Community structures of fecal bacteria in cattle from different animal feeding operations

Microbiota of newborn calves and their mothers reveals possible transfer routes for newborn calves' gastrointestinal microbiota

The intestinal microbiota of newborns plays an important role in the development of immunity and metabolism. In livestock animals, knowledge of the intestinal microbiota is essential not only to prevent diseases but also to optimize weight gain and performance. The aim of our study was to examine faecal samples repeatedly within the first two days of life using 16S rRNA gene High Throughput Sequencing. Additionally, samples from the mouths of the calves and the vaginas, colostrum, and faeces of the dams were included to evaluate possible sources of the calf faecal microbiota. The calf faecal microbiota was highly variable during the first 48 hours post natum (p.n.). Significant changes were found in species diversity and richness, in copy numbers evaluated by qPCR and in predominant bacteria over time. The most pronounced changes occurred between 6 and 24 hours p.n. All calf faecal samples were dominated by Operational Taxonomic Units (OTUs) belonging to the family Enterobacteriaceae. Cow faecal samples showed significantly higher species richness, diversity, number of observed OTUs, and copy numbers compared to all other samples. OTUs belonging to the family Ruminococcaceae were most abundant in cow faecal and vaginal samples. Colostrum was dominated by Enhydrobacter affiliated OTUs. To identify possible inoculation routes for the calf microbiota, we analysed OTU sharing between samples. The calf microbiota during the first two days of life was clearly distinct from the dam's faecal microbiota. Furthermore, colostrum microbiota clearly differed from calf and cow faecal microbiota and thus most likely does not play an important role as inoculation source for calf microbiota during the first two days of life. In contrast, the cow vaginal and the calf faecal microbiota were more similar, suggesting that some of the calf faecal microbiota may derive from inoculation from the birth canal during birth.

Response of Beef Cattle Fecal Microbiota to Grazing on Toxic Tall Fescue

Tall fescue, the predominant southeastern United States cool-season forage grass, frequently becomes infected with an ergot alkaloid-producing toxic endophyte, Epichloë coenophialum Consumption of endophyte-infected fescue results in fescue toxicosis (FT), a condition that lowers beef cow productivity. Limited data on the influence of ergot alkaloids on rumen fermentation profiles or ruminal bacteria that could degrade the ergot alkaloids are available, but how FT influences the grazing bovine fecal microbiota or what role fecal microbiota might play in FT etiology and associated production losses has yet to be investigated. Here, we used 16S rRNA gene sequencing of fecal samples from weaned Angus steers grazing toxic endophyte-infected (E+; n = 6) or nontoxic (Max-Q; n = 6) tall fescue before and 1, 2, 14, and 28 days after pasture assignment. Bacteria in the Firmicutes and Bacteroidetes phyla comprised 90% of the Max-Q and E+ steer fecal microbiota throughout the trial. Early decreases in the Erysipelotrichaceae family and delayed increases of the Ruminococcaceae and Lachnospiraceae families were among the major effects of E+ grazing. E+ also increased abundances within the Planctomycetes, Chloroflexi, and Proteobacteria phyla and the Clostridiaceae family. Multiple operational taxonomic units classified as Ruminococcaceae and Lachnospiraceae were correlated negatively with weight gains (lower in E+) and positively with respiration rates (increased by E+). These data provide insights into how E+ grazing alters the Angus steer microbiota and the relationship of fecal microbiota dynamics with FT.IMPORTANCE Consumption of E+ tall fescue has an estimated annual $1 billion negative impact on the U.S. beef industry, with one driver of these costs being lowered weight gains. As global agricultural demand continues to grow, mitigating production losses resulting from grazing the predominant southeastern United States forage grass is of great value. Our investigation of the effects of E+ grazing on the fecal microbiota furthers our understanding of bovine fescue toxicosis in a real-world grazing production setting and provides a starting point for identifying easy-to-access fecal bacteria that could serve as potential biomarkers of animal productivity and/or FT severity for tall fescue-grazing livestock.

Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture

The production of dairy, meat, and fiber by ruminant animals relies on the biological processes occurring in soils, forage plants, and the animals' rumens. Each of these components has an associated microbiome, and these have traditionally been viewed as distinct ecosystems. However, these microbiomes operate under similar ecological principles and are connected via water, energy flows, and the carbon and nitrogen nutrient cycles. Here, we summarize the microbiome research that has been done in each of these three environments (soils, forage plants, animals' rumen) and investigate what additional benefits may be possible through understanding the interactions between the various microbiomes. The challenge for future research is to enhance microbiome function by appropriate matching of plant and animal genotypes with the environment to improve the output and environmental sustainability of pastoral agriculture.

Effect of dietary concentrate to forage ratios on ruminal bacterial and anaerobic fungal populations of cashmere goats

The rumen contains a highly complex microbial ecosystem that plays an important role in converting solar energy in plants into nutrients for ruminants and generates animal food products, such as meat and milk for humans. Therefore, understanding the effect of the dietary concentrate to forage (C:F) ratio on ruminal microbiota is of great significance for the growth and development of ruminants. In this study, changes in the ruminal bacterial and anaerobic fungal populations of Shaanbei white-cashmere (SWC) goats that were reared under different dietary C:F ratios were evaluated by high-throughput sequencing analysis. It was found that dietary C:F ratio has a significant impact on the composition of the ruminal bacteria in SWC goats. The levels of Actinobacteria and Proteobacteria were significantly increased (P < 0.05), whereas the level of Bacteroidetes was significantly decreased when the proportion of dietary concentrate was increased (P < 0.05); as the proportion of dietary concentrate increased, Prevotella, Selenomonas, and Treponema were significantly increased (P < 0.05), whereas Oscillospira and Succiniclasticum were significantly reduced (P < 0.05). Furthermore, different dietary C:F ratios significantly affected the composition of anaerobic fungi in SWC goats. As the proportion of dietary concentrate increased, Ascomycota, Basidiomycota, and Zygomycota were significantly increased (P < 0.05), while Neocallimastigomycota was significantly reduced (P < 0.05); the levels of Alternaria, Aspergillus, Neocallimastix, Orpinomyces, Piromyces, and Stachybotrys were significantly increased, while those of Candida, Penicillium, and Trichosporon were significantly decreased when the proportion of dietary concentrate increased (P < 0.05). These findings will help us to better understand the changes in ruminal bacterial and anaerobic fungal populations of SWC goats under different dietary C:F ratios, which could provide a theoretical basis for microecological regulation of SWC goats.

Porcine Feed Efficiency-Associated Intestinal Microbiota and Physiological Traits: Finding Consistent Cross-Locational Biomarkers for Residual Feed Intake

Optimal feed efficiency (FE) in pigs is important for economic and environmental reasons. Previous research identified FE-associated bacterial taxa within the intestinal microbiota of growing pigs. This study investigated whether FE-associated bacteria and selected FE-associated physiological traits were consistent across geographic locations (Republic of Ireland [ROI] [two batches of pigs, ROI1 and ROI2], Northern Ireland [NI], and Austria [AT]), where differences in genetic, dietary, and management factors were minimized. Pigs (n = 369) were ranked, within litter, on divergence in residual feed intake (RFI), and 100 extremes were selected (50 with high RFI and 50 with low RFI) across geographic locations for intestinal microbiota analysis using 16S rRNA amplicon sequencing and examination of FE-associated physiological parameters. Microbial diversity varied by geographic location and intestinal sampling site but not by RFI rank, except in ROI2, where more-feed-efficient pigs had greater ileal and cecal diversity. Although none of the 188 RFI-associated taxonomic differences found were common to all locations/batches, Lentisphaerae, Ruminococcaceae, RF16, Mucispirillum, Methanobrevibacter, and two uncultured genera were more abundant within the fecal or cecal microbiota of low-RFI pigs in two geographic locations and/or in both ROI batches. These are major contributors to carbohydrate metabolism, which was reflected in functional predictions. Fecal volatile fatty acids and salivary cortisol were the only physiological parameters that differed between RFI ranks. Despite controlling genetics, diet specification, dietary phases, and management practices in each rearing environment, the rearing environment, encompassing maternal influence, herd health status, as well as other factors, appears to impact intestinal microbiota more than FE.IMPORTANCE Interest in the role of intestinal microbiota in determining FE in pigs has increased in recent years. However, it is not known if the same FE-associated bacteria are found across different rearing environments. In this study, geographic location and intestinal sampling site had a greater influence on the pig gut microbiome than FE. This presents challenges when aiming to identify consistent reliable microbial biomarkers for FE. Nonetheless, seven FE-associated microbial taxa were common across two geographic locations and/or two batches within one location, and these indicated a potentially "healthier" and metabolically more capable microbiota in more-feed-efficient pigs. These taxa could potentially be employed as biomarkers for FE, although bacterial consortia, rather than individual taxa, may be more likely to predict FE. They may also merit consideration for use as probiotics or could be targeted by dietary means as a strategy for improving FE in pigs in the future.

Feeding Pasteurized Waste Milk to Preweaned Dairy Calves Changes Fecal and Upper Respiratory Tract Microbiota

In the present study bacterial communities from both, the gastrointestinal and respiratory tract of pre-weaned dairy calves fed two different milk-feeding programs were characterized using 16S rRNA gene sequencing. Twenty female Holstein calves (38.8 ± 1.40 kg of BW) were fed pasteurized waste milk (pWM) containing residues of various antimicrobials. Twenty additional calves (38.1 ± 1.19 kg of BW) were fed milk replacer (MR) with similar nutrient composition (27.5% crude protein, 32.1% fat) compared to waste milk (28.6% crude protein, 30.0% fat) from day 1 to weaning at day 49 of study. Fecal samples and nasal swabs were collected on day 42 only from calves that were not treated with therapeutic antibiotics throughout the study, which were 8 MR and 10 pWM calves. To assess the impact of the two feeding regimes on the fecal and nasal microbiota, α and β-diversity measures were calculated, and the relative abundance of operational taxonomic units (OTUs) at different taxonomic levels was determined for each sample. In general, Chao1, PD Whole Tree, and Shannon diversity indices were similar for the fecal and nasal bacterial communities of calves regardless of the feeding regime. However, principal coordinate analysis based on unweighted Unifrac distances indicated differences in the structure of bacterial communities of calves fed milk replacer compared with those from calves fed pasteurized waste milk. The relative abundance of the Streptococcaceae family and the genus Histophilus was greater (P < 0.05) in the nasal microbiota of calves fed milk replacer than in those fed pasteurized waste milk. However, the genus Prevotella tended (P = 0.06) to be more relatively abundant in the respiratory tract of calves fed pasteurized waste milk than in those fed milk replacer. Differences in relative abundances of bacterial taxa in gut microbiota were only observed at the phylum level, suggesting that antimicrobial residues present in waste milk have a non-specific influence at a lower taxonomical level.

Large-scale implementation of standardized quantitative real-time PCR fecal source identification procedures in the Tillamook Bay Watershed

Fecal pollution management remains one of the biggest challenges for water quality authorities worldwide. Advanced fecal pollution source identification technologies are now available that can provide quantitative information from many animal groups. As public interest in these methodologies grows, it is vital to use standardized procedures with clearly defined data acceptance metrics and conduct field studies demonstrating the use of these techniques to help resolve real-world water quality challenges. Here we apply recently standardized human-associated qPCR methods with custom data acceptance metrics (HF183/BacR287 and HumM2), along with established procedures for ruminant (Rum2Bac), cattle (CowM2 and CowM3), canine (DG3 and DG37), and avian (GFD) fecal pollution sources to (i) demonstrate the feasibility of implementing standardized qPCR procedures in a large-scale field study, and (ii) characterize trends in fecal pollution sources in the research area. A total of 602 water samples were collected over a one-year period at 29 sites along the Trask, Kilchis, and Tillamook rivers and tributaries in the Tillamook Bay Watershed (OR, USA). Host-associated qPCR results were combined with high-resolution geographic information system (GIS) land use and general indicator bacteria (E. coli) measurements to elucidate water quality fecal pollution trends. Results demonstrate the feasibility of implementing standardized fecal source identification qPCR methods with established data acceptance metrics in a large-scale field study leading to new investigative leads suggesting that elevated E. coli levels may be linked to specific pollution sources and land use activities in the Tillamook Bay Watershed.

Effect of Dietary Supplementation of Moringa Oleifera on the Production Performance and Fecal Methanogenic Community of Lactating Dairy Cows

Simple Summary

High-quality forages such as protein-rich ingredients are essential to maximize production performance in dairy production. However, enteric methane produced by methanogenesis represents a substantial waste of feed energy for ruminants. Thus, it is important to evaluate the environmental effect when such feed ingredients are used to provide necessary nutrients. The aim of the present study was to examine the effects of dietary supplementation of Moringa oleifera on the production performance and fecal methanogenic community in lactating cows. The study’s main results suggest that inclusion of Moringa oleifera improved milk fat content and changed the composition and diversity of methanogens. This study indicates that secondary metabolites from Moringa oleifera may regulate fermentation conditions and associations between some methanogens and other microbes. These findings provide basic information on the utilization of alternative forage resources for dairy cows and can help to better understand the regulation of microbial metabolic function and methane emissions.

Abstract

Development of alternative forage resources is of great importance to provide necessary nutrients and minimize greenhouse gas emissions in ruminant production. The aim of this study was to examine the effects of dietary supplementation of Moringa oleifera on the production performance and fecal methanogenic community in dairy cows using methyl-coenzyme M reductase α-subunit gene. Sixty-four cows were allocated to one of four treatments: basal diet without M. oleifera (control) or low (3% w/w, M3), medium (6%, M6), or high (9%, M9) supplementation with M. oleifera. This study demonstrated that different supplementation levels of Moringa oleifera in the diet achieved similar feed intake and milk production, but adding 6% of Moringa oleifera improved milk fat content. Two families, two phyla, three genera, and three species in total were identified among the four treatments. The fecal archaeal community in the control treatment was predominated by Methanobrevibacter (39.1% of the total sequence reads) followed by Methanosphaera and Methanocorpusculum at the genus level. The increased abundance of the Methanosphaera genus and Methanosphaera sp. ISO3-F5 species was induced by secondary metabolites of Moringa oleifera in the diet. Results indicated that Moringa oleifera supplementation not only improved dairy product quality but could also potentially reduce methane emissions.

Fecal Microbial Communities in a Large Representative Cohort of California Dairy Cows

Improved sequencing and analytical techniques allow for better resolution of microbial communities; however, the agriculture field lacks an updated analysis surveying the fecal microbial populations of dairy cattle in California. This study is a large-scale survey to determine the composition of the bacterial community present in the feces of lactating dairy cattle on commercial dairy operations. For the study, 10 dairy farms across northern and central California representing a variety of feeding and management systems were enrolled. The farms represented three typical housing types including five freestall, two drylot and three pasture-based management systems. Fresh feces were collected from 15 randomly selected cows on each farm and analyzed using 16S rRNA gene amplicon sequencing. This study found that housing type, individual farm, and dietary components significantly affected the alpha diversity of the fecal microbiota. While only one Operational Taxonomic Unit (OTU) was common among all the sampled individuals, 15 bacterial families and 27 genera were shared among 95% of samples. The ratio of the families Coriobacteriaceae to Bifidobacteriaceae was significantly different between housing types and farms with pasture fed animals having a higher relative abundance of Coriobacteriaceae. A majority of samples were positive for at least one OTU assigned to Enterobacteriaceae and 31% of samples contained OTUs assigned to Campylobacter. However, the relative abundance of both taxa was <0.1%. The microbial composition displays individual farm specific signatures, but housing type plays a role. These data provide insights into the composition of the core fecal microbiota of commercial dairy cows in California and will further generate hypotheses for strategies to manipulate the microbiome of cattle.

Highly Specific Sewage-Derived Bacteroides Quantitative PCR Assays Target Sewage-Polluted Waters

The identification of sewage contamination in water has primarily relied on the detection of human-associated Bacteroides using markers within the V2 region of the 16S rRNA gene. Despite the establishment of multiple assays that target the HF183 cluster (i.e., Bacteroides dorei) and other Bacteroides organisms (e.g., Bacteroides thetaiota omicron), the potential for more human-associated markers in this genus has not been explored in depth. We examined the Bacteroides population structure in sewage and animal hosts across the V4V5 and V6 hypervariable regions. Using near-full-length cloned sequences, we identified the sequences in the V4V5 and V6 hypervariable regions that are linked to the HF183 marker in the V2 region and found these sequences were present in multiple animals. In addition, the V4V5 and V6 regions contained human fecal marker sequences for organisms that were independent of the HF183 cluster. The most abundant Bacteroides in untreated sewage was not human associated but pipe derived. Two TaqMan quantitative PCR (qPCR) assays targeting the V4V5 and V6 regions of this organism were developed. Validation studies using fecal samples from seven animal hosts (n = 76) and uncontaminated water samples (n = 30) demonstrated the high specificity of the assays for sewage. Freshwater Bacteroides were also identified in uncontaminated water samples, demonstrating that measures of total Bacteroides do not reflect fecal pollution. A comparison of two previously described human Bacteroides assays (HB and HF183/BacR287) in municipal wastewater influent and sewage-contaminated urban water samples revealed identical results, illustrating the assays target the same organism. The detection of sewage-derived Bacteroides provided an independent measure of sewage-impacted waters.IMPORTANCE Bacteroides are major members of the gut microbiota, and host-specific organisms within this genus have been used extensively to gain information on pollution sources. This study provides a broad view of the population structure of Bacteroides within sewage to contextualize the well-studied HF183 marker for a human-associated Bacteroides The study also delineates host-specific sequence patterns across multiple hypervariable regions of the 16S rRNA gene to improve our ability to use sequence data to assess water quality. Here, we demonstrate that regions downstream of the HF183 marker are nonspecific but other potential human-associated markers are present. Furthermore, we show the most abundant Bacteroides in sewage is free living, rather than host associated, and specifically found in sewage. Quantitative PCR assays that target organisms specific to sewer pipes offer measures that are independent of the human microbiome for identifying sewage pollution in water.

Effects and immune responses of probiotic treatment in ruminants

Gut microbial colonization and establishment are vital to ruminant health and production. This review article focuses on current knowledge and methods used to understand and manipulate the gut microbial community in ruminant animals, with a special focus on probiotics treatment. This review highlights the most promising of studies in this area, including gut microbial colonization and establishment, effect of gastrointestinal tract microbial community on host mucosal innate immune function, impact of feeding strategies on gut microbial community, current probiotic treatments in ruminants, methods to manipulate the gut microbiota and associated antimicrobial compounds, and models and cell lines used in understanding the host immune response to probiotic treatments. As a lot of work in this area was done in humans and mice, this review article also includes up-to-date knowledge from relevant studies in human and mouse models. This review is a useful resource for scientists working in the areas of ruminant nutrition and health, and to researchers investigating the microbial ecology and its relation to animal health.

Human and animal microbial source tracking in a tropical river with multiple land use activities

The enhancement and restoration of the water quality of deteriorating surface water resources can be challenging, particularly for rivers with multiple usages, such as agriculture, animal husbandry, human residence, and industries. Recently, the performance of DNA-based microbial source tracking (MST) indicators detected by end-point and quantitative PCR assays for identifying sources of fecal pollution from human sewage, swine, and cattle and non-host-specific (universal) fecal pollution in the Tha Chin River basin, Thailand, was evaluated. The present study monitored these validated MST markers and various physicochemical and microbial water quality parameters in samples collected from twelve stations along the Tha Chin River during four sampling events in the wet and dry seasons. No significant difference in precipitation was observed between the wet and dry samplings. Universal markers (both PCR and qPCR) were detected in all 48 samples, indicating persistent and continuing fecal contamination. The sewage- and swine-specific qPCR marker concentrations did not vary among the sampling events, whereas cattle-specific qPCR markers were detected only in the wet season. Animal-specific markers were detected in the lower Tha Chin River section, which is characterized by intensive animal farming. Sewage-specific markers were also found in the lower section and near an upstream residential area. The high agreement (87.5-100%) between the PCR and qPCR results suggested that PCR could serve as a lower-cost MST screening test that requires less technical expertise. A multivariate analysis conducted using the survival analysis procedure to include censored data also emphasized the high pollution in the lower section of the river at all sampling events. Universal and swine-specific markers showed moderate correlations with microbial indicators, including total coliforms, fecal coliforms, E. coli, and enterococci. None of the MST markers or microbial parameters were associated with the measured physicochemical parameters. This study provides the first evaluation of MST markers for monitoring surface freshwater in Thailand, and the findings might aid the pollution surveillance of impaired water bodies and the development of strategies for improving their water quality.

The Bacterial Community Structure and Microbial Activity in a Traditional Organic Milpa Farming System Under Different Soil Moisture Conditions

Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, i.e., inorganic fertilization, tillage, crop residue removal and maize (Zea mays L.) monoculture, and traditional organic farmed soil "milpa," i.e., minimum tillage, rotation of maize, pumpkin (Cucurbita sp.) and beans (Phaseolus vulgaris L.) and organic fertilization were sampled. Both soils from the central highlands of Mexico were characterized and incubated aerobically at 5% field capacity (5%FC) and 100% field capacity (FC) for 45 days, while the C and N mineralization, enzyme activity and the bacterial community structure were monitored. After applying the different agricultural practices 3 years, the organic C content was 1.8-times larger in the milpa than in the conventional cultivated soil, the microbial biomass C 1.3-times, and C and N mineralization 2.0-times (mean for soil incubated at 5%FC and FC). The dehydrogenase, activity was significantly higher in the conventional cultivated soil than in the milpa soil when incubated at 5%FC, but not when incubated at FC. The relative abundance of Gemmatimonadetes was larger in the conventional cultivated soil than in the milpa soil in soil both at 5%FC and FC, while that of Bacteroidetes showed an opposite trend. The relative abundance of other groups, such as Nitrospirae and Proteobacteria, was affected by cultivation technique, but controlled by soil water content. The relative abundance of other groups, e.g., FBP, Gemmatimonadetes and Proteobacteria, was affected by water content, but the effect depended on agricultural practice. For soil incubated at FC, the xenobiotics biodegradation and metabolism related functions were higher in the milpa soil than in the conventional cultivated soil, and carbohydrate metabolism showed an opposite trend. It was found that agricultural practices and soil water content had a strong effect on soil characteristics, C and N mineralization, enzyme activity, and the bacterial community structure and its functionality. Decreases or increases in the relative abundance of bacterial groups when the soil water content decreased, i.e., from FC to 5%FC, was defined often by the cultivation technique, and the larger organic matter content in the milpa soil did not prevent large changes in the bacterial community structure when the soil was dried.

How Can We Define "Optimal Microbiota?": A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture

All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.

Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in “omic” data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

Synergetic action between the rumen microbiota and bovine health

Host-rumen-microbe interactions are essential components of many physiological processes, and therefore can affect ruminant health. Classical knowledge of rumen microbiology is based on culture-dependent methodologies, which only account for 10-20% of the rumen bacterial communities. While, the advancement in DNA sequencing and bioinformatics platforms provide novel approaches to investigate the composition and dynamics of the rumen microbiota. Recent studies demonstrated that the ruminal ecosystem is highly diverse and harbors numerous microbial communities. The composition of these microbial communities are affected by various environmental factors such as nutrition and different management strategies. Disturbance in the microbial ecology of the rumen is associated with the development of various diseases. Despite the flow of recent rumen-based studies, rumen microbiota is still not fully characterized. This review provides an overview of recent efforts to characterize rumen microbiota and its potential role in rumen health and disease. Moreover, the recent effects of dietary interventions and probiotics on rumen microbiota are discussed.

Metagenomic Analysis of Bacteria, Fungi, Bacteriophages, and Helminths in the Gut of Giant Pandas

To obtain full details of gut microbiota, including bacteria, fungi, bacteriophages, and helminths, in giant pandas (GPs), we created a comprehensive microbial genome database and used metagenomic sequences to align against the database. We delineated a detailed and different gut microbiota structures of GPs. A total of 680 species of bacteria, 198 fungi, 185 bacteriophages, and 45 helminths were found. Compared with 16S rRNA sequencing, the dominant bacterium phyla not only included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria but also Cyanobacteria and other eight phyla. Aside from Ascomycota, Basidiomycota, and Glomeromycota, Mucoromycota, and Microsporidia were the dominant fungi phyla. The bacteriophages were predominantly dsDNA Myoviridae, Siphoviridae, Podoviridae, ssDNA Inoviridae, and Microviridae. For helminths, phylum Nematoda was the dominant. In addition to previously described parasites, another 44 species of helminths were found in GPs. Also, differences in abundance of microbiota were found between the captive, semiwild, and wild GPs. A total of 1,739 genes encoding cellulase, β-glucosidase, and cellulose β-1,4-cellobiosidase were responsible for the metabolism of cellulose, and 128,707 putative glycoside hydrolase genes were found in bacteria/fungi. Taken together, the results indicated not only bacteria but also fungi, bacteriophages, and helminths were diverse in gut of giant pandas, which provided basis for the further identification of role of gut microbiota. Besides, metagenomics revealed that the bacteria/fungi in gut of GPs harbor the ability of cellulose and hemicellulose degradation.

Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period

The objective was to examine effects of treating commercial beef feedlot cattle with therapeutic doses of tulathromycin, a macrolide antimicrobial drug, on changes in the fecal resistome and microbiome using shotgun metagenomic sequencing. Two pens of cattle were used, with all cattle in one pen receiving metaphylaxis treatment (800 mg subcutaneous tulathromycin) at arrival to the feedlot, and all cattle in the other pen remaining unexposed to parenteral antibiotics throughout the study period. Fecal samples were collected from 15 selected cattle in each group just prior to treatment (Day 1), and again 11 days later (Day 11). Shotgun sequencing was performed on isolated metagenomic DNA, and reads were aligned to a resistance and a taxonomic database to identify alignments to antimicrobial resistance (AMR) gene accessions and microbiome content. Overall, we identified AMR genes accessions encompassing 9 classes of AMR drugs and encoding 24 unique AMR mechanisms. Statistical analysis was used to identify differences in the resistome and microbiome between the untreated and treated groups at both timepoints, as well as over time. Based on composition and ordination analyses, the resistome and microbiome were not significantly different between the two groups on Day 1 or on Day 11. However, both the resistome and microbiome changed significantly between these two sampling dates. These results indicate that the transition into the feedlot-and associated changes in diet, geography, conspecific exposure, and environment-may exert a greater influence over the fecal resistome and microbiome of feedlot cattle than common metaphylactic antimicrobial drug treatment.

High-Throughput Analysis Reveals Seasonal Variation of the Gut Microbiota Composition Within Forest Musk Deer (Moschus berezovskii)

The gut microbiota plays a key role in the nutritional ecology of ruminants, and host diet has a significant effect on these microbial communities. Longitudinal studies assessing variation of seasonal microbiota in animals can provide a comparative context for interpreting the adaptive significance of such changes. However, few studies have investigated the effects of seasonally-related dietary shifts on the gut microbial communities of endangered forest musk deer (FMD), and the national breeding programs need this information to promote the growth of captive populations. The present study applied bacterial 16S rRNA genes based on high-throughput sequencing to profile the fecal microbial communities of FMD across four seasons. Microbial diversity was higher in seasons with dry leaf diets (winter and spring) compared to seasons with fresh leaf diets (summer and autumn). The dominant microbial phyla were Firmicutes and Bacteroidetes, and the core bacterial taxa also comprised mostly (94.40% of shared OTUs) Firmicutes (37 taxa) and Bacteroidetes (6 taxa), which were relatively stable across different seasons. The Firmicutes-Bacteroidetes ratio declined in seasons with fresh leaf diets relative to seasons with dry leaf diets, and the dominant genera among the four seasons showed no significant variation in abundance. This work explores the seasonal variation in the microbial communities of FMD for the first time, and reveals how gut microbial community dynamics vary seasonally in accordance with differences in dietary plants (fresh and dry leaf). These results indicate that the annual cyclic reconfiguration of FMD gut microbiota could be associated with shifts in dietary nutrients, which is important information to inform captive FMD management.

A Comparative Study on the Faecal Bacterial Community and Potential Zoonotic Bacteria of Muskoxen (Ovibos moschatus) in Northeast Greenland, Northwest Greenland and Norway

Muskoxen (Ovibos moschatus) are ruminants adapted to a high-fibre diet. There is increasing interest in the role that gut microbes play in the digestion and utilization of these specialized diets but only limited data available on the gut microbiome of high-Arctic animals. In this study, we metabarcoded the 16S rRNA region of faecal samples from muskoxen of Northeast Greenland, Northwest Greenland and Norway, and quantified the effects of physiological and temporal factors on bacterial composition. We found significant effects of body mass, year of sampling and location on the gut bacterial communities of North East Greenland muskoxen. These effects were however dwarfed by the effects of location, emphasizing the importance of the local ecology on the gut bacterial community. Habitat alterations and rising temperatures may therefore have a considerable impact on muskoxen health and reproductive success. Moreover, muskoxen are hunted and consumed in Greenland, Canada and Alaska; therefore, this study also screened for potential zoonoses of food safety interest. A total of 13 potentially zoonotic genera were identified, including the genera Erysipelothrix and Yersinia implicated in recent mass die-offs of the muskoxen themselves.

Effect of Sugarcane Straw and Goat Manure on Soil Nutrient Transformation and Bacterial Communities

Crop residue and animal manure as a soil amendment have been recognized as a feasible agricultural practice owing to its contribution in improving the soil fertility (SF). The primary advantages of this practice are determined by the activities of soil microorganisms. However, goat manure (M), sugarcane straw (S), and goat manure plus straw (MS) amendments influence soil bacteria, their activities, and SF in clay-loam soil remains undefinable. Therefore, this study distinguished the efficacy of M, MS, and S amendment on soil enzyme activities and the availability of nutrients, including various bacterial populations in clay-loamy soil with respect to two different phases (50 and 100 days). In order to analyze the bacterial structure and their activities, we employed high-throughput sequencing (HTS) and soil enzyme activity (SEA) tests. Soil amended with M and MS not only significantly enhanced nutrient availability, including C, P, and N, soil pH, as well as SEA for C and N cycles in both phases. Additionally, the increase in nutrient availability was greater in M- and MS-amended soils in the second phase (100 days) compared to the M- and S-amended soils in the first phase (50 days). Moreover, plant growth promoting and lignocellulose degrading bacterial genera were enhanced under M- and MS-amended soil compared to S-amended soil in both phases. Distance-based redundancy analysis (dbRDA) showed that soil pH, carbon-nitrogen ratio (C:N), and nitrates (NO3−) were inducing the fewest changes, while total nitrogen (TN), total carbon (TC), available nitrogen (AN), available phosphorus (AP), total phosphorus (TP), available potassium (AK), and ammonium (NH4+) were the main operators in terms of change in bacterial populations. In general, we observed that M and MS are better amendment sources as compared to S amendment in order to enhance the SF in the clay-loamy soil in both phases, but greater fertility was exhibited in the second phase.

Human-Associated Lachnospiraceae Genetic Markers Improve Detection of Fecal Pollution Sources in Urban Waters

The human microbiome contains many organisms that could potentially be used as indicators of human fecal pollution. Here we report the development of two novel human-associated genetic marker assays that target organisms within the family Lachnospiraceae Next-generation sequencing of the V6 region of the 16S rRNA gene from sewage and animal stool samples identified 40 human-associated marker candidates with a robust signal in sewage and low or no occurrence in samples from nonhuman hosts. Two were chosen for quantitative PCR (qPCR) assay development using longer sequences (the V2 to V9 regions) generated from clone libraries. Validation of these assays with these markers, designated Lachno3 and Lachno12, was performed using fecal samples (n = 55) from cat, dog, pig, cow, deer, and gull sources, and the results were compared with those of established host-associated assays (the Lachno2 marker and two human Bacteroides markers, the HB and HF183/BacR287). Each of the established assays cross-reacted with samples from at least one other animal species, including animals common in urban areas. The Lachno3 and Lachno12 markers were primarily human associated; however, the Lachno12 marker demonstrated low levels of cross-reactivity with samples from select cows and nonspecific amplification with samples from pigs. This limitation may not be problematic when testing urban waters. These novel markers resolved ambiguous results from previous investigations of stormwater-impacted waters, demonstrating their utility. The complexity of the microbiome in humans and animals suggests that no single organism is strictly specific to humans, and the use of multiple complementary markers in combination will provide the highest resolution and specificity for assessing fecal pollution sources.IMPORTANCE Traditional fecal indicator bacteria do not distinguish animal from human fecal pollution, which is necessary to evaluate health risks and mitigate pollution sources. Assessing water in urban areas is challenging, since the water can be impacted by sewage, which has a high likelihood of carrying human pathogens, as well as pet and urban wildlife waste. We demonstrate that the Lachno3 and Lachno12 markers are human associated and highly specific for the detection of human fecal pollution from urban sources, offering reliable identification of fecal pollution sources in urban waters.

Shift in the microbial community composition of surface water and sediment along an urban river

Urban rivers represent a unique ecosystem in which pollution occurs regularly, leading to significantly altered of chemical and biological characteristics of the surface water and sediments. However, the impact of urbanization on the diversity and structure of the river microbial community has not been well documented. As a major tributary of the Yangtze River, the Jialing River flows through many cities. Here, a comprehensive analysis of the spatial microbial distribution in the surface water and sediments in the Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. The results revealed distinct differences in surface water bacterial composition along the river with a differential distribution of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Acidobacteria (P < 0.05). The bacterial diversity in sediments was significantly higher than their corresponding water samples. Additionally, archaeal communities showed obvious spatial variability in the surface water. The construction of the hydropower station resulted in increased Cyanobacteria abundance in the upstream (32.2%) compared to its downstream (10.3%). Several taxonomic groups of potential fecal indicator bacteria, like Flavobacteria and Bacteroidia, showed an increasing trend in the urban water. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and nitrogen metabolism in the urban water, indicating that urban discharges might act as the dominant selective force to alter the microbial communities. Redundancy analysis suggested that the microbial community structure was influenced by several environmental factors. TP (P < 0.01) and NO₃^- (P < 0.05), and metals (Zn, Fe) (P < 0.05) were the most significant drivers determining the microbial community composition in the urban river. These results highlight that river microbial communities exhibit spatial variation in urban areas due to the joint influence of chemical variables associated with sewage discharging and construction of hydropower stations.

Effect of Limit-Fed Diets With Different Forage to Concentrate Ratios on Fecal Bacterial and Archaeal Community Composition in Holstein Heifers

Limit-feeding of a high concentrate diet has been proposed as an effective method for improving feed efficiency and reducing total manure output of dairy heifers; meanwhile the effects of this method on hindgut microbiota are still unclear. This study investigated the effects of a wide range of dietary forage:concentrate ratios (F:C) on the fecal composition of bacteria and archaea in heifers using next-generation sequencing. Four diets with different F:C (80:20, 60:40, 40:60, and 20:80) were limit-fed to 24 Holstein heifers, and the fecal fermentation parameters and bacterial and archaeal communities were investigated. With increasing dietary concentrate levels, the fecal dry matter output, neutral detergent fiber (NDF) content, and proportion of acetate decreased linearly (P < 0.01), while the fecal starch content and proportions of propionate, butyrate, and total branched-chain volatile fatty acids (TBCVFAs) were increased (P ≤ 0.05). An increased concentrate level linearly increased (P = 0.02) the relative abundance of Proteobacteria, and linearly decreased (P = 0.02) the relative abundance of Bacteroidetes in feces. At the genus level, the relative abundance of unclassified Ruminococcaceae and Paludibacter which may have the potential to degrade forage decreased linearly (q ≤ 0.02) with increasing dietary concentrate levels, while the relative abundance of Roseburia and Succinivibrio which may be non-fibrous carbohydrate degrading bacteria increased linearly (q ≤ 0.05). Some core microbiota operational taxonomic units (OTUs) also showed significant association with fecal VFAs, NDF, and/or acid detergent fiber (ADF) content. Meanwhile, the relative abundance of most detected taxa in archaea were similar across different F:C, and only Methanosphaera showed a linear decrease (P = 0.01) in high concentrate diets. Our study provides a better understanding of fecal fermentation parameters and microbiota under a wide range of dietary F:C. These findings support the potential for microbial manipulation by diet, which could enhance feed digestibility and relieve environmental problems associated with heifer rearing.

Fecal microbiome of periparturient dairy cattle and associations with the onset of Salmonella shedding

Non-typhoidal Salmonella enterica is a zoonotic pathogen with critical importance in animal and public health. The persistence of Salmonella on farms affects animal productivity and health, and represents a risk for food safety. The intestinal microbiota plays a fundamental role in the colonization and invasion of this ubiquitous microorganism. To overcome the colonization resistance imparted by the gut microbiome, Salmonella uses invasion strategies and the host inflammatory response to survive, proliferate, and establish infections with diverse clinical manifestations. Cattle serve as reservoirs of Salmonella, and periparturient cows have high prevalence of Salmonella shedding; however, little is known about the association between the gut microbiome and the onset of Salmonella shedding during the periparturient period. Thus, the objective of this study was to assess the association between changes in bacterial communities and the onset of Salmonella shedding in cattle approaching parturition. In a prospective cohort study, fecal samples from 98 dairy cows originating from four different farms were collected at four time points relative to calving (-3 wks, -1 wk, +1 wk, +3 wks). All 392 samples were cultured for Salmonella. Sequencing of the V4 region of the 16S rRNA gene using the Illumina platform was completed to evaluate the fecal microbiome in a selected sample subset. Analyses of microbial composition, diversity, and structure were performed according to time points, farm, and Salmonella onset status. Individual cow fecal microbiomes, predominated by Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria phyla, significantly changed before and after parturition. Microbial communities from different farms were distinguishable based on multivariate analysis. Although there were significant differences in some bacterial taxa between Salmonella positive and negative samples, our results did not identify differences in the fecal microbial diversity or structure for cows with and without the onset of Salmonella shedding. These data suggest that determinants other than the significant changes in the fecal microbiome influence the periparturient onset of Salmonella shedding in dairy cattle.

Core gut microbiota in Jinhua pigs and its correlation with strain, farm and weaning age

Gut microbial diversity and the core microbiota of the Jinhua pig, which is a traditional, slow-growing Chinese breed with a high body-fat content, were examined from a total of 105 fecal samples collected from 6 groups of pigs at 3 weaning ages that originated from 2 strains and were raised on 3 different pig farms. The bacterial community was analyzed following high-throughput pyrosequencing of 16S rRNA genes, and the fecal concentrations of short-chain fatty acids (SCFAs) were measured by gas chromatograph. Our results showed that Firmicutes and Bacteroidetes were the dominant phyla, and Lactobacillus, Streptococcus, Clostridium, SMB53, and Bifidobacterium were the most abundant genera. Fifteen predominant genera present in every Jinhua pig sample constituted a phylogenetic core microbiota and included the probiotics Lactobacillus and Bifidobacterium, and the SCFA-producing bacteria Clostridium, Prevotella, Bacteroides, Coprococcus, Roseburia, Ruminococcus, Blautia, and Butyricicoccus. Comparisons of the microbiota compositions and SCFA concentrations across the 6 groups of pigs demonstrated that genetic background and weaning age affected the structure of the gut microbiota more significantly than the farm. The relative abundance of the core genera in the pigs, including Lactobacillus, Clostridium, Prevotella, Bacteroides, Roseburia, Ruminococcus, Blautia, and Butyricicoccus varied dramatically in pigs among the 2 origins and 3 weaning ages, while Oscillospira, Megasphaera, Parabacteroides, and Corynebacterium differed among pigs from different farms. Interestingly, there was a more significant influence of strain and weaning age than of rearing farm on the SCFA concentrations. Therefore, strain and weaning age appear to be the more important factors shaping the intestinal microbiome of pigs.

Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds

Microbial source tracking (MST) DNA-based assays have been used to successfully solve fecal pollution problems in many countries, particularly in developed nations. However, their application in developing countries has been limited but continues to increase. In this study, sixteen endpoint and quantitative PCR (qPCR) assays targeting universal and human-, swine-, and cattle-specific Bacteroidales gene markers were modified for endpoint PCR, evaluated for their performance with sewage and fecal samples from the Tha Chin watershed and subsequently validated with samples from the Chao Phraya watershed, Thailand. Sample sizes of 81 composite samples (from over 1620 individual samples) of farm animals of each type as well as 19 human sewage samples from the Tha Chin watershed were calculated using a stratified random sampling design to achieve a 90% confidence interval and an expected prevalence (i.e., desired assay's sensitivity) of 0.80. The best universal and human-, swine-, and cattle-specific fecal markers were BacUni EP, HF183/BFDrev EP, Pig-2-Bac EP, and Bac3 assays, respectively. The detection limits for these assays ranged from 30 to 3000 plasmid copies per PCR. The positive predictive values were high in universal and swine- and cattle-specific markers (85-100%), while the positive predictive value of the human-specific assay was 52.2%. The negative predictive values in all assays were relatively high (90.8-100%). A suite of PCR assays in Thailand was established for potential MST use in environmental waters, which supports the worldwide applicability of Bacteroidales gene markers. This study also emphasizes the importance of using a proper sample size in assessing the performance of MST markers in a new geographic region.

Invited review: Learning from the future-A vision for dairy farms and cows in 2067

The world's population will reach 10.4 billion in 2067, with 81% residing in Africa or Asia. Arable land available for food production will decrease to 0.15 ha per person. Temperature will increase in tropical and temperate zones, especially in the Northern Hemisphere, and this will push growing seasons and dairy farming away from arid areas and into more northern latitudes. Dairy consumption will increase because it provides essential nutrients more efficiently than many other agricultural systems. Dairy farming will become modernized in developing countries and milk production per cow will increase, doubling in countries with advanced dairying systems. Profitability of dairy farms will be the key to their sustainability. Genetic improvements will include emphasis on the coding genome and associated noncoding epigenome of cattle, and on microbiomes of dairy cattle and farmsteads. Farm sizes will increase and there will be greater lateral integration of housing and management of dairy cattle of different ages and production stages. Integrated sensors, robotics, and automation will replace much of the manual labor on farms. Managing the epigenome and microbiome will become part of routine herd management. Innovations in dairy facilities will improve the health of cows and permit expression of natural behaviors. Herds will be viewed as superorganisms, and studies of herds as observational units will lead to improvements in productivity, health, and well-being of dairy cattle, and improve the agroecology and sustainability of dairy farms. Dairy farmers in 2067 will meet the world's needs for essential nutrients by adopting technologies and practices that provide improved cow health and longevity, profitable dairy farms, and sustainable agriculture.

Differential Microbial Communities of Omnivorous and Herbivorous Cattle in Southern China

In Hong Kong, cattle were traditionally raised by farmers as draft animals to plough rice fields. Due to urbanization in the 20th century, they were gradually abandoned and became wild cattle straying in suburban Hong Kong. Recently, these cattle were observed to have become omnivorous by eating leftover barbeque food waste in country parks. Microbiome analysis was performed on fecal samples of the omnivorous cattle using deep sequencing and the resulting microbiome was compared with that of traditional herbivorous cattle in Southern China. A more diverse gut microbiome was observed in the omnivorous cattle, suggesting that microbiota diversity increases as diet variation increases. At the genus level, the relative abundance of Anaeroplasma, Anaerovorax, Bacillus, Coprobacillus and Solibacillus significantly increased and those of Anaerofustis, Butyricimonas, Campylobacter, Coprococcus, Dehalobacterium, Phascolarctobacterium, rc4.4, RFN20, Succinivibrio and Turicibacter significantly decreased in the omnivorous group. The increase in microbial community levels of Bacillus and Anaerovorax likely attributes to the inclusion of meat in the diet; while the decrease in relative abundance of Coprococcus, Butyricimonas, Succinivibrio, Campylobacter and Phascolarctobacterium may reflect the reduction in grass intake. Furthermore, an increased consumption of resistant starch likely resulted in the increase in abundance of Anaeroplasma. In conclusion, a significant change in the gut microbial community was observed in the omnivorous cattle, suggesting that diet may be one of the factors that may signal an adaptation response by the cattle to maintain feed efficiency as a consequence of the change in environment.

Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters

Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma. Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass.

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

BACKGROUND

Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known to which extent and how specifically soil and plant microbiomes can be manipulated through different cropping practices. Here, we investigated soil and wheat root microbial communities in a cropping system experiment consisting of conventional and organic managements, both with different tillage intensities.

RESULTS

While microbial richness was marginally affected, we found pronounced cropping effects on community composition, which were specific for the respective microbiomes. Soil bacterial communities were primarily structured by tillage, whereas soil fungal communities responded mainly to management type with additional effects by tillage. In roots, management type was also the driving factor for bacteria but not for fungi, which were generally determined by changes in tillage intensity. To quantify an "effect size" for microbiota manipulation, we found that about 10% of variation in microbial communities was explained by the tested cropping practices. Cropping sensitive microbes were taxonomically diverse, and they responded in guilds of taxa to the specific practices. These microbes also included frequent community members or members co-occurring with many other microbes in the community, suggesting that cropping practices may allow manipulation of influential community members.

CONCLUSIONS

Understanding the abundance patterns of cropping sensitive microbes presents the basis towards developing microbiota management strategies for smart farming. For future targeted microbiota management-e.g., to foster certain microbes with specific agricultural practices-a next step will be to identify the functional traits of the cropping sensitive microbes.

Toward Forensic Uses of Microbial Source Tracking

The science of microbial source tracking has allowed researchers and watershed managers to go beyond general indicators of fecal pollution in water such as coliforms and enterococci, and to move toward an understanding of specific contributors to water quality issues. The premise of microbial source tracking is that characteristics of microorganisms that are strongly associated with particular host species can be used to trace fecal pollution to particular animal species (including humans) or groups, e.g., ruminants or birds. Microbial source tracking methods are practiced largely in the realm of research, and none are approved for regulatory uses on a federal level. Their application in the conventional sense of forensics, i.e., to investigate a crime, has been limited, but as some of these methods become standardized and recognized in a regulatory context, they will doubtless play a larger role in applications such as total maximum daily load assessment, investigations of sewage spills, and contamination from agricultural practices.

Comparison of antimicrobial resistance genes in feedlots and urban wastewater

The use of antibiotics in livestock production in North America and possible association with elevated abundance of detectable antimicrobial resistance genes (ARG) is a growing concern. Real-time, quantitative PCR (RT-qPCR) was used to determine the relative abundance and diversity of ARG in fecal composite and catch basin samples from 4 beef feedlots in Alberta. Samples from a surrounding waterway and municipal wastewater treatment plants were also included to compare the ARG profile of urban environments and fresh water with that of feedlots. The relative abundance of 18 resistance genes across 5 antibiotic families including sulfonamides, tetracyclines, macrolides, fluoroquinolones, and β-lactams was examined. Sulfonamide, fluoroquinolone, and β-lactam resistance genes predominated in wastewater treatment samples, while tetracycline resistance genes predominated in cattle fecal composite samples. These results reflect the types of antibiotic that are used in cattle versus humans, but other factors such as co-selection of ARG and variation in the composition of bacterial communities associated with these samples may also play a role.

Interactions of the Hindgut Mucosa-Associated Microbiome with Its Host Regulate Shedding of Escherichia coli O157:H7 by Cattle

Cattle are the primary carrier of Escherichia coli O157:H7, a foodborne human pathogen, and those shedding >10⁴ CFU/gram of feces of E. coli O157:H7 are defined as supershedders (SS). This study investigated the rectoanal junction (RAJ) mucosa-associated microbiota and its relationship with host gene expression in SS and in cattle from which E. coli O157:H7 was not detected (nonshedders [NS]), aiming to elucidate the mechanisms involved in supershedding. In total, 14 phyla, 66 families, and 101 genera of RAJ mucosa-associated bacteria were identified and Firmicutes (61.5 ± 7.5%), Bacteroidetes (27.9 ± 6.4%), and Proteobacteria (5.5 ± 2.1%) were the predominant phyla. Differential abundance analysis of operational taxonomic units (OTUs) identified 2 OTUs unique to SS which were members of Bacteroides and Clostridium and 7 OTUs unique to NS which were members of Coprococcus, Prevotella, Clostridium, and Paludibacter Differential abundance analysis of predicted microbial functions (using PICRUSt [phylogenetic investigation of communities by reconstruction of unobserved states]) revealed that 3 pathways had higher abundance (log₂ fold change, 0.10 to 0.23) whereas 12 pathways had lower abundance (log₂ fold change, -0.36 to -0.20) in SS. In addition, we identified significant correlations between expression of 19 differentially expressed genes and the relative abundance of predicted microbial functions, including nucleic acid polymerization and carbohydrate and amino acid metabolism. Our findings suggest that differences in RAJ microbiota at both the compositional and functional levels may be associated with E. coli O157:H7 supershedding and that certain microbial groups and microbial functions may influence RAJ physiology of SS by affecting host gene expression.IMPORTANCE Cattle with fecal E. coli O157:H7 at >10⁴ CFU per gram of feces have been defined as the supershedders, and they are responsible for the most of the E. coli O157:H7 spread into farm environment. Currently, no method is available for beef producers to eliminate shedding of E. coli O157:H7 in cattle, and the lack of information about the mechanisms of supershedding greatly impedes the development of effective methods. This study investigated the role of the rectoanal junction (RAJ) mucosa-associated microbiome in E. coli O157:H7 shedding, and our results indicated that the compositions and functions of RAJ microbiota differed between supershedders and nonshedders. The identified relationship between the differentially abundant microbes and 19 previously identified differentially expressed genes suggests the role of host-microbial interactions involved in E. coli O157:H7 supershedding. Our findings provide a fundamental understanding of the supershedding phenomenon which is essential for the development of strategies, such as the use of directly fed microbials, to reduce E. coli O157:H7 shedding in cattle.

Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals

In this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.

Mass mortality events and the role of necrophagous invertebrates

Scale is important in understanding and applying concepts in ecology. Historically, the mechanisms regulating necrophagous arthropod community structure have been well explored on a single vertebrate carcass. However, practically nothing is known of whether such findings can be extrapolated to cases where large numbers of carcasses have been introduced into an ecosystem at a single time point. With the increasing incidences of mass mortality events (MMEs), understanding how scale effects community assembly of necrophagous insects and the resulting bottom-up or top-down effects on the impacted ecosystem are of utmost importance. Unfortunately, MMEs are unpredictable, making their study nearly impossible within a robust experimental framework. The objectives of this paper are to provide a brief overview of what is known with regards to ecological responses to carrion, opine on the ramifications of MMEs on local communities, and provide a brief overview of knowledge gaps, avenues for future research, and a potential study systems for rigorous MME experiments.

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle

In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and control animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level. However, treated cattle had reduced abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachnospiraceae in the gut of treated steers was reduced. Functional analysis of the data indicates that there was only minimal impact due to the treatment in the rumen. Genes involved in detoxification were significantly increased in the rumen of AB steers. But the relative abundance of these genes was < 0.3%. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.

Microbiome-Metabolome Responses to a High-Grain Diet Associated with the Hind-Gut Health of Goats

Studies on the effect of a high-concentrate (HC) diet on the hindgut microbiota and metabolome of ruminants are rarely reported. We used 454 pyrosequencing of 16S rDNA genes and gas chromatography-mass spectrometry to evaluate the effects of long-term feeding (HL) or short-term (HS) feeding of an HC diet on changes in bacterial microbiota and their metabolites in the hindgut, with Guanzhong goat as a ruminant model. Results indicated that an HC diet decreased bacterial diversity and induced metabolic disorder in the hindgut. The levels of lactate, endotoxin (lipopolysaccharide, LPS), and volatile fatty acid concentrations were higher in the intestinal digesta of the HC goats than in those of the LC goats (P < 0.05). The level of beta-alanine decreased, whereas the levels of stigmasterol and quinic acid decreased in the cecal and colonic digesta of the HC goats. At the genus level, the abundance of Clostridium and Turicibacter was significantly increased in both the colonic and cecal digesta of the HC goats. Several potential relationships between metabolites and several microbial species were revealed in this study. The mRNA expression of the genes functionally associated with nutrients transport, including NHE2, NHE3, MCT1, and MCT4 were significantly downregulated in the colonic mucosa by the HC diet (P < 0.05). The expression levels of the genes related to the inflammatory response, including TLR4, MYD88, TNF-α, and IL-1β were markedly upregulated in the cecal mucosa by the HC diet (P < 0.05). Our results indicate that an HC diet induces microbiota dysbiosis, metabolic disorders, and mucosal damage in the hindgut of goats.

The impact of the bovine faecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle

AIMS

The objective of this study was to determine if the faecal microbiome has an association with Escherichia coli O157:H7 prevalence and enumeration.

METHODS AND RESULTS

Pyrosequencing analysis of faecal microbiome was performed from feedlot cattle fed one of three diets: (i) 94 heifers fed low concentrate (LC) diet, (ii) 142 steers fed moderate concentrate (MC) diet, and (iii) 132 steers fed high concentrate (HC) diet. A total of 322 585 OTUs were calculated from 2,411,122 high-quality sequences obtained from 368 faecal samples. In the LC diet group, OTUs assigned to the orders Clostridiales and RF39 (placed within the class Mollicutes) were positively correlated with both E. coli O157:H7 prevalence and enumeration. In the MC diet group, OTUs assigned to Prevotella copri were positively correlated with both E. coli O157:H7 prevalence and enumeration, whereas OTUs assigned to Prevotella stercorea were negatively correlated with both E. coli O157:H7 prevalence and enumeration. In both the MC diet group and the HC diet group, OTUs assigned to taxa placed within Clostridiales were both positively and negatively correlated with both E. coli O157:H7 prevalence and enumeration. However, all correlations were weak. In both the MC diet group and the HC diet group, stepwise linear regression through backward elimination analyses indicated that these OTUs were significantly correlated (P < 0·001) with prevalence or enumeration, explaining as much as 50% of variability in E. coli O157:H7 prevalence or enumeration.

CONCLUSIONS

Individual colonic bacterial species have little impact on E. coli O157:H7 shedding but collectively groups of bacteria were strongly associated with pathogen shedding.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacterial groups in the bovine colon may impact faecal shedding of the zoonotic pathogen E. coli O157:H7, and manipulation of the intestinal microbiota to alter these bacteria may reduce shedding of this pathogen and foodborne illnesses.

Fecal microbiota of lambs fed purple prairie clover (Dalea purpurea Vent.) and alfalfa (Medicago sativa)

The present study assessed the effect of purple prairie clover (PPC) and PPC condensed tannins (CT) on the fecal microbiota of lambs using high-throughput 16S rRNA gene pyrosequencing. A total of 18 individual lambs were randomly divided into three groups and fed either green chop alfalfa (Alf), a 40:60 (DM basis; Mix) mixture of Alf and PPC, or Mix supplemented with polyethylene glycol (Mix-P) for 18 days. Fecal samples were collected on days 13 through 18 using digital rectal retrieval. The DNA of fecal samples was extracted and the microbial 16S rRNA gene amplicons were sequenced using 454 pyrosequencing. Regardless of diet, the bacterial community was dominated by Firmicutes and Bacteroidetes with many sequences unclassified at the genus level. Forage type and CT had no effect on the fecal microbial composition at the phylum level or on α-diversity. Compared to the Alf diet, the Mix diet reduced the relative abundance of Akkermansia (P = 0.03) and Asteroleplasma (P = 0.05). Fecal microbial populations in Alf and Mix-P clustered separately from each other when assessed using unweighted UniFrac (P < 0.05). These results indicate that PPC CT up to 36 g/kg DM in the diet had no major effect on fecal microbial flora at the phyla level and exerted only minor effects on the genera composition of fecal microbiota in lambs.

Microbial community composition along the digestive tract in forage- and grain-fed bison

BACKGROUND

Diversity and composition of microbial communities was compared across the 13 major sections of the digestive tract (esophagus, reticulum, rumen, omasum, abomasum, duodenum, jejunum, ileum, cecum, ascending colon, transverse colon, descending colon, and rectum) in two captive populations of American bison (Bison bison), one of which was finished on forage, the other on grain.

RESULTS

Microbial diversity fell to its lowest levels in the small intestine, with Bacteroidetes reaching their lowest relative abundance in that region, while Firmicutes and Euryarchaeota attained their highest relative abundances there. Gammaproteobacteria were most abundant in the esophagus, small intestine, and colon. The forage-finished bison population exhibited higher overall levels of diversity, as well as a higher relative abundance of Bacteroidetes in most gut sections. The grain-finished bison population exhibited elevated levels of Firmicutes and Gammaproteobacteria. Within each population, different sections of the digestive tract exhibited divergent microbial community composition, although it was essentially the same among sections within a given region of the digestive tract. Shannon diversity was lowest in the midgut. For each section of the digestive tract, the two bison populations differed significantly in microbial community composition.

CONCLUSIONS

Similarities among sections indicate that the esophagus, reticulum, rumen, omasum, and abomasum may all be considered to house the foregut microbiota; the duodenum, jejunum, and ileum may all be considered to house the small intestine or midgut microbiota; and the cecum, ascending colon, transverse colon, descending colon, and rectum may all be considered to house the hindgut microbiota. Acid from the stomach, bile from the gall bladder, digestive enzymes from the pancreas, and the relatively low retention time of the small intestine may have caused the midgut's low microbial diversity. Differences in microbial community composition between populations may have been most strongly influenced by differences in diet (forage or grain). The clinical condition of the animals used in the present study was not evaluated, so further research is needed to establish whether the microbial profiles of some bison in this study are indeed indicative of dysbiosis, a predisposing factor to ruminal acidosis and its sequelae.

Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine keratoconjunctivitis

Infectious bovine keratoconjunctivitis (IBK) is an important production limiting disease in cattle. Moraxella bovis has historically been considered the primary causal agent; however, vaccines have not been consistently shown as effective in controlling disease incidence. The purpose of this study was to examine the bacterial community of calf eyes prior to disease onset using high-throughput sequencing of 16S ribosomal RNA and determine if it was associated with IBK occurrence. The study was designed as a case-control nested within a randomized controlled trial (RCT). Eye swabs were collected from all spring-born calves without clinical signs of IBK (t₀ swabs) on a research farm with a previous history of IBK disease outbreaks. At follow-up or weaning, calves were diagnosed as IBK positive or negative. The lag time between enrollment swabs (t₀) and IBK diagnosis ranged from approximately one to three months. Cases were randomly selected from IBK positive calves and controls were selected from IBK negative calves (i.e. calves that did not exhibit clinical signs of IBK throughout the course of the RCT). Analysis of the fold-change differences between cases and controls did not reveal large-scale distinctions in bacterial composition. However, principal component analysis suggested bacterial composition differences between calf management groups, which were based on dam parity. Moraxella was found to be among the top ten most abundant genera in our population; however, the difference in abundance was not significant between the cases and controls. No large-scale differences in the bacterial communities of calves that did or did not develop IBK were observed in our population. Nevertheless, it remains unclear whether the "natural" bacterial population of the calf might ultimately impact disease status. Further study is warranted to examine bacterial taxa that were observed to be significantly more abundant in the cases or controls as potential vaccines/therapeutic targets.

Comparison of the Performance of Different Microbial Source Tracking Markers among European and North African Regions

Microbial source tracking (MST) has been extensively used to detect the sources of fecal pollution in water. The inclusion of MST in water management strategies improves the ecological status of the ecosystem and human and animal health under interdisciplinary analysis in all aspects of health care for humans, animals, and the environment (One Health approach). In this study, the performance of MST markers targeting host-specific Bacteroidales (HF183 and Rum-2-Bac) and species (HMBif and CWBif) were evaluated in raw sewage collected from human, ruminant, swine, and poultry sources in Tunisia, Cyprus, Ireland, and Spain. In addition, the ratio between somatic coliphages and bacteriophages infecting GA17 (SOMCPH/GA17PH) was measured in Tunisia and Spain. The obtained results showed variability of the bacterial markers between the four countries, suggesting that their usefulness could be affected by several conditions (dietary habits, agricultural practices, and climatic conditions) that differ between countries. The Rum-2-Bac marker stood out as a valid MST tool, particularly in Ireland, whereas CWBif was the best option in Tunisia, Spain, and Cyprus. The human-specific HMBif marker showed good sensitivity and specificity in Tunisia, Spain, and Ireland, whereas HF183 showed a low specificity. However, HF183 was suggested as a good human marker in Ireland and Cyprus because of its higher concentration than HMBif. Regarding viral markers, the ratio of SOMCPH/GA17PH showed a clear discrimination between human and nonhuman samples. The combined use of molecular bacterial markers and the ratio of SOMCPH/GA17PH may improve the success of MST.

Changes in the fecal microbiota of beef cattle caused by change in management and the use of virginiamycin as a growth promoter

Several factors are known to affect the intestinal microbiota of cattle. However, how these changes occur over time is poorly understood. This study aimed to investigate the consequences of entrance into a feedlot and the effects of virginiamycin used as a growth promoter on the bovine fecal microbiota. Two batches of beef cattle (B1, n=50 and B2, n=36) entering a feedlot operation were randomly divided into two pens: one receiving virginiamycin and one group not receiving antibiotic (control group). Fecal samples were collected at arrival, mid feedlot and at exit to slaughter. The V4 region of 16S rRNA gene was amplified and sequenced. Escherichia coli strains isolated in samples from arrival and exit of B2 were also isolated and used as indicators of antimicrobial susceptibility. Marked changes in membership and structure of fecal microbiota occurred following entrance into the feedlot. At mid feedlot, virginiamycin affected bacterial community membership, but not structure, suggesting that the antibiotic had a stronger effect on the rare, but not on the most abundant species. The use of virginiamycin had no demonstrable effect on antibiotic resistance in E. coli. The differences found between batches are suggestive that variations in study conditions are important and can strongly affect the intestinal microbiota.