain-energy parameter:

h = 1 3 V 0 (S 11 -S 12 )(P c -P a ) 2 .
(

) 5
The first term in the r.h.s. of Eq. 4 is the stress-independent ordering energy U el . The second term is the elastic work of the applied stress when the configuration is changed from disorder ( η = 0 ) to partial order ( η = 0 ). Eq. 4 shows that Zener ordering along direction 3 ( η > 0 ) is favoured when a tensile stress is applied along that direction ( σ η > 0 , H el decreases); it is disfavoured when a compressive stress is applied along the same direction ( σ η < 0 , H el increases).

From Eqs. 3 and 5 we notice that the equilibrium state of order, obtained from minimising function H el (η, ζ ) at given c and σ, does not depend on the elastic stiffness of the host matrix, but only on the deviatoric part of the dipole moment tensor, via the ratio (P c -P a ) /V 0 .

All material parameters entering the elasticity model were extracted from high-accuracy DFT calculations. Their values are gathered in Table 1 . The dipole moment tensor was computed using the residual stress method [START_REF] Varvenne | [END_REF] : a supercell containing one carbon atom in a bcc-Fe matrix was relaxed, while maintaining the shape and volume of the cell identical to that of carbon-free iron. On account of the carbon insertion, a residual stress σ builds up at the cell boundary. The dipole moment tensor P is related to the residual stress by P = -V σ, where V is the volume of the supercell.

Correction of the image forces due to the periodic boundary conditions was applied by varying the supercell size and performing a parabolic fit of the residual stress as function of 1 /V .

Table 1

Lattice parameter a 0 (in nm), elastic compliances S i j (in GPa -1 ) and dipole moments P a , c (in eV) computed by DFT. Volumes V 0 , V C , V (in eV/GPa) and strain-energy parameter h (in eV) used in the elasticity calculations. Contribution of the short-range carbon-carbon interactions to the enthalpy was written as a pairwise Ising-type model:

a 0 S 11 S 12 P a P c V 0 V C V h 0.
H nn = 1 2
V i j , where V i j is the interaction energy between two carbon atoms indexed i and j. The V i j 's were computed by DFT up to the 19th coordination shell [36] . To evaluate H nn (η, ζ ) , 250,0 0 0 carbon atoms were randomly distributed over the 3 octahedral sublattices according to the specified order parameters and the summation was performed numerically.

The ordering enthalpy computed with the elasticity model coincides well with the decreasing parabolic profile obtained by SQS-DFT ( Fig. 2 top), and even better when the C-C pairwise contribution is added. The coincidence remains satisfactory in case of applied stress ( Fig. 3 ): although a slight shift is observed, the influence of the order state is well rendered by the elasticity and pairwise interactions model. We conclude that elasticity captures ∼85% of the ordering enthalpy, while pairwise interactions have a minority contribution of ∼15%. The latter moderate effect is qualitatively in line with the findings of Yan et al. [26] . On the other hand, the influence of ordering on the lattice parameters is perfectly rendered by the elasticity model ( Fig. 2 bottom). As expected from elasticity theory, short-range interactions play a negligible role on the carbon-induced homogeneous strain [START_REF] Khachaturyan | Theory of structural transformations in solids[END_REF] .

To generalise our investigation to all possible states of order, surface plots of the reduced ordering enthalpy H el /h c 2 were computed with the elasticity model for selected values of the reduced applied stress σV /h c ( Fig. 4 ). In the stress-free condition ( σ = 0 ), H el exhibits three degenerate stable states characterised by the ( η, ζ ) pairs (-0 . 5 , -1) , (-0 . 5 , 1) and (1,0). These pairs represent respectively the fully Zener-ordered variants Z1, Z2 and Z3. We see that when a tensile stress is applied ( σ > 0 ), the degeneracy is lifted and the stable state is the Zener-ordered variant Z3. In case of compressive stress ( σ < 0 ) variants Z1 and Z2 are the two degenerate stable states. These variants are oriented transversaly to the applied compressive stress. Owing to the downward concavity of the enthalpy surfaces, all partially ordered states are unstable, including the disordered structure (0,0) and the inverse-Zener structure (-0 . 5 , 0) , and this regardless the applied stress.

We have demonstrated that full Zener order is always energetically more favorable than any other state of order, while disorder and inverse-Zener order are unstable. This conclusion is true as long as the carbon atoms are randomly distributed in each sublattice. We did not investigate secondary ordering, i.e. ordering in one or more sublattices, possibly occurring at some specific carbon stoichiometries. Such phenomenon was evidenced experimentally [START_REF] Taylor | [END_REF] and theoretically [22,25,26,38] . However, secondary ordering is expected to affect only marginally the ordering enthalpies, es-pecially at low-carbon content, thus not invalidating our general conclusions.

Chen et al. reported the experimental evidence of cubic or nontetragonal martensite formed at room temperature in plastically deformed quenched martensite [7] , as well as in deformationinduced nanograined martensite [8] . These results apparently contradict our finding that Zener order is expected in martensite, whatever the applied stress. However, the present paper is limited to investigating the 0 K states of a defect-free crystal. At finite temperature, martensite orders on the condition that its carbon content be higher than a critical value. According to literature, this value lies in the range of 0.8 to 2.9 at% at room temperature. Chen et al.'s material may not reach the criterion. Indeed, although their nominal carbon is high, carbon atoms are likely to have migrated to the deformation-induced dislocations and/or to the nanograin boundaries during room-temperature ageing or sample preparation, thus decreasing solute carbon down to a subcritical value.

Our first-principles investigation leads to the conclusion that Zener-ordered configurations of body-centered Fe-C are always energetically favoured compared to disordered or partially ordered ones. This finding supports Zener's theory of ordering. Comparison with mean-field elasticity and Ising-type modelling confirms that Zener ordering is mostly driven by the long-range carboncarbon strain interaction, while short-range carbon-carbon interactions play a minor role. These conclusions remain true when tensile or compressive stress is applied.

Fig. 1 .

 1 Fig. 1. The Zener order-disorder transition transforms bcc-ferrite (left) into bctmartensite (right) and vice-versa. Fe atoms are in gray, preferred carbon sites are coloured according to their sublattice (RGB code).

  range order parameters η and ζ defined by cη = c 3 -1 2 (c 1 + c 2 ) and cζ = c 2c 1 . Parameter η quantifies the degree of Zener order along crystal direction [001], while ζ quantifies the unequal occupancy in directions [100] and [010]. In the mean-field approach, a state of order is characterised by the pair of parameters (η, ζ ) . The case (1,0) represents full Zener order along direction

Fig. 2 .

 2 Fig. 2. Ordering enthalpy (top) and lattice parameters (bottom) as function of Zener-order parameter η ( ζ = 0 ) in stress-free Fe-8.6at%C. SQS-DFT is compared to elasticity and pairwise interactions and to experimental data from Cheng [49] . Error bars indicate the standard deviations.

Fig. 3 .

 3 Fig. 3. Ordering enthalpy of various states of order under tensile or compressive stress in Fe-8.6at%C and schematics of the relaxed cell shape (arrows represent the state of order). Fully Zener-ordered configurations are the most stable ones in all cases.

Fig. 4 .

 4 Fig.4. Ordering enthalpy (in units of h c 2 ) as function of the order parameters η and ζ . From left to right: σ = -1 , 0 and 1 (in units of h c/V ). The gray triangle drawn at ordinate -1 represents all accessible states of order. Z1, Z2 and Z3 fully-ordered variants (coloured points) are the stable states when no stress is applied (centre). Tension along axis 3 stabilises longitudinal variant Z3 (right), while compression stabilises both transverse variants Z1 and Z2 (left).

Acknowledgements

This work was supported by the Agence Nationale de la Recherche (contract C-TRAM ANR-18-CE92-0021 ). Centre de Calcul Intensif d'Aix-Marseille is acknowledged for granting access to its high performance computing resources. The authors thank C. Arnold for his technical assistance in compiling the VASP code.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Supplementary material

Supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.scriptamat.2020.