Exploring the Rumen and Cecum Microbial Community from Fetus to Adulthood in Goat

Arthropods to Eutherians: A Historical and Contemporary Comparison of Sparse Prenatal Microbial Communities Among Animalia Species

Since the advent of next-generation sequencing, investigators worldwide have sought to discern whether a functional and biologically or clinically relevant prenatal microbiome exists. One line of research has led to the hypothesis that microbial DNA detected in utero/in ovo or prior to birth/hatching is a result of contamination and does not belong to viable and functional microbes. Many of these preliminary evaluations have been conducted in humans, mice, and nonhuman primates due to sample and specimen availability. However, a comprehensive review of the literature across animal species suggests organisms that maintain an obligate relationship with microbes may act as better models for interrogating the selective pressures placed on vertical microbial transfer over traditional laboratory species. To date, studies in humans and viviparous laboratory species have failed to illustrate the clear presence and transfer of functional microbes in utero. Until a ground truth regarding the status and relevance of prenatal microbes can be ascertained, it is salient to conduct parallel investigations into the prevalence of a functional prenatal microbiome across the developmental lifespan of multiple organisms in the kingdom Animalia. This comprehensive understanding is necessary not only to determine the role of vertically transmitted microbes and their products in early human health but also to understand their full One Health impact. This review is among the first to compile such comprehensive primary conclusions from the original investigator's conclusions, and hence collectively illustrates that prenatal microbial transfer is supported by experimental evidence arising from over a long and rigorous scientific history encompassing a breadth of species from kingdom Animalia.

Impact of feeding dried distillers' grains with solubles diet on microbiome and metabolome of ruminal and cecal contents in Guanling yellow cattle

Dried distillers' grains with solubles (DDGS) are rich in nutrients, and partially alternative feeding of DDGS effectively reduces cost of feed and improves animals' growth. We used 16S rDNA gene sequencing and LC/MS-based metabolomics to explore the effect of feeding cattle with a basal diet (BD) and a Jiang-flavor DDGS diet (replaces 25% concentrate of the diet) on microbiome and metabolome of ruminal and cecal contents in Guanling yellow cattle. The results showed that the ruminal and cecal contents shared the same dominance of Bacteroidetes, Firmicutes and Proteobacteria in two groups. The ruminal dominant genera were Prevotella_1, Rikenellaceae_RC9_gut_group, and Ruminococcaceae_UCG-010; and the cecal dominant genera were Ruminococcaceae_UCG-005, Ruminococcaceae_UCG-010, and Rikenellaceae_RC9_gut_group. Linear discriminant analysis effect size analysis (LDA > 2, P < 0.05) revealed the significantly differential bacteria enriched in the DDGS group, including Ruminococcaceae_UCG_012, Prevotellaceae_UCG_004 and Anaerococcus in the ruminal contents, which was associated with degradation of plant polysaccharides. Besides, Anaerosporobacter, Anaerovibrio, and Caproiciproducens in the cecal contents were involved in fatty acid metabolism. Compared with the BD group, 20 significantly different metabolites obtained in the ruminal contents of DDGS group were down-regulated (P < 0.05), and based on them, 4 significantly different metabolic pathways (P < 0.05) were enriched including "Linoleic acid metabolism," "Biosynthesis of unsaturated fatty acids," "Taste transduction," and "Carbohydrate digestion and absorption." There were 65 significantly different metabolites (47 were upregulated, 18 were downregulated) in the cecal contents of DDGS group when compared with the BD group, and 4 significantly different metabolic pathways (P < 0.05) were enriched including "Longevity regulating pathway," "Bile secretion," "Choline metabolism in cancer," and "HIF-1 signaling pathway." Spearman analysis revealed close negative relationships between the top 20 significantly differential metabolites and Anaerococcus in the ruminal contents. Bacteria with high relevance to cecal differential metabolites were Erysipelotrichaceae_UCG-003, Dielma, and Solobacterium that affect specific metabolic pathways in cattle. Collectively, our results suggest that feeding cattle with a DDGS diet improves the microbial structure and the metabolic patterns of lipids and carbohydrates, thus contributing to the utilization efficiency of nutrients and physical health to some extent. Our findings will provide scientific reference for the utilization of DDGS as feed in cattle industry.

Physical, Metabolic, and Microbial Rumen Development in Goat Kids: A Review on the Challenges and Strategies of Early Weaning

The digestive system of newborn ruminant functions is similar to monogastric animals, and therefore milk flows into the abomasum instead of rumen for digestion. The rumen undergoes tremendous changes over time in terms of structure, function, and microbiome. These changes contribute to the smooth transition from the dependence on liquid diets to solid diets. Goat kids are usually separated at early ages from their dams in commercial intensive systems. The separation from dams minimizes the transfer of microbiota from dams to newborns. In this review, understanding how weaning times and methodologies could affect the normal development and growth of newborn goats may facilitate the development of new feeding strategies to control stress in further studies.

Exploring the digesta- and mucosa-associated microbial community dynamics in the rumen and hindgut of goats from birth to adult

Recently, the relationship between the goat host and its gastrointestinal microbiome has emerged as a hallmark of host-microbiota symbiosis, which was indispensable for the proper physiological function that convert the plant biomass to livestock products. However, little integrative information about the establishment of gastrointestinal microflora in goats exists. Herein, we characterized the colonizing process of the bacterial community in the digesta and mucosa of the rumen, cecum, and colon of the cashmere goat from birth to adulthood to compare its spatiotemporal difference via 16S rRNA gene sequencing. A total of 1,003 genera belonging to 43 phyla were identified. Principal coordinate analysis unveiled the similarity of microbial community between or within each age group increased and gradually developed toward mature whatever in digesta or mucosa. In the rumen, the composition of the bacterial community in digesta differed significantly from in mucosa across age groups; whereas in the hindgut, there was a high similarity of bacterial composition between the in digesta and mucosa in each age group before weaning, while the bacterial community structure differed markedly between these two types of samples after weaning. Taxonomic analysis indicated that 25 and 21 core genera coexisted in digesta and mucosa of the rumen and hindgut, respectively; but their abundances differed considerably by GIT region and/or age. In digesta, as goats aged, a lower abundance of Bacillus was observed with higher abundances of Prevotella 1 and Rikenellaceae RC9 in the rumen; while in the hindgut, the genera Escherichia-Shigella, Variovorax, and Stenotrophomonas decreased and Ruminococcaceae UCG-005, Ruminococcaceae UCG-010, and Alistipes increased with age increased. In mucosa, the rumen showed microbial dynamics with increases of Butyrivibrio 2 and Prevotellaceae UCG-001 and decreases of unclassified_f_Pasteurellaceae; while the genera Treponema 2 and Ruminococcaceae UCG-010 increased and Escherichia-Shigella decreased in the hindgut as goats aged. These results shed light on the colonization process of microbiota in the rumen and hindgut, which mainly include the initial, transit, and mature phases. Furthermore, there is a significant difference in the microbial composition between in digesta and mucosa, and both these exhibit a considerable spatiotemporal specificity.

Reproductive Microbiomes in Domestic Livestock: Insights Utilizing 16S rRNA Gene Amplicon Community Sequencing

Advancements in 16S rRNA gene amplicon community sequencing have vastly expanded our understanding of the reproductive microbiome and its role in fertility. In humans, Lactobacillus is the overwhelmingly dominant bacteria within reproductive tissues and is known to be commensal and an indicator of fertility in women and men. It is also known that Lactobacillus is not as largely abundant in the reproductive tissues of domestic livestock species. Thus, the objective of this review is to summarize the research to date on both female and male reproductive microbiomes in domestic livestock species (i.e., dairy cattle, beef cattle, swine, small ruminants, and horses). Having a comprehensive understanding of reproductive microbiota and its role in modulating physiological functions will aid in the development of management and therapeutic strategies to improve reproductive efficiency.

Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives

The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.

Age-dependent changes of hindgut microbiota succession and metabolic function of Mongolian cattle in the semi-arid rangelands

Dietary changes have significant effects on gut microbiota and host health. Weaning is an important stage of dietary change in ruminants. The gastrointestinal tract (GIT) microbiota of calf in the early life undergo some changes, and the plasticity of the calf is beneficial to cope with these changes and challenges. However, the complex development of hindgut microorganisms in post-weaning ruminants is not fully understood. In this study, we used 16S rRNA sequencing and untargeted metabolomic analysis to determine the cecal and colonic bacterial community and associated metabolome of Mongolian cattle at age of the 5th (at weaning), 18th, and 36th months. Moreover, the maturation patterns of the hindgut bacterial community and the dynamic changes of metabolites were also explored. Sequencing results showed that Firmicutes and Bacteroidetes were the dominant phyla in the cecum and colon. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that were stage-specific in the cecum and colon. The relative abundance of Ruminococcaceae, a microbial family related to fiber degradation, gradually increased with age in the cecum, while the relative abundance of Bacteroides and Alistipes, which are related to immunity, gradually increased in the colon. The differential metabolites in the cecum and colon were mainly enriched in steroid hormone biosynthesis, primary bile acid biosynthesis, and arachidonic acid metabolism between different ages of Mongolian cattle after weaning. Consequently, this dual omics analysis provided important information on the changes in microbial and metabolite interactions in Mongolian cattle after weaning. The microorganisms and metabolites in the cecum and colon further enhanced the abiotic stress resistance of Mongolian cattle to the harsh environment. The information obtained in this study is of great significance for future strategies of cecum and colon microbiota regulation of post-weaning Mongolian cattle in the harsh Mongolian Plateau ecosystem.

Does the Amniotic Fluid of Mice Contain a Viable Microbiota?

The existence of an amniotic fluid microbiota (i.e., a viable microbial community) in mammals is controversial. Its existence would require a fundamental reconsideration of fetal in utero exposure to and colonization by microorganisms and the role of intra-amniotic microorganisms in fetal immune development as well as in pregnancy outcomes. In this study, we determined whether the amniotic fluid of mice harbors a microbiota in late gestation. The profiles of the amniotic fluids of pups located proximally or distally to the cervix were characterized through quantitative real-time PCR, 16S rRNA gene sequencing, and culture (N = 21 dams). These profiles were compared to those of technical controls for bacterial and DNA contamination. The load of 16S rRNA genes in the amniotic fluid exceeded that in controls. Additionally, the 16S rRNA gene profiles of the amniotic fluid differed from those of controls, with Corynebacterium tuberculostearicum being differentially more abundant in amniotic fluid profiles; however, this bacterium was not cultured from amniotic fluid. Of the 42 attempted bacterial cultures of amniotic fluids, only one yielded bacterial growth – Lactobacillus murinus. The 16S rRNA gene of this common murine-associated bacterium was not detected in any amniotic fluid sample, suggesting it did not originate from the amniotic fluid. No differences in the 16S rRNA gene load, 16S rRNA gene profile, or bacterial culture were observed between the amniotic fluids located Proximally and distally to the cervix. Collectively, these data indicate that, although there is a modest DNA signal of bacteria in murine amniotic fluid, there is no evidence that this signal represents a viable microbiota. While this means that amniotic fluid is not a source of microorganisms for in utero colonization in mice, it may nevertheless contribute to fetal exposure to microbial components. The developmental consequences of this observation warrant further investigation.

Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission?

Agriculture is responsible for a great share of the anthropogenic sources of greenhouse gases that, by warming the earth, threaten its biodiversity. Among greenhouse gas emissions, enteric CH4 from livestock is an important target to slow down climate changes. The CH4 is originated from rumen fermentation and its concentration is affected by several factors, including genetics and nutrition. Ruminants have an extraordinary symbiosis with microorganisms (bacteria, fungi, and protozoa) that ferment otherwise indigestible carbohydrates, from which they obtain energy to grow and continue actively producing, among other products, volatile fatty acids, CO2 and H2. Detrimental ruminal accumulation of H2 is avoided by methanogenesis carried out by Archaea methanogens. Importantly, methanogenesis is not the only H2 sink pathway. In fact, other bacteria can reduce substrates using metabolic hydrogen formed during carbohydrate fermentation, namely propionate production and reductive acetogenesis, thus lowering the CH4 produced. Although the complexity of rumen poses challenges to mitigate CH4 production, the emergence of sequencing techniques that allow the study of microbial communities, gene expression, and metabolome are largely contributing to unravel pathways and key players in the rumen. Indeed, it is now recognized that in vivo emissions of CH4 are correlated to microbial communities, and particularly with the abundance of methanogens, several bacterial groups, and  their genes. The goal of CH4 mitigation is to work in favor of the natural processes, without compromising rumen function, animal health, and productivity. Notwithstanding, the major challenge continues to be the feasibility and affordability of the proposed solutions.

Age Matters: Community Assembly in the Pig Fecal Microbiome in the First Month of Life

Despite the wealth of research into strategies for microbiome modulation, studies of microbiome management in pig hosts have found mixed results. A refined understanding of the patterns of microbiome assembly during the host’s early life, when management strategies are most commonly applied, is necessary for the development of successful management practices. Here, we study the development of the pig gut microbial community in a monitoring experiment, sampling the microbiome of pigs in a commercial farm intensively during the first month of life. We found that the community’s taxonomic richness increased linearly with host age. Furthermore, rapid changes across communities occurred in stages, and non-linear patterns in relative abundance were commonly observed among dominant taxa across host age, consistent with primary succession. Our results highlight the importance of understanding the patterns of microbiome assembly during host development, and identify successional stages as windows of opportunity for future research.