Ruminant Gut Research Articles

A metagenomic catalogue of the ruminant gut archaeome

While the ruminant gut archaeome regulates the gut microbiota and hydrogen balance, it is also a major producer of the greenhouse gas methane. However, ruminant gut archaeome diversity within the gastrointestinal tract (GIT) of ruminant animals worldwide remains largely underexplored. Here, we construct a catalogue of 998 unique archaeal genomes recovered from the GITs of ruminants, utilizing 2270 metagenomic samples across 10 different ruminant species. Most of the archaeal genomes (669/998 = 67.03%) belong to Methanobacteriaceae and Methanomethylophilaceae (198/998 = 19.84%). We recover 47/279 previously undescribed archaeal genomes at the strain level with completeness of >80% and contamination of <5%. We also investigate the archaeal gut biogeography across various ruminants and demonstrate that archaeal compositional similarities vary significantly by breed and gut location. The catalogue contains 42,691 protein clusters, and the clustering and methanogenic pathway analysis reveal strain- and host-specific dependencies among ruminant animals. We also find that archaea potentially carry antibiotic and metal resistance genes, mobile genetic elements, virulence factors, quorum sensors, and complex archaeal viromes. Overall, this catalogue is a substantial repository for ruminant archaeal recourses, providing potential for advancing our understanding of archaeal ecology and discovering strategies to regulate methane production in ruminants.

Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization

BackgroundRuminant gut microbiota are critical in ecological adaptation, evolution, and nutrition utilization because it regulates energy metabolism, promotes nutrient absorption, and improves immune function. To study the functional roles of key gut microbiota in sheep and goats, it is essential to construct reference microbial gene catalogs and high-quality microbial genomes database.ResultsA total of 320 fecal samples were collected from 21 different sheep and goat breeds, originating from 32 distinct farms. Metagenomic deep sequencing and binning assembly were utilized to construct a comprehensive microbial genome information database for the gut microbiota. We successfully generated the largest reference gene catalogs for gut microbiota in sheep and goats, containing over 162 million and 82 million nonredundant predicted genes, respectively, with 49 million shared nonredundant predicted genes and 1138 shared species. We found that the rearing environment has a greater impact on microbial composition and function than the host’s species effect. Through subsequent assembly, we obtained 5810 medium- and high-quality metagenome-assembled genomes (MAGs), out of which 2661 were yet unidentified species. Among these MAGs, we identified 91 bacterial taxa that specifically colonize the sheep gut, which encode polysaccharide utilization loci for glycan and mucin degradation.ConclusionsBy shedding light on the co-symbiotic microbial communities in the gut of small ruminants, our study significantly enhances the understanding of their nutrient degradation and disease susceptibility. Our findings emphasize the vast potential of untapped resources in functional bacterial species within ruminants, further expanding our knowledge of how the ruminant gut microbiota recognizes and processes glycan and mucins.4UTuEuRwTx7UvdwKUcENuWVideo

Red seaweed as an abundant, natural methanogenesis inhibitor for industrial biorefinery

Acidogenic fermentation offers a means to renewably refine biomass to volatile fatty acids from which industrial chemicals can be sustainably derived. Small molecules (bromoethane sulfonate) are used in the literature to inhibit methanogenesis and improve fatty acid yields but are impractical at industrial scale due to cost. The red seaweed Asparagopsis taxiformis has been shown to provide methanogenesis inhibition in the microbiome of the ruminant gut over short retention times (up to 72 h), but its suitability for bioreactor control has not been previously characterised. This study investigated the responses of both rumen fluid and anaerobic digester sludge to various Asparagopsis doses. In rumen fluid, doses of ≥5% Asparagopsis showed equivalent inhibition to bromoethane sulfonate at retention times under 30 days, producing VFA of both similar yields and qualities to this standard inhibitor. Digester sludge was not found to respond to Asparagopsis treatment at the levels tested, suggesting a specificity of treatment to microbial community. These data support the application of Asparagopsis as a scalable reactor control agent for rumen-driven fermenter configurations.

Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans.

Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multienzymatic cellulosome structures capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut, potentially during domestication where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations but are rare in populations from industrialized societies thus indicating potential disappearance in response to the westernized lifestyle.

Microencapsulation technology for delivery of enzymes in ruminant feed.

The ruminant digestive system is uniquely designed to make efficient use of high-fibre feed, including forages. Between 40 to 100% of the ruminant diet consists of forages which are high in fibre and up to 70% of this may remain undigested in the ruminant gut, with substantial impact on feed utilisation rate and productivity and the economic and environmental sustainability of livestock production systems. In ruminants, feed costs can make up to 70% of the overall cost of producing an animal product. Increasing feed utilisation efficiency, i.e., more production with less feed lowers feeding costs and improves livestock economic viability. Strategies for improving nutrient utilisation in animal feed has been investigated over the years. Incorporation of fibre digesting enzymes in the feed to facilitate the digestion of the residual fibre in hind gut is one of the proposed strategies. However, delivering such enzymes to the hind gut in active state is challenging due to the unfavourable biochemical environment (pH, microbial proteases) of ruminant's gastrointestinal tract. This review discusses the potential application of microencapsulation for protected and targeted delivery of enzymes into the hind gut of ruminants.

Ruminant gut microbiota: importance, development, and alternative therapeutics for dysbiosis

The microbiome is a population of microbes that colonized in mammalian gut. During the first few years of life, the gut microbiome undergoes alteration and is very diverse in adulthood, depends upon various of circumstances. Gut microbes, particularly gut flora in ruminants, are receiving more and more attention. Intestinal microbes, particularly ruminant microorganisms, have attracted an increasing amount of attention as high-throughput sequencing technology has improved and costs have decreased, whether in the fundamental research or application fields. The ruminant microbiome changes in conjunction with its host and it is influenced by inter-microbial interactions, environmental exposures, and host properties. However, any organism's core functional microbiome is much more conventional. Unfortunately, the fragile growth ratio of the microbial culture is susceptible to incursions under illness circumstances, which may affect the abundance of various microbial species, resulting to dysbiosis. As a result, the purpose of this review is to provide a broad summary of the relevance of ruminant gut microorganisms, as well as to investigate variables that influence the microbiota and alternative therapeutics such as probiotics, prebiotics, fecal transplantation, and rumen transfiguration, all of which have been shown to be effective in addressing dysbiosis.

360 The Ability of an Enhanced Zeolite-Based Flow Agent to Mitigate the Effects of Ergot-Like Alkaloids Consumed by Beef Cattle

Abstract Aluminosilicate-based flow agents, like zeolites, may impact digestion of ergot-like alkaloids in the ruminant gut. Twenty-four steers (226 ± 27.6 kg) were used in a 21-d experiment to test the effects of an enhanced zeolite-based flow agent (KALLSIL, Kemin Industries, Des Moines, IA) on site of ergot-like alkaloid excretion, serum prolactin, rectal temperature, respiration rate, and nutrient digestibility. Treatments were control (E+) or enhanced zeolite inclusion (E+Z; 2 g/kg, DM basis). Steers were fed a TMR at 1.85% of BW (DM-basis). Tall-fescue seed was included in the diet at 11.14%, providing 465 µg of ergovaline/kg DM. Steers had no ORTS during the experiment. Rectal temperature and respiration rate were recorded daily at 0700 and 1200 h from steers housed tie stalls in a room kept at (18.5°C ± 0.33°C, 32.6% ± 2.19%). Serum was harvested from blood collected on d-1, 7, 14, and 21 to measure prolactin. On d-21 jugular catheters were placed to measure prolactin following the infusion of thyrotropin-releasing hormone (TRH; 1 µg/kg BW). Spot samples of feces and urine were collected every 8 h from d 17-20, with 2-hour advancement each day to determine digestibility, N balance, and recovery of ergot-like alkaloids. Digestion and N balance was not affected by treatment (P ≥ 0.16). Enhanced zeolite tended (P = 0.15) to increase recovery of ergovaline. Prolactin concentration decreased over time (P &amp;lt; 0.01), but was greater (P = 0.01) at each time point for E+Z steers. Following the infusion of TRH, prolactin tended (P = 0.11) to be greater for E+Z. Rectal temperatures and respiration rates were not affected (P ≥ 0.89) by E+Z. Results from this study indicate that enhanced zeolite inclusion tended to increase recovery of ergot-like alkaloids in feces and increased serum prolactin when offered to beef steers in a diet containing ergot-like alkaloids.

Characterization of gut microbiota dysbiosis of diarrheic adult yaks through 16S rRNA gene sequences.

The ruminant gut microbial community has a strong impact on host health and can be altered during diarrhea disease. As an indigenous breed of the Tibetan Plateau, domestic yak displays a high diarrhea rate, but little research has been done to characterize the bacterial microbial structure in diarrheic yaks. In the present study, a total of 30 adult yaks, assigned to diarrhea (case, N = 15) and healthy (control, N = 15) groups, were subjected to gut microbiota profiling using the V3–V4 regions of the 16S rRNA gene. The results showed that the gut microbiome of the case group had a significant decrease in alpha diversity. Additionally, differences in beta diversity were consistently observed for the case and control groups, indicating that the microbial community structure was changed due to diarrhea. Bacterial taxonomic analysis indicated that the Bacteroidetes, Firmicutes, and Proteobacteria were the three most dominant phyla in both groups but different in relative abundance. Especially, the proportion of Proteobacteria in the case group was increased as compared with the control group, whereas Spirochaetota and Firmicutes were significantly decreased. At the genus level, the relative abundance of Escherichia-Shigella and Prevotellaceae_UCG-003 were dramatically increased, whereas that of Treponema, p-2534-18B5_gut_group, and Prevotellaceae_UCG-001 were observably decreased with the effect of diarrhea. Furthermore, based on our linear discriminant analysis (LDA) effect size (LEfSe) results, Alistipes, Solibacillus, Bacteroides, Prevotellaceae_UCG_003, and Bacillus were significantly enriched in the case group, while the other five genera, such as Alloprevotella, RF39, Muribaculaceae, Treponema, and Enterococcus, were the most preponderant in the control group. In conclusion, alterations in gut microbiota community composition were associated with yak diarrhea, differentially represented bacterial species enriched in case animals providing a theoretical basis for establishing a prevention and treatment system for yak diarrhea.

Sheep vaccinated against paratuberculosis have increased levels of B cells infiltrating the intestinal tissue

Systemic immunisation delivered subcutaneously is currently used to control paratuberculosis, a chronic enteritis of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). These vaccines do not provide complete protection and a small cohort of animals still succumb to clinical disease. The aim of this study was to assess mycobacterial infection site-specific variations in immune cells in vaccinated sheep that did or did not develop the disease following controlled exposure to MAP. Immunohistochemical staining of terminal ileum demonstrated that vaccination increased infiltration of CD4 + T cells and B cells. Infiltration of large numbers of CD4 + T and B cells was also seen in sheep that successfully cleared infection. Vaccination promoted the polarisation of macrophages to an M1 activation state. The presence of certain cells at the site of infection, especially CD4 + T cells, is likely to contribute to vaccine success by increasing the speed and potency of the local immune response. Systemic immunisation against MAP can alter the composition of innate and adaptive immune cell populations at the predilection site for MAP infection in the ileum one year after vaccination. This informs understanding of the impact of vaccination at the site of infection and also the duration of vaccine-elicited changes. This information may assist vaccine development and allow targeting of protective immune responses in the gut of ruminants.

Indwelling robots for ruminant health monitoring: A review of elements

Maximizing the health, productivity, and sustainability of ruminant animals is an essential societal goal for a variety of reasons including food security, impact on the environment, and global nutrition; however, monitoring the metabolism of ruminant animals is currently a time-consuming and imprecise process. An indwelling robot residing within the ruminant gut would likely revolutionize metabolic monitoring in ruminants by providing a new level of detail into the complex and stratified chemistry of fermentation that goes on hour by hour. Indwelling robots could become an essential tool for ruminant health monitoring because many of the health, productivity, and sustainability challenges experienced by ruminants can be indicated and potentially influenced by changes in biomarkers within the rumen. We believe next-generation ruminant health monitoring will evolve from continuous biomarker measurement, reliable data transmission, and precise locomotion, all of which can be enabled by advances in indwelling ruminal robot design. Within this review, we summarize the requirements of and progress toward engineering advancements necessary to develop field-deployable robots for ruminant metabolic monitoring. The vital elements of an autonomous indwelling medical robot include locomotion, localization, wireless data transmission, and wireless power transfer. The state-of-the-art technologies associated with each element are articulated in this review. The comprehensive techniques of locomotion, the approaches for precise localization, as well as technologies for wireless power and data transmission that will make the indwelling robot entirely autonomous are enunciated, with a special focus on ruminants. The evaluated indices are potentially useful not only to assess the health of the ruminant but also to refine and standardize the assessment protocols. The overview presented in this article on the advances, imperative requirements, and challenges enables the deployment of the ruminal robot for health monitoring in ruminants.

A brief history of ruminant gut microbiological research

Increasing attention is paying to gut microorganisms, especially gut microflora in ruminants. Here, we explored the literature related to the study of ruminant intestinal microorganisms, in order to answer the questions as follows: (1) what are the distributions of research power in terms of countries, authors, and keywords? (2) what is the frontier research? Our analysis showed ruminant gut microbiological research experienced two stages: germination, and rapid development, GUAN LL, CHAUCHEYRAS-DURAND F, SUEN G were the top three local impact authors and the most relevant authors. USA, China, France and Canada were the main countries. The main keywords were diversity, bacteria, gastrointestinal-tract, rumen, and fermentation. Fungi and bacteria in rumen and intestinal and the evolution of microorganisms in rumen and intestine may need to be strengthened.

Isolation, Description and Genome Analysis of a Putative Novel Methylobacter Species (‘Ca. Methylobacter coli’) Isolated from the Faeces of a Blackbuck (Indian Antelope)

Enteric fermentation of methane by ruminant animals represents a major source of anthropogenic methane. Significantly less information is available on the existence of methanotrophs in the gut of ruminants. Therefore, detailed strain descriptions of methanotrophs isolated from ruminant faeces or gut are rare. We present a first report on the enrichment and isolation of a methanotroph, strain BlB1, from the faeces of an Indian antelope (blackbuck). The 16S rRNA gene sequence of strain BlB1 showed the highest identity (98.40% identity) to Methylobacter marinus A45T and Methylobacter luteus NCIMB 11914T. Strain BlB1 showed coccoidal cells (1.5–2 µm in diameter), which formed chains or aggregates of 3–4 cells of light yellow-coloured colonies on agarose when incubated with methane in the gas phase. The draft genome of BlB1 (JADMKV01) is 4.87 Mbp in size, with a G + C content of 51.3%. The draft genome showed 27.4% digital DNA-DNA hybridization (DDH) and 83.07% average nucleotide identity (ANIb) values with that of its closest phylogenetic neighbour, Methylobacter marinus A45T. Due to the lower values of DDH and ANIb with the nearest species, and &lt;98.7% 16S rRNA gene sequence identity, we propose that strain BlB1 belongs to a novel species of Methylobacter. However, as the culture has to be maintained live and resisted cryopreservation, deposition in culture collections was not possible and hence we propose a Candidatus species name, ‘Ca. Methylobacter coli’ BlB1. ‘Ca. Methylobacter coli’ BlB1 would be the first described methanotroph from ruminants worldwide, with a sequenced draft genome. This strain could be used as a model for studies concerning methane mitigation from ruminants.

Microbiome Analysis Reveals the Dynamic Alternations in Gut Microbiota of Diarrheal Giraffa camelopardalis.

The ruminant gut microbial community's importance has been widely acknowledged due to its positive roles in physiology, metabolism, and health maintenance. Diarrhea has been demonstrated to cause adverse effects on gastrointestinal health and intestinal microecosystem, but studies regarding diarrheal influence on gut microbiota in Giraffa camelopardalis have been insufficient to date. Here, this study was performed to investigate and compare gut microbial composition and variability between healthy and diarrheic G. camelopardalis. The results showed that the gut microbial community of diarrheal G. camelopardalis displayed a significant decrease in alpha diversity, accompanied by distinct alterations in taxonomic compositions. Bacterial taxonomic analysis indicated that the dominant bacterial phyla (Proteobacteria, Bacteroidetes, and Firmicutes) and genera (Escherichia Shigella and Acinetobacter) of both groups were the same but different in relative abundance. Specifically, the proportion of Proteobacteria in the diarrheal G. camelopardalis was increased as compared with healthy populations, whereas Bacteroidetes, Firmicutes, Tenericutes, and Spirochaetes were significantly decreased. Moreover, the relative abundance of one bacterial genus (Comamonas) dramatically increased in diarrheic G. camelopardalis, whereas the relative richness of 18 bacterial genera decreased compared with healthy populations. Among them, two bacterial genera (Ruminiclostridium_5 and Blautia) cannot be detected in the gut bacterial community of diarrheal G. camelopardalis. In summary, this study demonstrated that diarrhea could significantly change the gut microbial composition and diversity in G. camelopardalis by increasing the proportion of pathogenic to beneficial bacteria. Moreover, this study first characterized the distribution of gut microbial communities in G. camelopardalis with different health states. It contributed to providing a theoretical basis for establishing a prevention and treatment system for G. camelopardalis diarrhea.

The effects of phytochemicals on methanogenesis: insights from ruminant digestion and implications for industrial biogas digesters management

The overarching objective of this review is to compare methanogenesis in ruminant gut systems and industrial digesters that employ plants, crops and their processing residues or by-products as feedstocks. An important consideration is the presence of phytochemicals in these feedstocks, with the understanding that depending on the type and quantities, these phytochemicals affect the activity of biomass degrading microorganisms to varying extents. This review aims to evaluate currently available knowledge on the effects of phytochemicals in ruminants’ methanogenesis as well as industrial anaerobic digestion processes. Technology and scale up in industrial fermentation have always benefited from our understanding of natural biological processes as such, knowledge from the process of methanogenesis in the gastrointestinal tract of ruminants can be used to make inferences about the performance of industrial digester systems for biogas production. This is particularly important when the same feedstock is used in both systems. Thus, in this review, comparisons of the two methane generating systems are discussed with an emphasis on phytochemical inhibitory effects on microorganisms that are involved in anaerobic digestion.

Strategies for glycan acquisition by Bacteroidetes in the soil: The carbohydrate enzymology of Chitinophaga pinensis

The secretion of extracellular enzymes by soil microbes is rate-limiting in the global recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant bacterial phylum, just like in human and animal intestines. The enzymology of Bacteroidetes in the dynamic and competitive soil environment is under-explored compared to their cousins from the human and ruminant gut ecosystems. We are exploring carbohydrate binding and deconstruction by Chitinophaga pinensis. This species was isolated from the leaf litter of a pine forest, and our ongoing microbiological, biochemical, and proteomic analyses show that C. pinensis has a marked metabolic preference for carbohydrates (glycans) of microbial, rather than plant, origin. The species has a repertoire of enzymes that degrade components of the fungal cell wall, and we are characterising several important enzyme activities, including some with unusual substrate specificity. Several features of the C. pinensis “cazome” make it note-worthy. In particular, there is a significantly reduced reliance on the Polysaccharide Utilisation Loci that define glycan acquisition in most well-studied gut symbiont Bacteroidetes. Instead, C. pinensis produces some large multi-modular enzymes that convey multiple complementary carbohydrate-binding and -degrading functions, and which are often secreted via the phylum-specific Type IX Secretion System. This presentation will highlight our latest enzyme characterisation data, discussed in the context of the environmental functions of soil bacteria, as well as the use of enzymes for industrial biotechnology.

Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies.

Shiga toxin-producing Escherichia coli (STEC) are a leading cause of foodborne outbreaks of human disease, but they reside harmlessly as an asymptomatic commensal in the ruminant gut. STEC serogroup O145 are difficult to isolate as routine diagnostic methods are unable to distinguish non-O157 serogroups due to their heterogeneous metabolic characteristics, resulting in under-reporting which is likely to conceal their true prevalence. In light of these deficiencies, the purpose of this study was a twofold approach to investigate enhanced STEC O145 diagnostic culture-based methods: firstly, to use a genomic epidemiology approach to understand the genetic diversity and population structure of serogroup O145 at both a local (New Zealand) (n = 47) and global scale (n = 75) and, secondly, to identify metabolic characteristics that will help the development of a differential media for this serogroup. Analysis of a subset of E. coli serogroup O145 strains demonstrated considerable diversity in carbon utilisation, which varied in association with eae subtype and sequence type. Several carbon substrates, such as D-serine and D-malic acid, were utilised by the majority of serogroup O145 strains, which, when coupled with current molecular and culture-based methods, could aid in the identification of presumptive E. coli serogroup O145 isolates. These carbon substrates warrant subsequent testing with additional serogroup O145 strains and non-O145 strains. Serogroup O145 strains displayed extensive genetic heterogeneity that was correlated with sequence type and eae subtype, suggesting these genetic markers are good indicators for distinct E. coli phylogenetic lineages. Pangenome analysis identified a core of 3,036 genes and an open pangenome of >14,000 genes, which is consistent with the identification of distinct phylogenetic lineages. Overall, this study highlighted the phenotypic and genotypic heterogeneity within E. coli serogroup O145, suggesting that the development of a differential media targeting this serogroup will be challenging.

Reducing protein content in the diet of growing goats: implications for nitrogen balance, intestinal nutrient digestion and absorption, and rumen microbiota

Reducing dietary CP content is an effective approach to reduce animal nitrogen excretion and save protein feed resources. However, it is not clear how reducing dietary CP content affects the nutrient digestion and absorption in the gut of ruminants, therefore it is difficult to accurately determine how much reduction in dietary CP content is appropriate. This study was conducted to investigate the effects of reduced dietary CP content on N balance, intestinal nutrient digestion and absorption, and rumen microbiota in growing goats. To determine N balance, 18 growing wether goats (25.0 ± 0.5 kg) were randomly assigned to one of three diets: 13.0% (control), 11.5% and 10.0% CP. Another 18 growing wether goats (25.0 ± 0.5 kg) were surgically fitted with ruminal, proximate duodenal, and terminal ileal fistulae and were randomly assigned to one of the three diets to investigate intestinal amino acid (AA) absorption and rumen microbiota. The results showed that fecal and urinary N excretion of goats fed diets containing 11.5% and 10.0% CP were lower than those of goats fed the control diet (P < 0.05). When compared with goats fed the control diet, N retention was decreased and apparent N digestibility in the entire gastrointestinal tract was increased in goats fed the 10% CP diet (P < 0.05). When compared with goats fed the control diet, the duodenal flow of lysine, tryptophan and phenylalanine was decreased in goats fed the 11.5% CP diet (P < 0.05) and that of lysine, methionine, tryptophan, phenylalanine, leucine, glutamic acid, tyrosine, essential AAs (EAAs) and total AAs (TAAs) was decreased in goats fed the 10.0% CP diet (P < 0.05). When compared with goats fed the control diet, the apparent absorption of TAAs in the small intestine was increased in goats fed the 11.5% CP diet (P < 0.05) and that of isoleucine, serine, cysteine, EAAs, non-essential AAs, and TAAs in the small intestine was increased in goats fed the 10.0% CP diet (P < 0.05). When compared with goats fed the control diet, the relative richness of Bacteroidetes and Fibrobacteres was increased and that of Proteobacteria and Synergistetes was decreased in the rumen of goats fed a diet with 10.0% CP. In conclusion, reducing dietary CP content reduced N excretion and increased nutrient utilization by improving rumen fermentation, enhancing nutrient digestion and absorption, and altering rumen microbiota in growing goats.

Hydrogenotrophic methanogens of the mammalian gut: Functionally similar, thermodynamically different-A modelling approach.

Methanogenic archaea occupy a functionally important niche in the gut microbial ecosystem of mammals. Our purpose was to quantitatively characterize the dynamics of methanogenesis by integrating microbiology, thermodynamics and mathematical modelling. For that, in vitro growth experiments were performed with pure cultures of key methanogens from the human and ruminant gut, namely Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanobacterium formicium. Microcalorimetric experiments were performed to quantify the methanogenesis heat flux. We constructed an energetic-based mathematical model of methanogenesis. Our model captured efficiently the dynamics of methanogenesis with average concordance correlation coefficients of 0.95 for CO2, 0.98 for H2 and 0.97 for CH4. Together, experimental data and model enabled us to quantify metabolism kinetics and energetic patterns that were specific and distinct for each species despite their use of analogous methane-producing pathways. Then, we tested in silico the interactions between these methanogens under an in vivo simulation scenario using a theoretical modelling exercise. In silico simulations suggest that the classical competitive exclusion principle is inapplicable to gut ecosystems and that kinetic information alone cannot explain gut ecological aspects such as microbial coexistence. We suggest that ecological models of gut ecosystems require the integration of microbial kinetics with nonlinear behaviours related to spatial and temporal variations taking place in mammalian guts. Our work provides novel information on the thermodynamics and dynamics of methanogens. This understanding will be useful to construct new gut models with enhanced prediction capabilities and could have practical applications for promoting gut health in mammals and mitigating ruminant methane emissions.

Different milk diets have substantial effects on the jejunal mucosal immune system of pre-weaning calves, as demonstrated by whole transcriptome sequencing

There is increasing evidence that nutrition during early mammalian life has a strong influence on health and performance in later life. However, there are conflicting data concerning the appropriate milk diet. This discrepancy particularly applies to ruminants, a group of mammals that switch from monogastric status to rumination during weaning. Little is known regarding how the whole genome expression pattern in the juvenile ruminant gut is affected by alternative milk diets. Thus, we performed a next-generation-sequencing-based holistic whole transcriptome analysis of the jejunum in male pre-weaned German Holstein calves fed diets with restricted or unlimited access to milk during the first 8 weeks of life. Both groups were provided hay and concentrate ad libitum. The analysis of jejunal mucosa samples collected 80 days after birth and four weeks after the end of the feeding regimes revealed 275 differentially expressed loci. While the differentially expressed loci comprised 67 genes encoding proteins relevant to metabolism or metabolic adaptation, the most distinct difference between the two groups was the consistently lower activation of the immune system in calves that experienced restricted milk access compared to calves fed milk ad libitum. In conclusion, different early life milk diets had significant prolonged effects on the intestinal immune system.

Streptococcus uberis: In vitro biofilm production in response to carbohydrates and skim milk

Streptococcus uberis has become one of the most important environmental pathogens associated with clinical and subclinical bovine mastitis. Biofilm confers to bacteria more resistance to physical and chemical agents as well as to different mechanisms of the innate immune system. The aim of this work was to evaluate the ability of in vitro biofilm production in 32 S. uberis isolates from bovine mastitis and identified by biochemical tests and subsequently confirmed by the amplification of the pauA gene. The isolates were cultivated in TMP broth and TMP broth with the addition of 0.5% glucose, 1% sucrose, 1% lactose or 0.5% skim milk in microtiter plates stained with crystal violet. We demonstrated that S. uberis isolated from bovine mastitis are able to produce biofilms in TMP broth and, also that biofilm formation by S. uberis can be significantly enhanced by the addition of 0.5% glucose or 1% sucrose to TMP broth. This may suggest that the carbohydrates in milk or within the ruminant gut might affect the growth mode of S. uberis. In addition, our results showed that in vitro biofilm production under different conditions of supplementation displays variation among the isolates and that each isolate shows a particular profile of biofilm production. This phenotypic heterogeneity in biofilm production exhibited by S. uberis could at least partly explain why this bacterium has the ability to adapt to different niches facilitating survival to diverse and stressful conditions.