Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.

/pdf/evolution-of-mammals-and-their-gut-microbes-11pxmpi1dr.pdf

Evolution of mammals and their gut microbes

The microbiota of an animal's intestinal tract plays important roles in the animal's overall health, productivity and well-being. There is still a scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for this lack of data relates to the expense of methods needed to generate such data. Here we have utilized a bacterial tag-encoded FLX 16s rDNA amplicon pyrosequencing (bTEFAP) approach that is able to perform diversity analyses of gastrointestinal populations. bTEFAP is relatively inexpensive in terms of both time and labor due to the implementation of a novel tag priming method and an efficient bioinformatics pipeline. We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows. Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the cattle, a total of 4 cows were found to be positive for Salmonella spp (tentative enterica) and 6 cows were positive for Campylobacter spp. (tentative lanienae). Using bTEFAP we have examined the microbiota in the feces of cattle. As these methods continue to mature we will better understand the ecology of the major populations of bacteria the lower intestinal tract. This in turn will allow for a better understanding of ways in which the intestinal microbiome contributes to animal health, productivity and wellbeing.

/pdf/evaluation-of-the-bacterial-diversity-in-the-feces-of-cattle-1i4g0u3vqx.pdf

Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

/pdf/rumen-microbial-community-composition-varies-with-diet-and-54ih8mnsfv.pdf

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

https://cyberleninka.org/article/n/1082452.pdf

Invited review: Enteric methane in dairy cattle production: Quantifying the opportunities and impact of reducing emissions

Ruminant production is under increased public scrutiny in terms of the importance of cattle and other ruminants as major producers of the greenhouse gas methane. Methanogenesis is performed by methanogenic archaea, a specialised group of microbes present in several anaerobic environments including the rumen. In the rumen, methanogens utilise predominantly H2 and CO2 as substrates to produce methane, filling an important functional niche in the ecosystem. However, in addition to methanogens, other microbes also have an influence on methane production either because they are involved in hydrogen (H2) metabolism or because they affect the numbers of methanogens or other members of the microbiota. This study explores the relationship between some of these microbes and methanogenesis and highlights some functional groups that could play a role in decreasing methane emissions. Dihydrogen (‘H2’ from this point on) is the key element that drives methane production in the rumen. Among H2 producers, protozoa have a prominent position, which is strengthened by their close physical association with methanogens, which favours H2 transfer from one to the other. A strong positive interaction was found between protozoal numbers and methane emissions, and because this group is possibly not essential for rumen function, protozoa might be a target for methane mitigation. An important function that is associated with production of H2 is the degradation of fibrous plant material. However, not all members of the rumen fibrolytic community produce H2. Increasing the proportion of non-H2 producing fibrolytic microorganisms might decrease methane production without affecting forage degradability. Alternative pathways that use electron acceptors other than CO2 to oxidise H2 also exist in the rumen. Bacteria with this type of metabolism normally occupy a distinct ecological niche and are not dominant members of the microbiota; however, their numbers can increase if the right potential electron acceptor is present in the diet. Nitrate is an alternative electron sinks that can promote the growth of particular bacteria able to compete with methanogens. Because of the toxicity of the intermediate product, nitrite, the use of nitrate has not been fully explored, but in adapted animals, nitrite does not accumulate and nitrate supplementation may be an alternative under some dietary conditions that deserves to be further studied. In conclusion, methanogens in the rumen co-exist with other microbes, which have contrasting activities. A better understanding of these populations and the pathways that compete with methanogenesis may provide novel targets for emissions abatement in ruminant production.

Microbial ecosystem and methanogenesis in ruminants

The phylogenetic diversity of the fecal bacterial community in Holstein cattle was determined by 16S ribosomal RNA gene sequence analysis. The sequences were affiliated with the following phyla: Firmicutes (81.3%), Bacteroidetes (14.4%), Actinobacteria (2.5%), and Proteobacteria (1.4%). The Clostridium leptum subgroup was the most phylogenetically diverse group in cattle feces. In addition, a number of previously uncharacterized and unidentified bacteria were recognized in clone libraries.

https://www.tandfonline.com/doi/pdf/10.1271/bbb.69.1793

Culture-independent analysis of fecal microbiota in cattle.

The objective of this study was to evaluate the effects of sarsaponin on methane production, ruminal fermentation, nutrient digestion and blood metabolites using three Holstein steers in a 3×3 Latin Square design. The steers were fed Sudangrass hay plus concentrate mixture at a ratio 1.5:1 twice daily, and sarsaponin (0, 0.5 and 1% of DM), which was given at 09:00 and 17:00 h daily by mixing with concentrate. Rumen samples were collected 0, 2, and 5 h after morning dosing. Ruminal pH was numerically decreased and numbers of protozoa were decreased linearly (p<0.01) by treatment. Ruminal ammonia-N was reduced (linear; p<0.05) and total VFA was increased (quadratic; p<0.05) at 2 and 5 h after sarsaponin dosing. The molar proportion of acetate was decreased (quadratic; p<0.05) and propionate was increased (linear; p<0.01) at all sampling times. Blood plasma glucose was increased and urea-N was decreased (linear; p<0.05) at 2 and 5 h after dosing. Methane was decreased by approximately 12.7% (linear; p<0.05). The apparent digestibility of DM and NDF were decreased (quadratic; p<0.05) and that of CP remained unchanged due to the sarsaponin. The numbers of cellulolytic bacteria were decreased (quadratic; p<0.05), while numbers of total viable bacteria remained unchanged due to the sarsaponin. These results show that sarsaponin can partially inhibit rumen methanogenesis in vivo and improve ruminal fermentation, which supports our previous in vitro results. (Asian-Aust. J. Anim. Sci. 2005. Vol 18, No. 12 : 1746-1751)

Sarsaponin Effects on Ruminal Fermentation and Microbes, Methane Production, Digestibility and Blood Metabolites in Steers

A real-time PCR approach was used in this study to clarify the populations of major bacterial species in the rumens of faunated and unfaunated cattle. The sensitivity of this novel real-time PCR assay was evaluated by using 10(1) to 10(8) plasmid copies of target bacteria. The numbers of plasmid copies of Ruminococcus albus, Ruminococcus flavefaciens, Prevotella ruminicola, and the CUR-E cluster were higher in the unfaunated than in the faunated rumens. The CUR-E cluster belongs to the Clostridium group. In contrast, Fibrobacter succinogenes was higher in the faunated than in the unfaunated rumens. Although it is well known that an absence of protozoa brings about an increase in the bacterial population, it was clarified here that an absence of protozoa exerted differential effects on the populations of cellulolytic bacteria in cattle rumens (i.e., F. succinogenes, R. albus, and R. flavefaciens). In addition, real-time PCR analysis suggested that the CUR-E cluster was more prevalent in the unfaunated rumens.

Real-time PCR detection of the effects of protozoa on rumen bacteria in cattle.

The effects of including essential oil cyclodextrin (CD) complexes on ruminal methane and hydrogen production, volatile fatty acid (VFA) and protozoa were studied in vitro. The essential oil CD complexes used in the present study were both αCD and βCD with cineol, eucalyptus, menthol, peppermint, thyme and wasabi. Diluted rumen fluid (60 mL) was incubated anaerobically at 38°C for 6 h with the essential oil CD complex (1–40 mg as oil). Eucalyptus-αCD reduced methane production by 40% with 10 mg as oil along with decreasing the protozoal number and increasing total VFA and proportion of propionic acid. Both wasabi-αCD and wasabi-βCD reduced methane production by 85% and 97%, respectively, with 10 mg as oil, though they increased hydrogen production notably. The protozoal number was unchanged by wasabi-βCD and decreased to 50% by wasabi-αCD. Propionic acid was increased by both wasabi-αCD and wasabi-βCD. The other essential oil-CD showed no significant effect on reducing methane production. The combined use of 20 mM of fumaric acid with wasabi-αCD (1 mg as oil) caused about a 50% depression of methane production compared to the control without increasing hydrogen production. Fumaric acid was more effective than malic acid in reducing methane production. The addition of eucalyptus-αCD, wasabi-αCD or wasabi-βCD together with organic acid to rumen fluid turned out to be effective for reducing methane production with no increase in hydrogen production.

Effects of the essential oil cyclodextrin complexes on ruminal methane production in vitro

This experiment was designed to investigate the effects of different concentrations of cellobiose (CB) or a twin strain of Saccharomyces cerevisiae live cells (YST) (20, 40 and 60 mg/60 mL), and CB + YST (60 + 20, 60 + 40, 60 + 60 mg/60 mL) on mixed ruminal microorganism fermentation in vitro. Ruminal fluid was collected from a cow, mixed with phosphate buffer (1:2) and incubated (60 mL) anaerobically at 38°C for 24 h with or without supplement plus 400 mg (dry matter (DM) basis) substrate (hay plus concentrate, 1.5:1). The medium pH numerically decreased with CB and CB + YST, but was unchanged with YST. The total volatile fatty acid and proportion of propionate increased (P < 0.05) in all cases. The pro- portion of acetate decreased (P < 0.05) with CB and CB + YST, but increased (P < 0.05) with YST and that of butyrate increased (P < 0.05) with CB and CB + YST, but decreased (P < 0.05) with YST. Ammonia-N decreased (P < 0.05) with CB and CB + YST, but was unchanged with YST. The number of protozoa was unchanged, and that of cellulolytic bacteria increased (P < 0.05) in all cases. Total gas production increased (P < 0.05) in all cases. Methane decreased, hydrogen was unchanged by YST and both gases were unchanged by CB and CB + YST. The in vitro disappearance of DM and neutral detergent fiber increased (P < 0.05) by 11.2% and 8.9%, 9% and 8.5%, and 12.1% and 10.2% in the case of CB, YST and CB + YST, respectively. Therefore, the dietary supplementation of CB and/or YST may improve ruminal fermentation and digestibility.

Hisao Itabashi

Papers

Culture-independent analysis of fecal microbiota in cattle.

Sarsaponin Effects on Ruminal Fermentation and Microbes, Methane Production, Digestibility and Blood Metabolites in Steers

Real-time PCR detection of the effects of protozoa on rumen bacteria in cattle.

Effects of the essential oil cyclodextrin complexes on ruminal methane production in vitro

Increase of ruminal fiber digestion by cellobiose and a twin strain of Saccharomyces cerevisiae live cells in vitro