16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs

Establishment of methanogen bacterial interactions during the preweaning period of dairy cattle

Ruminant livestock are major contributors to anthropogenic methane emissions in the United States and worldwide. Enteric methane is generated by methanogenic archaea residing in ruminant digestive tracts. Information on when methanogens colonize the gut and when they begin to interact with bacteria during the early phases of the ruminant life cycle is less explored. The objectives of this study were (i) to investigate the composition of the methanogenic archaeal community at birth and through the weaning transition and (ii) to determine if and when the methanogenic archaea begin to interact with bacteria in the lower gut of neonatal dairy calves. Ten female Holstein calves (approximately 45kg birth weight) were enrolled in the study. Fecal samples were collected every two weeks (Wk 2, 4, 6, 8, 10, and 12) between birth and weaning and analyzed for methanogenic archaeal diversity via 16S rRNA amplicon sequencing and quantitative real-time PCR (RT-qPCR). Estimates of alpha diversity (Observed species, and Shannon diversity index) and beta diversity (weighted and unweighted UniFrac distances) showed significant differences (P < 0.05) between archaeal communities across timepoints. Both 16S rRNA amplicon sequencing and RT-qPCR analyses revealed Methanobrevibacter was the most prevalent genus at Wk2, Wk4, and Wk6, whereas Methanosphaera gradually increased with time and was most abundant at Wk10 and Wk12. Correlation analysis revealed that Methanobrevibacter and Methanosphaera were inversely correlated with each other and formed distinct cohorts with specific bacterial lineages similar to those reported in the mature rumen, thus revealing that these associations are established during the preweaning period. Therefore, the preweaning period presents a window of opportunity to interfere with early-life methanogenic colonization with the ultimate goal of reducing enteric methane emissions without perturbing ruminal function later in the life of dairy cattle.

Dynamic changes in fecal microbiota in donkey foals during weaning: From pre-weaning to post-weaning

Introduction

A better understanding of the microbiota community in donkey foals during the weaning transition is a prerequisite to optimize gut function and improve feed efficiency. The objective of the present study was to investigate the dynamic changes in fecal microbiota in donkey foals from pre-to post-weaning period.

Methods

A total of 27 fecal samples of donkey foals were collected in the rectum before morning feeding at pre-weaning (30 days of age, PreW group, n = 9), dur-weaning (100 days of age, DurW group, n = 9) and post-weaning (170 days of age, PostW group, n = 9) period. The 16S rRNA amplicon sequencing were employed to indicate the microbial changes during the weaning period.

Results

In the present study, the cessation of breastfeeding gradually and weaning onto plant-based feeds increased the microbial diversity and richness, with a higher Shannon, Ace, Chao and Sobs index in DurW and PostW than in PreW (p < 0.05). The predominant bacterial phyla in donkey foal feces were Firmicutes (>50.5%) and Bacteroidota (>29.5%), and the predominant anaerobic fungi and archaea were Neocallimastigomycota and Euryarchaeota. The cellulolytic related bacteria including phylum Firmicutes, Spirochaetota and Fibrobacterota and genus norank_f_F082, Treponema, NK4A214_group, Lachnospiraceae_AC2044_group and Streptococcus were increased from pre-to post-weaning donkey foals (p < 0.05). Meanwhile, the functions related to the fatty acid biosynthesis, carbohydrate metabolism and amino acid biosynthesis were significantly enriched in the fecal microbiome in the DurW and PostW donkeys. Furthermore, the present study provided the first direct evidence that the initial colonization and establishment of anaerobic fungi and archaea in donkey foals began prior to weaning. The relative abundance of Orpinomyces were the highest in DurW donkey foals among the three groups (p < 0.01). In terms of archaea, the abundance of Methanobrevibacter were higher in PreW than in DurW and PostW (p < 0.01), but the abundance of Methanocorpusculum were significantly increased in DurW and PostW compared to PreW donkey foals (p < 0.01).

Discussion

Altogether, the current study contributes to a comprehensive understanding of the development of the microbiota community in donkey foals from pre-to post-weaning period, which may eventually result in an improvement of the digestion and feed efficiency in donkeys.

Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome

Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.

Cross-reactivity of antibodies to different rumen methanogens demonstrated using immunomagnetic capture technology

Methane is produced in the rumen of ruminant livestock by methanogens, accounting for approximately 14.5% of anthropogenic greenhouse gas emissions in terms of global warming potential. The rumen contains a diversity of methanogens species, and only a few of these have been cultured. Immunomagnetic capture technology (ICT) is a simple and effective method to capture and concentrate target organisms in samples containing complex microflora. We hypothesized that antibody-coated magnetic beads could be used to demonstrate antibody specificity and cross-reactivity to methanogens in rumen samples. Sheep polyclonal antibodies raised against four isolates of rumen dwelling methanogens, Methanobrevibacter ruminantium strain M1, Methanobrevibacter sp. AbM4, Methanobrevibacter sp. D5, and Methanobrevibacter sp. SM9 or an equal mix of all four isolates, were used to coat paramagnetic beads. ICT was used together with flow cytometry and qPCR to optimize key parameters: the ratio of antibody to beads, coupling time between antibody and paramagnetic beads to produce immunomagnetic beads (IMBs), and optimal incubation time for the capture of methanogen cells by IMBs. Under optimized conditions, IMBs bound strongly to their respective isolates and showed a degree of cross-reactivity with isolates of other Methanobrevibacter spp. in buffer and in rumen fluid, and with resident methanogens in rumen content samples. The evidence provided here indicates that this method can be used to study the interaction of antibodies with antigens of rumen methanogens, to understand antigen cross-reactivity and antibody binding efficiency for the evaluation of antigens used for the development of a broad-spectrum anti-methanogen vaccine for the abatement of methane production.

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom

Archaea are common constituents of the gut microbiome of humans, ruminants, and termites but little is known about their diversity and abundance in other animals. Here, we analyse sequencing and quantification data of archaeal and bacterial 16S rRNA genes from 250 species of animals covering a large taxonomic spectrum. We detect the presence of archaea in 175 animal species belonging to invertebrates, fish, amphibians, birds, reptiles and mammals. We identify five dominant gut lineages, corresponding to Methanobrevibacter, Methanosphaera, Methanocorpusculum, Methanimicrococcus and "Ca. Methanomethylophilaceae". Some archaeal clades, notably within Methanobrevibacter, are associated to certain hosts, suggesting specific adaptations. The non-methanogenic lineage Nitrososphaeraceae (Thaumarchaeota) is frequently present in animal samples, although at low abundance, but may have also adapted to the gut environment. Host phylogeny, diet type, fibre content, and intestinal tract physiology are major drivers of the diversity and abundance of the archaeome in mammals. The overall abundance of archaea is more influenced by these factors than that of bacteria. Methanogens reducing methyl-compounds with H2 can represent an important fraction of the overall methanogens in many animals. Together with CO2-reducing methanogens, they are influenced by diet and composition of gut bacteria. Our results provide key elements toward our understanding of the ecology of archaea in the gut, an emerging and important field of investigation.

Novel Methanobacterium Strain Induces Severe Corrosion by Retrieving Electrons from Fe0 under a Freshwater Environment

Methanogens capable of accepting electrons from Fe⁰ cause severe corrosion in anoxic conditions. In previous studies, all iron-corrosive methanogenic isolates were obtained from marine environments. However, the presence of methanogens with corrosion ability using Fe⁰ as an electron donor and their contribution to corrosion in freshwater systems is unknown. Therefore, to understand the role of methanogens in corrosion under anoxic conditions in a freshwater environment, we investigated the corrosion activities of methanogens in samples collected from groundwater and rivers. We enriched microorganisms that can grow with CO₂/NaHCO₃ and Fe⁰ as the sole carbon source and electron donor, respectively, in ground freshwater. Methanobacterium sp. TO1, which induces iron corrosion, was isolated from freshwater. Electrochemical analysis revealed that strain TO1 can uptake electrons from the cathode at lower than −0.61 V vs SHE and has a redox-active component with electrochemical potential different from those of other previously reported methanogens with extracellular electron transfer ability. This study indicated the corrosion risk by methanogens capable of taking up electrons from Fe⁰ in anoxic freshwater environments and the necessity of understanding the corrosion mechanism to contribute to risk diagnosis.

Presence of Adult Companion Goats Favors the Rumen Microbial and Functional Development in Artificially Reared Kids

Newborn dairy ruminants are usually separated from their dams after birth and fed on milk replacer. This lack of contact with adult animals may hinder the rumen microbiological and physiological development. This study evaluates the effects of rearing newborn goat kids in contact with adult companions on the rumen development. Thirty-two newborn goat kids were randomly allocated to two experimental groups which were reared either in the absence (CTL) or in the presence of non-lactating adult goats (CMP) and weaned at 7 weeks of age. Blood and rumen samples were taken at 5, 7, and 9 weeks of age to evaluate blood metabolites and rumen microbial fermentation. Next-generation sequencing was carried out on rumen samples collected at 7 weeks of age. Results showed that CTL kids lacked rumen protozoa, whereas CMP kids had an abundant and complex protozoal community as well as higher methanogen abundance which positively correlated with the body weight and blood β-hydroxybutyrate as indicators of the physiological development. CMP kids also had a more diverse bacterial community (+132 ASVs) and a different structure of the bacterial and methanogen communities than CTL kids. The core rumen bacterial community in CMP animals had 53 more ASVs than that of CTL animals. Furthermore, the number of ASVs shared with the adult companions was over 4-fold higher in CMP kids than in CTL kids. Greater levels of early rumen colonizers Proteobacteria and Spirochaetes were found in CTL kids, while CMP kids had higher levels of Bacteroidetes and other less abundant taxa (Veillonellaceae, Cyanobacteria, and Selenomonas). These findings suggest that the presence of adult companions facilitated the rumen microbial development prior to weaning. This accelerated microbial development had no effect on the animal growth, but CMP animals presented higher rumen pH and butyrate (+45%) and ammonia concentrations than CTL kids, suggesting higher fibrolytic and proteolytic activities. CMP kids also had higher blood β-hydroxybutyrate (+79%) and lower blood glucose concentrations (-23%) at weaning, indicating an earlier metabolic development which could favor the transition from pre-ruminant to ruminant after the weaning process. Further research is needed to determine the effects of this intervention in more challenging farm conditions.

Cashew nut shell liquid potentially mitigates methane emission from the feces of Thai native ruminant livestock by modifying fecal microbiota

The methane-mitigating potency of cashew nutshell liquid (CNSL) was evaluated by investigating gas production from batch cultures using feces from Thai native ruminants that had been incubated for different periods. Feces was obtained from four Thai native cattle and four swamp buffaloes reared under practical feeding conditions at the Kasetsart University farm, Thailand. Fecal slurry from the same farm was also included in the analysis. CNSL addition successfully suppressed the methane production potential of feces from both ruminants by shifting short chain fatty acid profiles towards propionate production. Methane mitigation continued for almost 150 days, although the degree of mitigation was more apparent from Day 0 to Day 30. Bacterial and archaeal community shifts with CNSL addition were observed in feces from both ruminants; specifically, Bacteroides increased, whereas Lachnospiraceae and Ruminococcaceae decreased in feces to which CNSL was added. Fecal slurry did not show marked changes in gas production with CNSL addition. The findings showed that the addition of CNSL to the feces of ruminants native to the Southeast Asian region can suppress methane emission. Because CNSL can be easily obtained as a byproduct of the local cashew industry in this region, its on-site application might be ideal.

Comparison of enteric methane yield and diversity of ruminal methanogens in cattle and buffaloes fed on the same diet

An in vivo study was conducted to compare the enteric methane emissions and diversity of ruminal methanogens in cattle and buffaloes kept in the same environment and fed on the same diet. Six cattle and six buffaloes were fed on a similar diet comprising Napier (Pennisetum purpureum) green grass and concentrate in 70:30. After 90 days of feeding, the daily enteric methane emissions were quantified by using the SF6 technique and ruminal fluid samples from animals were collected for the diversity analysis. The daily enteric methane emissions were significantly greater in cattle as compared to buffaloes; however, methane yields were not different between the two species. Methanogens were ranked at different taxonomic levels against the Rumen and Intestinal Methanogen-Database. The archaeal communities in both host species were dominated by the phylum Euryarchaeota; however, Crenarchaeota represented <1% of the total archaea. Methanogens affiliated with Methanobacteriales were most prominent and their proportion did not differ between the two hosts. Methanomicrobiales and Methanomassillicoccales constituted the second largest group of methanogens in cattle and buffaloes, respectively. Methanocellales (Methanocella arvoryza) were exclusively detected in the buffaloes. At the species level, Methanobrevibacter gottschalkii had the highest abundance (55-57%) in both the host species. The relative abundance of Methanobrevibacter wolinii between the two hosts differed significantly. Methanosarcinales, the acetoclastic methanogens were significantly greater in cattle than the buffaloes. It is concluded that the ruminal methane yield in cattle and buffaloes fed on the same diet did not differ. With the diet used in this study, there was a limited influence (<3.5%) of the host on the structure of the ruminal archaea community at the species level. Therefore, the methane mitigation strategies developed in either of the hosts should be effective in the other. Further studies are warranted to reveal the conjunctive effect of diet and geographical locations with the host on ruminal archaea community composition.

Inoculation with rumen fluid in early life accelerates the rumen microbial development and favours the weaning process in goats

BACKGROUND

Newborn ruminants possess an underdeveloped rumen which is colonized by microorganisms acquired from adult animals and the surrounding environment. This microbial transfer can be limited in dairy systems in which newborns are separated from their dams at birth. This study explores whether the direct inoculation of fresh or autoclaved rumen fluid from adult goats to newborn kids has a beneficial effect on rumen microbial development and function.

RESULTS

Repetitive inoculation of young kids with fresh rumen fluid from adult goats adapted to forage (RFF) or concentrate diets (RFC) accelerated microbial colonization of the rumen during the pre-weaning period leading to high protozoal numbers, a greater diversity of bacterial (+ 234 OTUs), methanogens (+ 6 OTUs) and protozoal communities (+ 25 OTUs) than observed in control kids (CTL) without inoculation. This inoculation also increased the size of the core bacterial and methanogens community and the abundance of key rumen bacteria (Ruminococcaceae, Fibrobacteres, Veillonellaceae, Rikenellaceae, Tenericutes), methanogens (Methanobrevibacter ruminantium, Methanomicrobium mobile and Group 9), anaerobic fungi (Piromyces and Orpinomyces) and protozoal taxa (Enoploplastron, Diplodinium, Polyplastron, Ophryoscolex, Isotricha and Dasytricha) before weaning whereas CTL kids remained protozoa-free through the study. Most of these taxa were positively correlated with indicators of the rumen microbiological and physiological development (higher forage and concentrate intakes and animal growth during the post-weaning period) favoring the weaning process in RFF and RFC kids in comparison to CTL kids. Some of these microbiological differences tended to decrease during the post-weaning period, although RFF and RFC kids retained a more complex and matured rumen microbial ecosystem than CTL kids. Inoculation with autoclaved rumen fluid promoted lower development of the bacterial and protozoal communities during the pre-weaning period than using fresh inocula, but it favored a more rapid microbial development during the post-weaning than observed for CTL kids.

CONCLUSIONS

This study demonstrated that inoculation of young ruminants with fresh rumen fluid from adult animals accelerated the rumen microbial colonization which was associated with an earlier rumen functional development. This strategy facilitated a smoother transition from milk to solid feed favoring the animal performance during post-weaning and minimizing stress.

Phytogenic Additives Can Modulate Rumen Microbiome to Mediate Fermentation Kinetics and Methanogenesis Through Exploiting Diet-Microbe Interaction

Ruminants inhabit the consortia of gut microbes that play a critical functional role in their maintenance and nourishment by enabling them to use cellulosic and non-cellulosic feed material. These gut microbes perform major physiological activities, including digestion and metabolism of dietary components, to derive energy to meet major protein (65-85%) and energy (ca 80%) requirements of the host. Owing to their contribution to digestive physiology, rumen microbes are considered one of the crucial factors affecting feed conversion efficiency in ruminants. Any change in the rumen microbiome has an imperative effect on animal physiology. Ruminal microbes are fundamentally anaerobic and produce various compounds during rumen fermentation, which are directly used by the host or other microbes. Methane (CH4) is produced by methanogens through utilizing metabolic hydrogen during rumen fermentation. Maximizing the flow of metabolic hydrogen in the rumen away from CH4 and toward volatile fatty acids (VFA) would increase the efficiency of ruminant production and decrease its environmental impact. Understanding of microbial diversity and rumen dynamics is not only crucial for the optimization of host efficiency but also required to mediate emission of greenhouse gases (GHGs) from ruminants. There are various strategies to modulate the rumen microbiome, mainly including dietary interventions and the use of different feed additives. Phytogenic feed additives, mainly plant secondary compounds, have been shown to modulate rumen microflora and change rumen fermentation dynamics leading to enhanced animal performance. Many in vitro and in vivo studies aimed to evaluate the use of plant secondary metabolites in ruminants have been conducted using different plants or their extract or essential oils. This review specifically aims to provide insights into dietary interactions of rumen microbes and their subsequent consequences on rumen fermentation. Moreover, a comprehensive overview of the modulation of rumen microbiome by using phytogenic compounds (essential oils, saponins, and tannins) for manipulating rumen dynamics to mediate CH4 emanation from livestock is presented. We have also discussed the pros and cons of each strategy along with future prospective of dietary modulation of rumen microbiome to improve the performance of ruminants while decreasing GHG emissions.

Seasonal and Nutrient Supplement Responses in Rumen Microbiota Structure and Metabolites of Tropical Rangeland Cattle

This study aimed to characterize the rumen microbiota structure of cattle grazing in tropical rangelands throughout seasons and their responses in rumen ecology and productivity to a N-based supplement during the dry season. Twenty pregnant heifers grazing during the dry season of northern Australia were allocated to either N-supplemented or un-supplemented diets and monitored through the seasons. Rumen fluid, blood, and feces were analyzed before supplementation (mid-dry season), after two months supplementation (late-dry season), and post supplementation (wet season). Supplementation increased average daily weight gain (ADWG), rumen NH3-N, branched fatty acids, butyrate and acetic:propionic ratio, and decreased plasma δ15N. The supplement promoted bacterial populations involved in hemicellulose and pectin degradation and ammonia assimilation: Bacteroidales BS11, Cyanobacteria, and Prevotella spp. During the dry season, fibrolytic populations were promoted: the bacteria Fibrobacter, Cyanobacteria and Kiritimatiellaeota groups; the fungi Cyllamyces; and the protozoa Ostracodinium. The wet season increased the abundances of rumen protozoa and fungi populations, with increases of bacterial families Lachnospiraceae, Ruminococcaceae, and Muribaculaceae; the protozoa Entodinium and Eudiplodinium; the fungi Pecoramyces; and the archaea Methanosphera. In conclusion, the rumen microbiota of cattle grazing in a tropical grassland is distinctive from published studies that mainly describe ruminants consuming better quality diets.

Comparative Microbiome Analysis Reveals the Ecological Relationships Between Rumen Methanogens, Acetogens, and Their Hosts

Ruminant methane, which is generated by methanogens through the consumption of hydrogen and supports the normal function of the rumen ecosystem, is a major source of greenhouse gases. Reductive acetogenesis by acetogens is a possible alternative sink that can dispose of hydrogen for acetate production. However, the distribution of rumen methanogens and acetogens along with the relationships among methanogens, acetogens, and their host are poorly understood. Therefore, we investigated the rumen methanogen and acetogen communities of 97 individual animals representing 14 ruminant species within three ruminant families Cervidae (deer), Bovidae (bovid), and Moschidae (musk deer). The results showed that the Methanobrevibacter spp. and acetogens associated with Eubacteriaceae were the most widespread methanogens and acetogens, respectively. However, other methanogens and acetogens exhibited host specificity in the rumen of reindeer and Chinese muntjac deer. Acetogen and methanogen communities were not correlated in these species, and the phylosymbiosis signature between host phylogeny and the composition of both communities was lacking. The abundance of Methanobrevibacter gottschalkii was negatively correlated with the degree of papillation of the rumen wall. Finally, co-occurrence analysis showed that the variation of the predicted methane yields was characterized by the interactive patterns between methanogens, acetogens, and concentrations of rumen metabolites. Our results show that rumen methanogen and acetogen communities have low compositional interdependence and do not exhibit parallel host evolution, which suggests that the strategies for mitigating methane production should be based on a species-specific rumen microbiota analysis.

A meta-analysis of the bovine gastrointestinal tract microbiota

The bovine gastrointestinal (GI) tract microbiota has important influences on animal health and production. Presently, a large number of studies have used high-throughput sequencing of the archaeal and bacteria 16S rRNA gene to characterize these microbiota under various experimental parameters. By aggregating publically available archaeal and bacterial 16S rRNA gene datasets from 52 studies we were able to determine taxa that are common to nearly all microbiota samples from the bovine GI tract as well as taxa that are strongly linked to either the rumen or feces. The methanogenic genera Methanobrevibacter and Methanosphaera were identified in nearly all fecal and rumen samples (> 99.1%), as were the bacterial genera Prevotella and Ruminococcus (≥ 92.9%). Bacterial genera such as Alistipes, Bacteroides, Clostridium, Faecalibacterium and Escherichia/Shigella were associated with feces and Fibrobacter, Prevotella, Ruminococcus and Succiniclasticum with the rumen. As expected, individual study strongly affected the bacterial community structure, however, fecal and rumen samples did appear separated from each other. This meta-analysis provides the first comparison of high-throughput sequencing 16S rRNA gene datasets generated from the bovine GI tract by multiple studies and may serve as a foundation for improving future microbial community research with cattle.

Supplementation of live yeast based feed additive in early life promotes rumen microbial colonization and fibrolytic potential in lambs

Rumen microbiota is of paramount importance for ruminant digestion efficiency as the microbial fermentations supply the host animal with essential sources of energy and nitrogen. Early separation of newborns from the dam and distribution of artificial milk (Artificial Milking System or AMS) could impair rumen microbial colonization, which would not only affect rumen function but also have possible negative effects on hindgut homeostasis, and impact animal health and performance. In this study, we monitored microbial communities in the rumen and the feces of 16 lambs separated from their dams from 12 h of age and artificially fed with milk replacer and starter feed from d8, in absence or presence of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. Microbial groups and targeted bacterial species were quantified by qPCR and microbial diversity and composition were assessed by 16S rDNA amplicon sequencing in samples collected from birth to 2 months of age. The fibrolytic potential of the rumen microbiota was analyzed with a DNA microarray targeting genes coding for 8 glycoside hydrolase (GH) families. In Control lambs, poor establishment of fibrolytic communities was observed. Microbial composition shifted as the lambs aged. The live yeast supplement induced significant changes in relative abundances of a few bacterial OTUs across time in the rumen samples, among which some involved in crucial rumen function, and favored establishment of Trichostomatia and Neocallimastigaceae eukaryotic families. The supplemented lambs also harbored greater abundances in Fibrobacter succinogenes after weaning. Microarray data indicated that key cellulase and hemicellulase encoding-genes were present from early age in the rumen and that in the Supplemented lambs, a greater proportion of hemicellulase genes was present. Moreover, a higher proportion of GH genes from ciliate protozoa and fungi was found in the rumen of those animals. This yeast combination improved microbial colonization in the maturing rumen, with a potentially more specialized ecosystem towards efficient fiber degradation, which suggests a possible positive impact on lamb gut development and digestive efficiency.

Maternal versus artificial rearing shapes the rumen microbiome having minor long-term physiological implications

Increasing productivity is a key target in ruminant science which requires better understanding of the rumen microbiota. This study investigated how maternal versus artificial rearing shapes the rumen microbiota using 24 sets of triplet lambs. Lambs within each sibling set were randomly assigned to natural rearing on the ewe (NN); ewe colostrum for 24 h followed by artificial milk feeding (NA); and colostrum alternative and artificial milk feeding (AA). Maternal colostrum feeding enhanced VFA production at weaning but not thereafter. At weaning, lambs reared on milk replacer had no rumen protozoa and lower microbial diversity, whereas natural rearing accelerated the rumen microbial development and facilitated the transition to solid diet. Differences in the rumen prokaryotic communities disappear later in life when all lambs were grouped on the same pasture up to 23 weeks of age. However, NN animals retained higher fungal diversity and abundances of Piromyces, Feramyces and Diplodiniinae protozoa as well as higher feed digestibility (+4%) and animal growth (+6.5%) during the grazing period. Nevertheless, no correlations were found between rumen microbiota and productive outcomes. These findings suggest that the early life nutritional intervention determine the initial rumen microbial community, but the persistence of these effects later in life is weak.

Heterogeneous development of methanogens and the correlation with bacteria in the rumen and cecum of sika deer (Cervus nippon) during early life suggest different ecology relevance

BACKGROUND

Enteric methane from the ruminant livestock is a significant source in global greenhouse gas emissions, which is mainly generated by the methanogens inhabiting the rumen and cecum. Sika deer (Cervus nippon) not only produces less methane than bovine, but they also harbor a distinct methanogen community. Whereas, knowledge of methanogens colonization in the rumen and cecum of sika deer is relatively still unknown, which could provide more insights to the manipulation of gut microbiota during early life.

RESULTS

Here, we examined the development of bacteria and methanogens in the rumen and cecum of juvenile sika deer from birth to post-weaning (1 day, 42 days and 70 days, respectively) based on next generation sequencing. The results showed that the facultative anaerobic bacteria were decreased and the cellulolytic bacteria were increased. However, methanogens established soon after birth thrived through the whole developmental period, indicating a different succession process than bacteria in the GIT, and the limited role of age and dietary change on GIT methanogens. We also found Methanobrevibacter spp. (Mean relative abundance = 44.2%) and Methanocorpusculum spp. (Mean relative abundance = 57.5%) were dominated in the rumen and cecum, respectively. The methanogens also formed specific correlations with bacteria under different niches, suggesting a role of ecology niche on methanogen community.

CONCLUSIONS

This study contributes to our knowledge about the microbial succession in GIT of sika deer, that may facilitate the development of targeted strategies to improve GIT function of sika deer.

Methanogenesis in animals with foregut and hindgut fermentation: a review

Methane is the main greenhouse-gas contributor to global warming in the livestock sector; it is generated by anaerobic fermentation in the different sections of the gut, and the methane concentration differs significantly among species. Methane is produced only by certain types of microorganisms called methanogens. The species composition of methanogenic archaea population is largely affected by the diet, geographical location, host and the section of the gut. Consequently, methane production, either measured as total grams emitted per day or per bodyweight mass, differs greatly among animal species. The main difference in methanogenic activity among different gut sections and animal species is the substrate fermented and the metabolic pathway to complete anaerobic fermentation of plant material. The three main substrates used by methanogens are CO2, acetate and compounds containing methyl groups. The three dominant orders of methanogens in gut environments are Methanomicrobiales, Methanobacteriales and Methanosarcinales. They normally are present in low numbers (below 3% of total microbiome). The present review will describe the main metabolic pathways and methanogens involved in CH4 production in the gut of different host-animal species, as well as discuss general trends that influence such emissions, such as geographical distribution, feed composition, section of the gut, host age and diurnal and season variation. Finally, the review will describe animal species (large and small domestic ruminants, wild ruminants, camelids, pigs, rabbits, horses, macropods, termites and humans) specificities in the methanogen diversity and their effects on methane emission.

RUMINANT NUTRITION SYMPOSIUM: Tiny but mighty: the role of the rumen microbes in livestock production

The microbes inhabiting the rumen convert low-quality, fibrous, plant material into useable energy for the host ruminant. Consisting of bacteria, protozoa, fungi, archaea, and viruses, the rumen microbiome composes a sophisticated network of symbiosis essential to maintenance, immune function, and overall production efficiency of the host ruminant. Robert Hungate laid the foundation for rumen microbiome research. This area of research has expanded immensely with advances in methodology and technology that have not only improved the ability to describe microbes in taxonomic and density terms but also characterize populations of microbes, their functions, and their interactions with each other and the host. The interplay between the rumen microbiome and the host contributes to variation in many phenotypic traits expressed by the host animal. A better understanding of how the rumen microbiome influences host health and performance may lead to novel strategies and treatments for trait improvement. Furthermore, elucidation of maternal, genetic, and environmental factors that influence rumen microbiome establishment and development may provide novel insights into possible mechanisms for manipulating the rumen microbial composition to enhance long-term host health and performance. The potential for these tiny but mighty rumen microbes to play a role in improving livestock production is appreciated despite being relatively obscure.

Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract

The impact of maternal microbial influences on the early choreography of the neonatal calf microbiome were investigated. Luminal content and mucosal scraping samples were collected from ten locations in the calf gastrointestinal tract (GIT) over the first 21 days of life, along with postpartum maternal colostrum, udder skin, and vaginal scrapings. Microbiota were found to vary by anatomical location, between the lumen and mucosa at each GIT location, and differentially enriched for maternal vaginal, skin, and colostral microbiota. Most calf sample sites exhibited a gradual increase in α-diversity over the 21 days beginning the first few days after birth. The relative abundance of Firmicutes was greater in the proximal GIT, while Bacteroidetes were greater in the distal GIT. Proteobacteria exhibited greater relative abundances in mucosal scrapings relative to luminal content. Forty-six percent of calf luminal microbes and 41% of mucosal microbes were observed in at-least one maternal source, with the majority being shared with microbes on the skin of the udder. The vaginal microbiota were found to harbor and uniquely share many common and well-described fibrolytic rumen bacteria, as well as methanogenic archaea, potentially indicating a role for the vagina in populating the developing rumen and reticulum with microbes important to the nutrition of the adult animal.

Air-Dried Brown Seaweed, Ascophyllum nodosum, Alters the Rumen Microbiome in a Manner That Changes Rumen Fermentation Profiles and Lowers the Prevalence of Foodborne Pathogens

Maintaining product safety and reducing the carbon footprint of production are two sustainability goals of the livestock industry. The objective of this study was to study the impact of Tasco, a product derived from the brown macroalga Ascophyllum nodosum, on the rumen microbiome and its function. The inclusion of Tasco altered both rumen and fecal microbiota levels without affecting rumen fermentation. Tasco reduced fecal Escherichia coli populations and specifically reduced the prevalence of Shiga toxin-producing E. coli O45, O103, O111, and O121 in feces. The findings of this study highlight the application of Tasco as a potential feed additive to reduce pathogen shedding in rams without interfering with ruminal metabolism.

The use of Tasco (air-dried Ascophyllum nodosum) as a feed supplement for ruminants has been reported to affect rumen fermentation and reduce Escherichia coli O157:H7 shedding in feces, but the mode of action behind this phenomenon is unclear. In this study, the effects of four Tasco levels (0, 1, 3, and 5%) on rumen microbiota and rumen/fecal E. coli O serogroups in rams were investigated. Rumen total bacteria and archaea were linearly reduced (P < 0.001) and protozoa were linearly increased (P < 0.001) by increasing levels of Tasco. The relative abundances of seven bacterial species and one protozoal species differed among Tasco levels. With Tasco, 14 predicted metabolic pathways were enriched while only 3 were suppressed. A lower ruminal butyrate concentration is possibly associated with enrichment of the “butanoate metabolism” pathway in Tasco-fed rams. The ruminal total E. coli population was linearly reduced (P < 0.001) by Tasco. Supplementation with Tasco only completely eliminated O121 in the rumen and feces, and higher levels of Tasco (3 and 5%) reduced fecal shedding of serogroups O45, O103, and O111 even though these serogroups were present in the rumen. Our results suggest that Tasco effectively reduced pathogenic E. coli but had only minimal impacts on rumen fermentation in rams.

IMPORTANCE Maintaining product safety and reducing the carbon footprint of production are two sustainability goals of the livestock industry. The objective of this study was to study the impact of Tasco, a product derived from the brown macroalga Ascophyllum nodosum, on the rumen microbiome and its function. The inclusion of Tasco altered both rumen and fecal microbiota levels without affecting rumen fermentation. Tasco reduced fecal Escherichia coli populations and specifically reduced the prevalence of Shiga toxin-producing E. coli O45, O103, O111, and O121 in feces. The findings of this study highlight the application of Tasco as a potential feed additive to reduce pathogen shedding in rams without interfering with ruminal metabolism.

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

The aim of this work was to evaluate the effect of feeding management during the first month of life (natural with the mother, NAT, or artificial with milk replacer, ART) on the rumen microbial colonization and the host innate immune response. Thirty pregnant goats carrying two fetuses were used. At birth one kid was taken immediately away from the doe and fed milk replacer (ART) while the other remained with the mother (NAT). Kids from groups received colostrum during first 2 days of life. Groups of four kids (from ART and NAT experimental groups) were slaughtered at 1, 3, 7, 14, 21 and 28 days of life. On the sampling day, after slaughtering, the rumen content was sampled and epithelial rumen tissue was collected. Pyrosequencing analyses of the bacterial community structure on samples collected at 3, 7, 14 and 28 days showed that both systems promoted significantly different colonization patterns (P = 0.001). Diversity indices increased with age and were higher in NAT feeding system. Lower mRNA abundance was detected in TLR2, TLR8 and TLR10 in days 3 and 5 compared to the other days (7, 14, 21 and 28). Only TLR5 showed a significantly different level of expression according to the feeding system, presenting higher mRNA abundances in ART kids. PGLYRP1 showed significantly higher abundance levels in days 3, 5 and 7, and then experienced a decline independently of the feeding system. These observations confirmed a highly diverse microbial colonisation from the first day of life in the undeveloped rumen, and show that the colonization pattern substantially differs between pre-ruminants reared under natural or artificial milk feeding systems. However, the rumen epithelial immune development does not differentially respond to distinct microbial colonization patterns.

Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves

At birth, calves display an underdeveloped rumen that eventually matures into a fully functional rumen as a result of solid food intake and microbial activity. However, little is known regarding the gradual impact of pre-weaning diet on the establishment of the rumen microbiota. Here, we employed next-generation sequencing to investigate the effects of the inclusion of starter concentrate (M: milk-fed vs. MC: milk plus starter concentrate fed) on archaeal, bacterial and anaerobic fungal communities in the rumens of 45 crossbred dairy calves across pre-weaning development (7, 28, 49, and 63 days). Our results show that archaeal, bacterial, and fungal taxa commonly found in the mature rumen were already established in the rumens of calves at 7 days old, regardless of diet. This confirms that microbiota colonization occurs in the absence of solid substrate. However, diet did significantly impact some microbial taxa. In the bacterial community, feeding starter concentrate promoted greater diversity of bacterial taxa known to degrade readily fermentable carbohydrates in the rumen (e.g., Megasphaera, Sharpea, and Succinivribrio). Shifts in the ruminal bacterial community also correlated to changes in fermentation patterns that favored the colonization of Methanosphaera sp. A4 in the rumen of MC calves. In contrast, M calves displayed a bacterial community dominated by taxa able to utilize milk nutrients (e.g., Lactobacillus, Bacteroides, and Parabacteroides). In both diet groups, the dominance of these milk-associated taxa decreased with age, suggesting that diet and age simultaneously drive changes in the structure and abundance of bacterial communities in the developing rumen. Changes in the composition and abundance of archaeal communities were attributed exclusively to diet, with more highly abundant Methanosphaera and less abundant Methanobrevibacter in MC calves. Finally, the fungal community was dominated by members of the genus SK3 and Caecomyces. Relative anaerobic fungal abundances did not change significantly in response to diet or age, likely due to high inter-animal variation and the low fiber content of starter concentrate. This study provides new insights into the colonization of archaea, bacteria, and anaerobic fungi communities in pre-ruminant calves that may be useful in designing strategies to promote colonization of target communities to improve functional development.

Compositional and functional dynamics of the bovine rumen methanogenic community across different developmental stages

Methanogenic archaea in the bovine rumen are responsible for the reduction of carbon molecules to methane, using various electron donors and driving the electron flow across the microbial food webs. Thus, methanogens play a key role in sustaining rumen metabolism and function. Research of rumen methanogenic archaea typically focuses on their composition and function in mature animals, while studies of early colonization and functional establishment remain scarce. Here, we investigated the metabolic potential and taxonomic composition of the methanogenic communities across different rumen developmental stages. We discovered that the methanogenesis process changes with age and that the early methanogenic community is characterized by a high activity of methylotrophic methanogenesis, likely performed by members of the order Methanosarcinales, exclusively found in young rumen. In contrast, higher hydrogenotrophic activity was observed in the mature rumen, where a higher proportion of exclusively hydrogenotrophic taxa are found. These findings suggest that environmental filtering acts on the archaeal communities and select for different methanogenic lineages during different growth stages, affecting the functionality of this ecosystem. This study provides a better understanding of the compositional and metabolic changes that occur in the rumen microbiome from its initial stages of colonization and throughout the animals' life.

Investigation and manipulation of metabolically active methanogen community composition during rumen development in black goats

This study was performed to investigate the initial colonization of metabolically active methanogens and subsequent changes in four fractions: the rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) from 1 to 60 d after birth, and manipulate methanogen community by early weaning on 40 d and supplementing rhubarb from 40 to 60 d in black goats. The RNA-based real-time quantitative PCR and 16S rRNA amplicon sequencing were employed to indicate the metabolically active methanogens. Results showed that active methanogens colonized in RL and RE on 1 d after birth. RP and RE contained the highest and lowest density of methanogens, respectively. Methanobrevibacter, Candidatus Methanomethylophilus, and Methanosphaera were the top three genera. The methanogen communities before weaning differed from those post weaning and the structure of the methanogen community in RE was distinct from those in the other three fractions. The discrepancies in the distribution of methanogens across four fractions, and various fluctuations in abundances among four fractions according to age were observed. The addition of rhubarb significantly (P < 0.05) reduced the abundances of Methanimicrococcus spp. in four fractions on 50 d, but did not change the methanogen community composition on 60 d.

Changes in Metabolically Active Bacterial Community during Rumen Development, and Their Alteration by Rhubarb Root Powder Revealed by 16S rRNA Amplicon Sequencing

The objective of this present study was to explore the initial establishment of metabolically active bacteria and subsequent evolution in four fractions: rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) through early weaning and supplementing rhubarb root powder in 7 different age groups (1, 10, 20, 38, 41, 50, and 60 d) during rumen development. Results of the 16S rRNA sequencing based on RNA isolated from the four fractions revealed that the potentially active bacterial microbiota in four fractions were dominated by the phyla Proteobacteria, Firmicutes, and Bacteroidetes regardless of different ages. An age-dependent increment of Chao 1 richness was observed in the fractions of RL and RE. The principal coordinate analysis (PCoA) indicated that samples in four fractions all clustered based on different age groups, and the structure of the bacterial community in RE was distinct from those in other three fractions. The abundances of Proteobacteria decreased significantly (P < 0.05) with age, while increases in the abundances of Firmicutes and Bacteroidetes were noted. At the genus level, the abundance of the predominant genus Mannheimia in the Proteobacteria phylum decreased significantly (P < 0.05) after 1 d, while the genera Quinella, Prevotella, Fretibacterium, Ruminococcus, Lachnospiraceae NK3A20 group, and Atopobium underwent different manners of increases and dominated the bacterial microbiota across four fractions. Variations of the distributions of some specific bacterial genera across fractions were observed, and supplementation of rhubarb affected the relative abundance of various genera of bacteria.

Dietary pea fiber increases diversity of colonic methanogens of pigs with a shift from Methanobrevibacter to Methanomassiliicoccus-like genus and change in numbers of three hydrogenotrophs

BACKGROUND

Pea fiber (PF) is a potential fibrous supplement in swine production. The influence of dietary PF on microbial community in the colon of pigs remains largely unexplored. Methanogens in the hindgut of monogastric animals play important roles in degradation of dietary fibers and efficient removal of microbial metabolic end product H2. Understanding the impact of dietary PF on the structure of colonic methanogens may help understand the mechanisms of microbe-mediated physiological functions of PF. This study investigated the influence of PF on the diversity and quantity and/or activity of colonic methanongens of piglets and finishing pigs. Four archaeal 16S rRNA clone libraries were constructed for piglets and finishers fed with control (Piglet-C and Finisher-C) or PF diet (Piglet-P and Finisher-P).

RESULTS

There were 195, 190, 194 and 196 clones obtained from the library Piglet-C, Piglet-P, Finisher-C and Finisher-P, respectively, with corresponding 12, 11, 11 and 16 OTUs (operational taxonomic units). Significant differences of Shannon Index among the four libraries were found (P < 0.05). Libshuff analysis showed that the archaeal community structure among the four libraries were significantly different (P < 0.0001). The predominant methanogens shifted from Methanobrevibacter to Methanobrevibacter and Methanomassiliicoccus-like genus as a result of dietary PF. Supplementation of PF significantly increased the copy numbers of mcrA and dsrA genes (P < 0.05).

CONCLUSIONS

Alteration of methanogenic community structure may lead to functional transition from utilization of H2/CO2 to employment of both H2/CO2 and methanol/CO2. Quantification of three functional genes (mcrA, dsrA and fhs) of methanogens, sulfate-reducing bacteria (SRB) and acetogens revealed that dietary PF also increased the activity of methanogens and SRB,probably associated with increased proportion of Methanomassiliicoccus luminyensis-species. Further study is required to examine the interaction between specific methanogens and SRB during fermentation of dietary PF.

Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota

Cystic fibrosis is often associated with intestinal inflammation due to several factors, including altered gut microbiota composition. In this study, we analyzed the fecal microbiota among patients with cystic fibrosis of 10–22 years of age, and compared the findings with age-matched healthy subjects. The participating patients included 14 homozygotes and 14 heterozygotes with the delF508 mutation, and 2 heterozygotes presenting non-delF508 mutations. We used PCR-DGGE and qPCR to analyze the presence of bacteria, archaea and sulfate-reducing bacteria. Overall, our findings confirmed disruption of the cystic fibrosis gut microbiota. Principal component analysis of the qPCR data revealed no differences between homozygotes and heterozygotes, while both groups were distinct from healthy subjects who showed higher biodiversity. Archaea were under the detection limit in all homozygotes subjects, whereas methanogens were detected in 62% of both cystic fibrosis heterozygotes and healthy subjects. Our qPCR results revealed a low frequency of sulfate-reducing bacteria in the homozygote (13%) and heterozygote (13%) patients with cystic fibrosis compared with healthy subjects (87.5%). This is a pioneer study showing that patients with cystic fibrosis exhibit significant reduction of H₂-consuming microorganisms, which could increase hydrogen accumulation in the colon and the expulsion of this gas through non-microbial routes.

Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs

The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. The results obtained clearly demonstrate that comparability of community profiles established using different primer pairs is difficult. 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis. This finding, previously shown for Bacteria, was as well observed for the archaeal domain.

Exploring the Goat Rumen Microbiome from Seven Days to Two Years

Rumen microbial communities play important roles in feed conversion and the physiological development of the ruminants. Despite its significance, little is known about the rumen microbial communities at different life stages after birth. In this study, we characterized the rumen bacterial and the archaeal communities in 11 different age groups (7, 15, 30, 60, 90, 120, 150, 180, 360, 540 and 720 days old) of a crossbred F1 goats (n = 5 for each group) by using an Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. We found that the bacterial communities were mainly composed of Bacteroidetes, Firmicutes, and Proteobacteria across all age groups. The relative abundance of Firmicutes was stable across all age groups. While changes in relative abundance were observed in Bacteroidetes and Proteobacteria, these two phyla reached a stable stage after weaning (day 90). Euryarchaeota (82%) and Thaumarchaeota (15%) were the dominant phyla of Archaea. Crenarchaeota was also observed, although at a very low relative abundance (0.68% at most). A clear age-related pattern was observed in the diversity of bacterial community with 59 OTUs associated with age. In contrast, no age-related OTU was observed in archaea. In conclusion, our results suggested that from 7 days to 2 years, the ruminal microbial community of our experimental goats underwent significant changes in response to the shift in age and diet.

Draft Genome Sequence of the Rumen Methanogen Methanobrevibacter olleyae YLM1

Methanobrevibacter olleyae YLM1 is a hydrogenotrophic methanogen, isolated from the rumen of a lamb. Its genome has been sequenced to provide information on the genomic diversity of rumen methanogens and support the development of approaches to reduce methane formation by ruminants.

Monitoring the microbial community shift throughout the shock changes of hydraulic retention time in an anaerobic moving bed membrane bioreactor

An anaerobic moving bed membrane bioreactor (AnMBMBR) fed with synthetic domestic wastewater was investigated under hydraulic retention time (HRT) shocks to assess the effects on the microbial (bacteria and archaea) community and reactor performance. 16S rDNA targeted polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach was optimized to relate the metabolic and community composition with biogas generation, methane content and COD removal efficiency. From the drastic decrease of HRT (from 8 h to 4 h), the methane production was significantly reduced due to the HRT shock, while the COD removal efficiency was not affected. The enhanced growth of homoacetogenic bacteria, Thermoanaerobacteraceae competes with methanogens under shock period. When the HRT was recovered to 8 h, the methane generation rate was higher than the initial operation before the shock HRT changes, which would be ascribed to the activity of new emerging hydrogenotrophic archaea, Methanocella sp. and Methanofollis sp.

High-throughput DNA sequencing of the moose rumen from different geographical locations reveals a core ruminal methanogenic archaeal diversity and a differential ciliate protozoal diversity

Moose rumen samples from Vermont, Alaska and Norway were investigated for methanogenic archaeal and protozoal density using real-time PCR, and diversity using high-throughput sequencing of the 16S and 18S rRNA genes. Vermont moose showed the highest protozoal and methanogen densities. Alaskan samples had the highest percentages of Methanobrevibacter smithii, followed by the Norwegian samples. One Norwegian sample contained 43 % Methanobrevibacter thaueri, whilst all other samples contained < 10 %. Vermont samples had large percentages of Methanobrevibacter ruminantium, as did two Norwegian samples. Methanosphaera stadtmanae represented one-third of sequences in three samples. Samples were heterogeneous based on gender, geographical location and weight class using analysis of molecular variance (AMOVA). Two Alaskan moose contained >70 % Polyplastron multivesiculatum and one contained >75 % Entodinium spp. Protozoa from Norwegian moose belonged predominantly (>50 %) to the genus Entodinium, especially Entodinium caudatum. Norwegian moose contained a large proportion of sequences (25–97 %) which could not be classified beyond family. Protozoa from Vermont samples were predominantly Eudiplodinium rostratum (>75 %), with up to 7 % Diploplastron affine. Four of the eight Vermont samples also contained 5–12 % Entodinium spp. Samples were heterogeneous based on AMOVA, principal coordinate analysis and UniFrac. This study gives the first insight into the methanogenic archaeal diversity in the moose rumen. The high percentage of rumen archaeal species associated with high starch diets found in Alaskan moose corresponds well to previous data suggesting that they feed on plants high in starch. Similarly, the higher percentage of species related to forage diets in Vermont moose also relates well to their higher intake of fibre.

Manipulating rumen microbiome and fermentation through interventions during early life: a review

The nutritional manipulations of the rumen microbiome to enhance productivity and health are rather limited by the resilience of the ecosystem once established in the mature rumen. Based on recent studies, it has been suggested that the microbial colonization that occurs soon after birth opens a possibility of manipulation with potential to produce lasting effects into adult life. This paper presents the state-of-the-art in relation to early life nutritional interventions by addressing three areas: the development of the rumen as an organ in regards to the nutrition of the new-born, the main factors that determine the microbial population that first colonizes and establishes in the rumen, and the key immunity players that contribute to shaping the commensal microbiota in the early stage of life to understand host-microbiome specificity. The development of the rumen epithelium and muscularization are differently affected by the nature of the diet and special care should be taken with regards to transition from liquid (milk) to solid feed. The rumen is quickly colonized by all type of microorganisms straight after birth and the colonization pattern may be influenced by several factors such as presence/absence of adult animals, the first solid diet provided, and the inclusion of compounds that prevent/facilitate the establishment of some microorganisms or the direct inoculation of specific strains. The results presented show how early life events may be related to the microbial community structure and/or the rumen activity in the animals post-weaning. This would create differences in adaptive capacity due to different early life experiences and leads to the idea of microbial programming. However, many elements need to be further studied such as: the most sensitive window of time for interventions, the best means to test long term effectiveness, the role of key microbial groups and host-immune regulations.

Rumen microbial communities influence metabolic phenotypes in lambs

The rumen microbiota is an essential part of ruminants shaping their nutrition and health. Despite its importance, it is not fully understood how various groups of rumen microbes affect host-microbe relationships and functions. The aim of the study was to simultaneously explore the rumen microbiota and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted) that differentially restricted the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure, notably Ruminococcaceae and Lachnospiraceae lower up to 6 folds, Prevotellaceae lower by ~40%, and Clostridiaceae and Veillonellaceae higher up to 10 folds compared to microbiota without protozoa. An orthogonal partial least squares-discriminant analysis of urinary metabolome matched differences in microbiota structure. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between methylotrophic methanogens Methanomassiliicoccales and trimethylamine N-oxide. These results stress the influence of gut microbes on animal phenotype and show the potential of metabolomics for monitoring rumen microbial functions.

Uptake of milk with and without solid feed during the monogastric phase: Effect on fibrolytic and methanogenic microorganisms in the gastrointestinal tract of calves

Microbial communities are affected by diet and play a role in the successful transition from milk to a solid diet. The response of microorganisms in the gastrointestinal tract of Holstein bull calves to the uptake of milk with solid feed (control treatment; CT), or milk without solid feed (milk-only treatment; MT) during the first 3 weeks of life was investigated. Samples were collected from the rumen (fluid and tissue), abomasum (fluid), cecum (fluid and tissue) and feces at 7, 14 and 20 days of age. Calf weight was higher on days 14 and 20 in the MT than the CT. In the rumen at 14 days, the fibrolytic bacteria Fibrobacter succinogenes and Prevotella ruminicola increased in the CT and Ruminococcus flavefaciens increased in the MT. This suggests that R. flavefaciens is not strictly fibrolytic and that it might use milk as a substrate or other microbial species might supply a substrate. Diet affected methanogens, but this may have been due to an indirect effect via an association with Geobacter spp. or other syntrophic partners. The treatments also affected microorganisms in the abomasum, cecum and feces. Our results contribute to an understanding of diet, microbes in the gastrointestinal tract and weaning.

Presence of Selected Methanogens, Fibrolytic Bacteria, and Proteobacteria in the Gastrointestinal Tract of Neonatal Dairy Calves from Birth to 72 Hours

The microbial communities in the gastrointestinal tract of a young calf are essential for the anatomical and physiological development that permits a transition from milk to solid feed. Selected methanogens, fibrolytic bacteria, and proteobacteria were quantified in the rumen fluid and tissue, abomasum fluid, cecum fluid and tissue, and feces of Holstein bull calves on day 0 (0-20 mins after birth), day 1 (24 ± 1 h after birth), day 2 (48 ± 1 h after birth), and day 3 (72 ± 1 h after birth). Methanogens, fibrolytic bacteria, and Geobacter spp. were found to be already present from birth, indicating that microbial colonization of the gastrointestinal tract occurred before or during delivery. The abundance of methanogens and Geobacter spp. differed between the days tested and between compartments of the digestive tract and feces, but such difference was not observed for fibrolytic bacteria. Our findings suggests that methanogens might have an alternative hydrogen provider such as Geobacter spp. during these early stages of postnatal development. In addition, fibrolytic bacteria were present in the rumen well before the availability of fibrous substrates, suggesting that they might use nutrients other than cellulose and hemicellose.

Archaeal microbiota population in piglet feces shifts in response to weaning: Methanobrevibacter smithii is replaced with Methanobrevibacter boviskoreani

Methanogens commonly inhabit swine intestine. We analyzed the gut archaeal population by extracting DNA from the feces of nine piglets. We performed PCR to target the V6-V8 region of the 16S rRNA gene. Subsequent denaturing gradient gel electrophoresis (DGGE) revealed the presence of Methanobrevibacter boviskoreani, which has not previously been identified in pigs. We confirmed these data with a PCR-DGGE analysis of the mcrA gene, and subsequent sequencing. At 63 days old, the only band in fecal samples corresponded to M. boviskoreani. The DGGE analysis also showed that Methanobrevibacter smithii, which was abundant at 28 days, was dramatically reduced at 42 days, and it completely disappeared at 63 days. To confirm these data, we quantified M. smithii and the total archaeal population by quantitative PCR (qPCR); moreover, we designed a new set of species-specific primers based on the 16S rRNA gene of M. boviskoreani. The qPCR results confirmed the reduction in M. smithii over time and a simultaneous increase in M. boviskoreani. At 63 days, the total numbers of archaea and M. boviskoreani genomes were comparable, which suggested that M. boviskoreani represented the dominant archaea. This work showed that the archaeal population shifted during weaning, and M. boviskoreani replaced M. smithii.

Rumen development process in goats as affected by supplemental feeding v. grazing: age-related anatomic development, functional achievement and microbial colonisation

The aim of the present study was to describe age-related changes in anatomic, functional and microbial variables during the rumen development process, as affected by the feeding system (supplemental feeding v. grazing), in goats. Goats were slaughtered at seven time points that were selected to reflect the non-rumination (0, 7 and 14 d), transition (28 and 42 d) and rumination (56 and 70 d) phases of rumen development. Total volatile fatty acid (TVFA) concentration (P= 0·002), liquid-associated bacterial and archaeal copy numbers (P< 0·01) were greater for supplemental feeding v. grazing, while rumen pH (P< 0·001), acetate molar proportion (P= 0·003) and solid-associated microbial copy numbers (P< 0·05) were less. Rumen papillae length (P= 0·097) and extracellular (P= 0·093) and total (P= 0·073) protease activity potentials in supplemented goats tended to be greater than those in grazing goats. Furthermore, from 0 to 70 d, irrespective of the feeding system, rumen weight, rumen wall thickness, rumen papillae length and area, TVFA concentration, xylanase, carboxymethylcellulase activity potentials, and microbial copy numbers increased (P< 0·01) with age, while the greatest amylase and protease activity potentials occurred at 28 d. Most anatomic and functional variables evolved progressively from 14 to 42 d, while microbial colonisation was fastest from birth to 28 d. These outcomes suggest that the supplemental feeding system is more effective in promoting rumen development than the grazing system; in addition, for both the feeding systems, microbial colonisation in the rumen is achieved at 1 month, functional achievement at 2 months, and anatomic development after 2 months.

Thermophilic anaerobic digestion of thermal pretreated sludge: role of microbial community structure and correlation with process performances

Thermal hydrolysis pretreatment coupled with Thermophilic Anaerobic Digestion (TAD) for Waste Activated Sludge (WAS) treatment is a promising combination to improve biodegradation kinetics during stabilization. However, to date there is a limited knowledge of the anaerobic biomass composition and its impact on TAD process performances. In this study, the structure and dynamics of the microbial communities selected in two semi-continuous anaerobic digesters, fed with untreated and thermal pretreated sludge, were investigated. The systems were operated for 250 days at different organic loading rate. 16S rRNA gene clonal analysis and Fluorescence In Situ Hybridization (FISH) analyses allowed us to identify the majority of bacterial and archaeal populations. Proteolytic Coprothermobacter spp. and hydrogenotrophic Methanothermobacter spp. living in strict syntrophic association were found to dominate in TAD process. The establishment of a syntrophic proteolytic pathway was favoured by the high temperature of the process and enhanced by the thermal pretreatment of the feeding sludge. Proteolytic activity, alone or with thermal pretreatment, occurred during TAD as proven by increasing concentration of soluble ammonia and soluble COD (sCOD) during the process. However, the availability of a readily biodegradable substrate due to pretreatment allowed to significant sCOD removals (more than 55%) corresponding to higher biogas production in the reactor fed with thermal pretreated sludge. Microbial population dynamics analysed by FISH showed that Coprothermobacter and Methanothermobacter immediately established a stable syntrophic association in the reactor fed with pretreated sludge in line with the overall improved TAD performances observed under these conditions.

Bacterial diversity dynamics associated with different diets and different primer pairs in the rumen of Kankrej cattle

The ruminal microbiome in herbivores plays a dominant role in the digestion of lignocellulose and has potential to improve animal productivity. Kankrej cattle, a popular native breed of the Indian subcontinent, were used to investigate the effect of different dietary treatments on the bacterial diversity in ruminal fractions using different primer pairs. Two groups of four cows were assigned to two primary diets of either dry or green forages. Each group was fed one of three dietary treatments for six weeks each. Dietary treatments were; K1 (50% dry/green roughage: 50% concentrate), K2 (75% dry/green roughage: 25% concentrate) and K3 (100% dry/green roughage). Rumen samples were collected using stomach tube at the end of each dietary period and separated into solid and liquid fractions. The DNA was extracted and amplified for V1–V3, V4–V5 and V6–V8 hypervariable regions using P1, P2 and P3 primer pairs, sequenced on a 454 Roche platform and analyzed using QIIME. Community compositions and the abundance of most bacterial lineages were driven by interactions between primer pair, dietary treatment and fraction. The most abundant bacterial phyla identified were Bacteroidetes and Firmicutes however, the abundance of these phyla varied between different primer pairs; in each primer pair the abundance was dependent on the dietary treatment and fraction. The abundance of Bacteroidetes in cattle receiving K1 treatment indicate their diverse functional capabilities in the digestion of both carbohydrate and protein while the predominance of Firmicutes in the K2 and K3 treatments signifies their metabolic role in fibre digestion. It is apparent that both liquid and solid fractions had distinct bacterial community patterns (P<0.001) congruent to changes in the dietary treatments. It can be concluded that the P1 primer pair flanking the V1–V3 hyper-variable region provided greater species richness and diversity of bacterial populations in the rumen of Kankrej cattle.

Methanogen prevalence throughout the gastrointestinal tract of pre-weaned dairy calves

The methanogenic community throughout the gastrointestinal tract (GIT) of pre-weaned calves has not been well studied. The current study firstly investigated the distribution and composition of the methanogenic community in the rumen, ileum, and colon of 3-4 week-old milk-fed dairy calves (n = 4) using 16S rRNA gene clone library analysis. The occurrence of methanogens in the GIT of pre-weaned calves was further validated by using PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and quantitative real-time PCR (qPCR) was applied to quantify the methanogenic community in the rumen, jejunum, ileum, cecum, colon and rectum of 8 3-4 week old animals. Both cloning libraries and PCR-DGGE revealed that phylotypes close to Methanobrevibacter were the main taxon along the GIT in pre-weaned sucking calves. The composition and abundance of methanogens varied significantly among individual animals, suggesting that host conditions may influence the composition of the symbiotic microbiota. Segregation of methanogenic communities throughout the GIT was also observed within individual animals, suggesting possible functional differences among methanogens residing in different GIT regions. This is the first study to analyze methanogenic communities throughout the GIT of milk-fed newborn dairy calves and reveal both their diversity and abundance. The identification of methanogens in the lower GIT of pre-weaned dairy calves warrants further investigation to better define methanogen roles in GIT function and their impact on host metabolism and health.

Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods

Ruminal archaeomes of two mature sheep grazing in the Scottish uplands were analysed by different sequencing and analysis methods in order to compare the apparent archaeal communities. All methods revealed that the majority of methanogens belonged to the Methanobacteriales order containing the Methanobrevibacter, Methanosphaera and Methanobacteria genera. Sanger sequenced 1.3 kb 16S rRNA gene amplicons identified the main species of Methanobrevibacter present to be a SGMT Clade member Mbb. millerae (≥91% of OTUs); Methanosphaera comprised the remainder of the OTUs. The primers did not amplify ruminal Thermoplasmatales-related 16S rRNA genes. Illumina sequenced V6–V8 16S rRNA gene amplicons identified similar Methanobrevibacter spp. and Methanosphaera clades and also identified the Thermoplasmatales-related order as 13% of total archaea. Unusually, both methods concluded that Mbb. ruminantium and relatives from the same clade (RO) were almost absent. Sequences mapping to rumen 16S rRNA and mcrA gene references were extracted from Illumina metagenome data. Mapping of the metagenome data to16S rRNA gene references produced taxonomic identification to Order level including 2–3% Thermoplasmatales, but was unable to discriminate to species level. Mapping of the metagenome data to mcrA gene references resolved 69% to unclassified Methanobacteriales. Only 30% of sequences were assigned to species level clades: of the sequences assigned to Methanobrevibacter, most mapped to SGMT (16%) and RO (10%) clades. The Sanger 16S amplicon and Illumina metagenome mcrA analyses showed similar species richness (Chao1 Index 19–35), while Illumina metagenome and amplicon 16S rRNA analysis gave lower richness estimates (10–18). The values of the Shannon Index were low in all methods, indicating low richness and uneven species distribution. Thus, although much information may be extracted from the other methods, Illumina amplicon sequencing of the V6–V8 16S rRNA gene would be the method of choice for studying rumen archaeal communities.

An antimethanogenic nutritional intervention in early life of ruminants modifies ruminal colonization by Archaea

The aim of this work was to study whether feeding a methanogen inhibitor from birth of goat kids and their does has an impact on the archaeal population colonizing the rumen and to what extent the impact persists later in life. Sixteen goats giving birth to two kids were used. Eight does were treated (D+) with bromochloromethane after giving birth and over 2 months. The other 8 goats were not treated (D−). One kid per doe in both groups was treated with bromochloromethane (k+) for 3 months while the other was untreated (k−), resulting in four experimental groups: D+/k+, D+/k−, D−/k+, and D−/k−. Rumen samples were collected from kids at weaning and 1 and 4 months after (3 and 6 months after birth) and from does at the end of the treating period (2 months). Pyrosequencing analyses showed a modified archaeal community composition colonizing the rumen of kids, although such effect did not persist entirely 4 months after; however, some less abundant groups remained different in treated and control animals. The different response on the archaeal community composition observed between offspring and adult goats suggests that the competition occurring in the developing rumen to occupy different niches offer potential for intervention.