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

Dietary type (carnivore, herbivore and omnivore) and animal species modulate the nutritional metabolome of terrestrial species

Ecometabolomics could be implemented as a powerful tool in molecular ecology studies, but it is necessary to know the baseline of certain metabolites and understand how different traits could affect the metabolome of the animals. Therefore, the main objective of this study was to provide values for the nutritional metabolome profile of different diet groups and animal species, as well as to study the differences in the metabolomic profile due to the effect of diet type and species. To achieve this goal, blood samples were taken from healthy animals (n = 43) of different species: lion (Panthera leo), jaguar (Panthera onca), chimpanzee (Pan troglodytes), bison (Bison bison), gazelle (Gazella cuvieri) and fallow deer (Dama dama), and with different types of diet (carnivore, herbivore and omnivore). Each blood sample was analysed to determine nutritional metabolites. The main results this study provides are the nutritional metabolic profile of these animals based on the type of diet and the animal species. A significant effect of the dietary type was found on nutritional metabolite levels, with those metabolites related to protein metabolism (total protein and creatine) being higher in carnivores. There is also an effect of the species on nutritional metabolites, observing a metabolome differentiation between lion and jaguar. In the case of herbivores, bison showed higher levels of uric acid and cholesterol, and lower urea levels than gazelle and fallow deer. More molecular ecology studies are needed to further the knowledge of the metabolism of these animals.

Effects of grain-based diets on the rumen and fecal bacterial communities of the North American bison (Bison bison)

To overcome the challenges of pasture-finishing of bison, producers commonly feed them with higher energy, grain-based diets to reach the desired market weight. However, decades of research on domesticated ruminants have shown that such diets can have profound effects on the composition of gut microbial communities. To gain further insight, the 16S rRNA gene-based study described in this report aimed to compare the composition of ruminal and fecal bacterial communities from two herds of bison heifers (n = 20/herd) raised on different ranches that were both transitioned from native pasture to a grain-based, free-choice diet for ~100 days prior to slaughter. Comparative analyses of operational taxonomic unit (OTU) composition, either by alpha diversity indices, principal coordinate analysis (PCoA), or on the most abundant individual OTUs, showed the dramatic effect of a diet on the composition of both rumen and fecal bacterial communities in bison. Indeed, feeding a grain-based diet resulted in a lower number of rumen and fecal bacterial OTUs, respectively, compared to grazing on pasture (p < 0.05). PCoA revealed that the composition of the rumen and fecal bacterial communities from the two herds was more similar when they were grazing on native pastures compared to when they were fed a grain-based, free-choice diet. Finally, a comparative analysis of the 20 most abundant OTUs from the rumen and fecal communities further showed that the representation of all these species-level bacterial groups differed (p < 0.05) between the two dietary treatments. Together, these results provide further insights into the rumen and fecal microbiomes of grazing bison and their response to grain-based diet regimens commonly used in intensive ruminant production systems.

Effects of sources and levels of dietary supplementary manganese on growing yak's in vitro rumen fermentation

Introduction

Manganese (Mn) is an essential trace element for livestock, but little is known about the optimal Mn source and level for yak.

Methods

To improve yak's feeding standards, a 48-h in vitro study was designed to examine the effect of supplementary Mn sources including Mn sulfate (MnSO₄), Mn chloride (MnCl₂), and Mn methionine (Met-Mn) at five Mn levels, namely 35 mg/kg, 40 mg/kg, 50 mg/kg, 60 mg/kg, and 70 mg/kg dry matter (includes Mn in substrates), on yak's rumen fermentation.

Results

Results showed that Met-Mn groups showed higher acetate (p < 0.05), propionate, total volatile fatty acids (p < 0.05) levels, ammonia nitrogen concentration (p < 0.05), dry matter digestibility (DMD), and amylase activities (p < 0.05) compared to MnSO4 and MnCl2 groups. DMD (p < 0.05), amylase activities, and trypsin activities (p < 0.05) all increased firstly and then decreased with the increase of Mn level and reached high values at 40-50 mg/kg Mn levels. Cellulase activities showed high values (p < 0.05) at 50-70 mg/kg Mn levels. Microbial protein contents (p < 0.05) and lipase activities of Mn-Met groups were higher than those of MnSO4 and MnCl2 groups at 40-50 mg/kg Mn levels.

Discussion

Therefore, Mn-met was the best Mn source, and 40 to 50 mg/kg was the best Mn level for rumen fermentation of yaks.

Effects of Two Different Straw Pellets on Yak Growth Performance and Ruminal Microbiota during Cold Season

The Tianzhu white yaks (Bos grunniens) live on the Qinghai-Tibet Plateau. During winter, a lack of resources and low nutritional levels seriously affect their growth performance. In this study, we aimed to explore the effect of supplementation straw pellets on the growth performance and ruminal microbiota of yaks. Overall, at 6 (6M, n = 24), 18 (18M, n = 26), 30 (30M, n = 20), 42 (42M, n = 24), and 54 (54M, n = 22) month old Tianzhu white yaks were selected (total n = 116) and divided into the mixed straw + grazing (MSG), corn straw + grazing (CSG), and the grazing control (G) groups according to age and gender. Their growth performance was measured as per different dietary treatments. The rumen microbial community structure and levels of VFAs were analyzed from the 6M, 30M, and 54M male yaks from each group. The supplementary diets led to an increase in the ADG, which was the highest in the MSG group. The MSG group exhibited the highest level of acetate and total VFAs (TVFAs) among the three groups (p < 0.05). In addition, the 16S rRNA sequencing results proved that the microbial composition was dominated by the members of Firmicutes and Bacteroidetes. Christensenellaceae R-7 group was significantly abundant in the CSG and MSG groups compared to the G group (p < 0.05). Principal coordinate analysis (PCoA) revealed that the bacterial community structure of rumen in the MSG and CSG groups was considerably different from that in the G group; 6M samples exhibited different rumen microbial diversity compared with the other samples. Correlation analysis revealed that Christensenellaceae_R-7_group was positively correlated with the levels of acetate, TVFAs, and ADG. These results demonstrated that mixed straw pellets improved the growth performance of yaks, increased the abundance of Christensenellaceae R-7_group involved in cellulose degradation in the rumen, and produced large amounts of VFAs, which were absorbed by yaks, thus increasing their ADG. This study provides new insights into the effects of straw pellet supplementation on the changes in the rumen microbiota and growth performance of yaks.

Molecular detection of feline hemoplasmas and retroviruses in free-roaming and shelter cats within a university campus

Objectives

The aim of the present study was to assess the frequency of hemoplasma, feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) infections in cats living in an on-campus shelter and free-roaming cats within a university campus in Brazil.

Methods

Blood samples were tested using quantitative PCR for hemoplasma, FIV and FeLV. Positive hemoplasma samples were sequenced. Associations between hemoplasma detection and living situation, sex, flea and/or tick parasitism, and coinfection with FIV and FeLV, were assessed using Fisher's exact test and the respective odds ratios were calculated.

Results

Overall, 6/45 (13.3%) cats tested positive: four (8.9%) were infected with 'Candidatus Mycoplasma haemominutum' and two (4.4%) with Mycoplasma haemofelis. All positive samples were from free-roaming cats (6/15; 40.0%) and had statistically significantly lower packed cell volumes (P = 0.037). Although 5/23 (21.7%) males and 1/22 (4.6%) females were positive, no statistically significant association between sex and hemoplasma infection was found (P = 0.19). Viral quantitative PCR (qPCR) was performed on 43/45 samples, among which 2/43 (4.7%) were positive for FIV and none for FeLV. Only one cat (2.3%) was coinfected with hemoplasma and FIV (P = 0.26). In addition, 4/6 (66.7%) cats that tested positive for hemoplasmas were infested by fleas (P = 0.0014) and/or ticks (P = 0.25).

Conclusions and relevance

These results show that even if the free-roaming cat population is clinically healthy and has adequate access to food, it may present flea infestation and hemoplasma infection with lower packed cell volume values.

Microbial colonization dynamics of the postnatal digestive tract of Bos indicus calves

The rumen and the jejunum of calves have distinct functional roles; the former is in the storage and fermentation of feed, and the latter is in transporting digesta to the ileum. It is unknown how nutrition changes the evolution of the microbiome of these organs after birth. We sequenced and characterized the entire microbiome of the rumen and the jejunum from Bos indicus calves of the Mexican Tropics to study their dynamics at Days 0, 7, 28, and 42 after birth. Operational taxonomic units (OTUs) belonging to 185 and 222 genera from 15 phylum were observed in the organs, respectively. The most abundant OTUs were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. We observed that proteobacterial species were outcompeted after the first week of life by Bacteroidetes and Firmicutes in the rumen and the jejunum, respectively. Moreover, Prevotella species were found to predominate in the rumen (36% of total OTUs), while the jejunum microbiome is composed of small proportions of several genera. Presumably, their high relative abundance assists in specialized functions and is more likely in fermentation since they are anaerobes. In summary, the rumen and the jejunum microbiomes were outcompeted by new microbiomes in a dynamic process that begins at birth.

Cecal microbiota of feedlot cattle fed a four-species Bacillus supplement

As commercial fed cattle consume large amounts of concentrate feedstuffs, hindgut health can be challenged. The objective of this study was to evaluate the effects of a commercially available Bacillus feed additive on cattle health outcomes and cecal microbiota of fed cattle at the time of harvest. Commercial cattle from a single feedlot were identified for characterization of cecal microbial communities using 16S ribosomal ribonucleic acid gene sequencing. All cattle were fed a common corn-based finishing diet. Control cattle (CON) were administered no treatment while treated cattle (TRT) were supplemented daily with 0.050 g of MicroSaf 4C 40 (2 billion colony forming units of Bacillus spp.; Phileo by Lesaffre, Milwaukee, WI). Immediately after harvest and evisceration, the cecal contents of cattle were sampled. After DNA extraction, amplification, and sequencing, reads from CON samples (N = 12) and TRT samples (N = 12) were assigned taxonomy using the SILVA 138 database. Total morbidity, first treatment of atypical interstitial pneumonia, and early shipments for harvest were decreased among TRT cattle compared to CON cattle (P ≤ 0.021). On average, cecal microbiota from TRT cattle had greater alpha diversity than microbiota from CON cattle as measured by Shannon diversity, Pielou's evenness, and feature richness (P < 0.010). Additionally, TRT microbial communities were different (P = 0.001) and less variable (P < 0.001) than CON microbial communities when evaluated by unweighted UniFrac distances. By relative abundance across all samples, the most prevalent phyla were Firmicutes (55.40%, SD = 15.97) and Bacteroidetes (28.17%, SD = 17.74) followed by Proteobacteria (6.75%, SD = 10.98), Spirochaetes (4.54%, SD = 4.85), and Euryarchaeota (1.77%, SD = 3.00). Spirochaetes relative abundance in TRT communities was greater than that in CON communities and was differentially abundant between treatments by ANCOM testing (W = 11); Monoglobaceae was the only family-level taxon identified as differentially abundant (W = 59; greater mean relative abundance in TRT group by 2.12 percentage points). Half (N = 6) of the CON samples clustered away from all other samples based on principal coordinates and represented cecal dysbiosis among CON cattle. The results of this study indicated that administering a four-species blend of Bacillus positively supported the cecal microbial communities of finishing cattle. Further research is needed to explore potential mechanisms of action of Bacillus DFM products in feedlot cattle.

A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

BACKGROUND

The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries.

RESULTS

Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes.

CONCLUSIONS

Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task. Video Abstract.

Effects of Concentrate Supplementation on Growth Performance, Rumen Fermentation, and Bacterial Community Composition in Grazing Yaks during the Warm Season

This study aimed to evaluate the effects of concentrate supplementation on the growth performance, serum biochemical parameters, rumen fermentation, and bacterial community composition of grazing yaks during the warm season. Eight male yaks (body weight, 123.96 ± 7.43 kg; 3-years) were randomly allocated to two treatments groups: grazing (n = 4, GY) and concentrate supplement group (n = 4, GYS). Concentrate supplementation increased the average daily gain (ADG) (p < 0.05). Glucose (GLU), total protein (TP), and aspartate aminotransferase (AST) serum concentrations were significantly higher in the GYS group than in the GY group (p < 0.05). Ammonia-N, MCP: microbial protein, and total volatile fatty acid concentrations were significantly higher in the GYS group than in the GY group (p < 0.01), whereas the pH and acetate: propionate values were significantly decreased (p < 0.01). The relative abundance of Firmicutes in the rumen fluid was significantly higher in the GYS group than in the GY group (p < 0.01). At the genus level, the relative abundances of Succiniclasticum, Prevotellaceae_UCG_003, Prevotellaceae_UCG_005, and Ruminococcus_1 were significantly greater in the GY group than in the GYS group (p < 0.01). In conclusion, concentrate supplementation improved yaks’ growth potential during the warm season, improved ruminal fermentation, and altered core bacteria abundance.

Variation in diet composition and its relation to gut microbiota in a passerine bird

Quality and quantity of food items consumed has a crucial effect on phenotypes. In addition to direct effects mediated by nutrient resources, an individual’s diet can also affect the phenotype indirectly by altering its gut microbiota, a potent modulator of physiological, immunity and cognitive functions. However, most of our knowledge of diet-microbiota interactions is based on mammalian species, whereas little is still known about these effects in other vertebrates. We developed a metabarcoding procedure based on cytochrome c oxidase I high-throughput amplicon sequencing and applied it to describe diet composition in breeding colonies of an insectivorous bird, the barn swallow (Hirundo rustica). To identify putative diet-microbiota associations, we integrated the resulting diet profiles with an existing dataset for faecal microbiota in the same individual. Consistent with previous studies based on macroscopic analysis of diet composition, we found that Diptera, Hemiptera, Coleoptera and Hymenoptera were the dominant dietary components in our population. We revealed pronounced variation in diet consumed during the breeding season, along with significant differences between nearby breeding colonies. In addition, we found no difference in diet composition between adults and juveniles. Finally, our data revealed a correlation between diet and faecal microbiota composition, even after statistical control for environmental factors affecting both diet and microbiota variation. Our study suggests that variation in diet induce slight but significant microbiota changes in a non-mammalian host relying on a narrow spectrum of items consumed.

Dominant remodelling of cattle rumen microbiome by Schedonorus arundinaceus (tall fescue) KY-31 carrying a fungal endophyte

Tall fescue KY-31 is an important primary forage for beef cattle. It carries a fungal endophyte that produces ergovaline, the main cause of tall fescue toxicosis that leads to major revenue loss for livestock producers. The MaxQ, an engineered cultivar, hosts an ergovaline nonproducing strain of the fungus and consequently is nontoxic. However, it is less attractive economically. It is not known how rumen microbiome processes these two forages towards nutrient generation and ergovaline transformation. We have analysed the rumen microbiome compositions of cattle that grazed MaxQ with an intervening KY-31 grazing period using the 16S rRNA-V4 element as an identifier and found that KY-31 remodelled the microbiome substantially, encompassing both cellulolytic and saccharolytic functions. The effect was not evident at the whole microbiome levels but was identified by analysing the sessile and planktonic fractions separately. A move from MaxQ to KY-31 lowered the Firmicutes abundance in the sessile fraction and increased it in planktonic part and caused an opposite effect for Bacteroidetes, although the total abundances of these dominant rumen organisms remained unchanged. The abundances of Fibrobacter, which degrades less degradable fibres, and certain cellulolytic Firmicutes such as Pseudobutyrivibrio and Butyrivibrio 2, dropped in the sessile fraction, and these losses were apparently compensated by increased occurrences of Eubacterium and specific Ruminococcaceae and Lachnospiraceae. A return to MaxQ restored the original Firmicutes and Bacteroidetes distributions. However, several KY-31 induced changes, such as the low abundance of Fibrobacter and Butyrivibrio two remained in place, and their substitutes maintained significant presence. The rumen microbiome was distinct from previously reported faecal microbiomes. In summary, KY-31 and MaxQ were digested in the cattle rumen with distinct consortia and the KY-31-specific features were dominant. The study also identified candidate ergovaline transforming bacteria. It highlighted the importance of analysing sessile and planktonic fractions separately.

FI: The Fecobiome Initiative

Animal husbandry has been key to the sustainability of human societies for millennia. Livestock animals, such as cattle, convert plants to protein biomass due to a compartmentalized gastrointestinal tract (GIT) and the complementary contributions of a diverse GIT microbiota, thereby providing humans with meat and dairy products. Research on cattle gut microbial symbionts has mainly focused on the rumen (which is the primary fermentation compartment) and there is a paucity of functional insight on the intestinal (distal end) microbiota, where most foodborne zoonotic bacteria reside. Here, we present the Fecobiome Initiative (or FI), an international effort that aims at facilitating collaboration on research projects related to the intestinal microbiota, disseminating research results, and increasing public availability of resources. By doing so, the FI can help mitigate foodborne and animal pathogens that threaten livestock and human health, reduce the emergence and spread of antimicrobial resistance in cattle and their proximate environment, and potentially improve the welfare and nutrition of animals. We invite all researchers interested in this type of research to join the FI through our website: www.fecobiome.com

Bacterial Community Characteristics in the Gastrointestinal Tract of Yak (Bos grunniens) Fully Grazed on Pasture of the Qinghai-Tibetan Plateau of China

Simple Summary

The Qinghai–Tibetan plateau is considered as the third Pole of the world and is characterized by low oxygen, high altitude, extreme cold weather and strong ultraviolet radiation. Yak, as the main domestic animals raised on the plateau, play various roles in local herdsmen’s lives by supplying necessities such as meat, milk and fuel. Yak are adapted to the harsh environment on the plateau; microbiota in gut equip the hosts with special abilities including adaptability, as illustrated by numerous research projects. Accordingly, the microbes in the gastrointestinal tract of yak must be characteristically profiled as a strategy to adapt to the environment. However, little is known about the microbial community in whole tract of yak; almost all of reported researches focused on rumen. Therefore, in the current study the bacterial community in the gastrointestinal tract of yak was explored using 16S rDNA amplicon sequencing technology, and the community profiling characteristic in each section was clearly elucidated.

Abstract

In the current research, samples of yak gastrointestinal tracts (GITs) were used to profile the bacterial compositional characteristics using high through-put sequencing technology of 16S RNA amplicon. A total of 6959 OTUs was obtained from 20,799,614 effective tags, among which 751 OTUs were shared by ten sections. A total of 16 known phyla were obtained in all samples—the most abundant phyla were Firmicutes (34.58%), Bacteroidetes (33.96%) and Verrucomicrobia (11.70%). At the genus level, a total of 66 genera were obtained—Rikenellaceae_RC9_gut_group (7.24%), Akkermansia (6.32%) and Ruminococcaceae_UCG-005 (6.14%) were the most abundant. Species of Observed (Sob), Shannon and Chao values of the Stomach were the greatest, followed by the large intestine, while small intestine had the lowest diversity (p < 0.05). Bacteroidete were more abundant in sections from rumen to duodenum; while Firmicutes were the most abundant in sections from jejunum. ABC transporters (7.82%), Aminoacyl-tRNA biosynthesis (4.85%) and Purine metabolism (3.77%) were the most abundant level-3 pathways in all samples. The results of associated correlation analysis indicated that rectum samples might be used as an estimator of rumen bacterial communities and fermentation. The results of this research enrich the current knowledge about the unique animals of the QTP and extend our insight into GITs microecology of various animals.

Accessing Dietary Effects on the Rumen Microbiome: Different Sequencing Methods Tell Different Stories

The current study employed both amplicon and shotgun sequencing to examine and compare the rumen microbiome in Angus bulls fed with either a backgrounding diet (BCK) or finishing diet (HG), to assess if both methods produce comparable results. Rumen digesta samples from 16 bulls were subjected for microbial profiling. Distinctive microbial profiles were revealed by the two methods, indicating that choice of sequencing approach may be a critical facet in studies of the rumen microbiome. Shotgun-sequencing identified the presence of 303 bacterial genera and 171 archaeal species, several of which exhibited differential abundance. Amplicon-sequencing identified 48 bacterial genera, 4 archaeal species, and 9 protozoal species. Among them, 20 bacterial genera and 5 protozoal species were differentially abundant between the two diets. Overall, amplicon-sequencing showed a more drastic diet-derived effect on the ruminal microbial profile compared to shotgun-sequencing. While both methods detected dietary differences at various taxonomic levels, few consistent patterns were evident. Opposite results were seen for the phyla Firmicutes and Bacteroidetes, and the genus Selenomonas. This study showcases the importance of sequencing platform choice and suggests a need for integrative methods that allow robust comparisons of microbial data drawn from various omic approaches, allowing for comprehensive comparisons across studies.

Analysis of Host Jejunum Transcriptome and Associated Microbial Community Structure Variation in Young Calves with Feed-Induced Acidosis

Diet-induced acidosis imposes a health risk to young calves. In this study, we aimed to investigate the host jejunum transcriptome changes, along with its microbial community variations, using our established model of feed-induced ruminal acidosis in young calves. Eight bull calves were randomly assigned to two diet treatments beginning at birth (a starch-rich diet, Aci; a control diet, Con). Whole-transcriptome RNA sequencing was performed on the jejunum tissues collected at 17 weeks of age. Ribosomal RNA reads were used for studying microbial community structure variations in the jejunum. A total of 853 differentially expressed genes were identified (402 upregulated and 451 downregulated) between the two groups. The cell cycle and the digestion and absorption of protein in jejunal tissue were affected by acidosis. Compared to the control, genera of Campylobacter, Burkholderia, Acidaminococcus, Corynebacterium, and Olsenella significantly increased in abundance in the Aci group, while Lachnoclostridium and Ruminococcus were significantly lower in the Aci group. Expression changes in the AXL gene were associated with the abundance variations of a high number of genera in jejunum. Our study provided a snapshot of the transcriptome changes in the jejunum and its associated meta-transcriptome changes in microbial communities in young calves with feed-induced acidosis.

Characterization of the bacterial microbiota across the different intestinal segments of the Qinghai semi-fine wool sheep on the Qinghai-Tibetan Plateau

Objective

The intestinal microbiota enhances nutrient absorption in the host and thus promotes heath. Qinghai semi-fine wool sheep is an important livestock raised in the Qinghai-Tibetan Plateau; however, little is known about the bacterial microbiota of its intestinal tract. The aim of this study was to detect the microbial characterization in the intestinal tract of the Qinghai semi-fine wool sheep.

Methods

The bacterial profiles of the six different intestinal segments (duodenum, jejunum, ileum, cecum, colon and rectum) of Qinghai semi-fine wool sheep were studied using 16S rRNA V3-V4 hypervariable amplicon sequencing.

Results

A total of 2,623,323 effective sequences were obtained, and 441 OTUs shared all six intestinal segments. The bacterial diversity was significantly different among the different intestinal segments, and the large intestine exhibited higher bacterial diversity than the small intestine. Firmicutes, Bacteroidetes, and Patescibacteria were the dominant phyla in these bacterial communities. Additionally, at the genus level, Prevotella_1, Candidatus_Saccharimonas, and Ruminococcaceae_UCG-005 were the most predominant genus in duodenal segment, jejunal and ileal segments, and cecal, colonic, and rectal segments, respectively. We predicted that the microbial functions and the relative abundance of the genes involved in carbohydrate metabolism were overrepresented in the intestinal segments of Qinghai semi-fine wool sheep.

Conclusion

The bacterial communities and functions differed among different intestinal segments. Our study is the first to provide insights into the composition and biological functions of the intestinal microbiota of Qinghai semi-fine wool sheep. Our results also provide useful information for the nutritional regulation and production development in Qinghai semi-fine wool sheep.

Dynamic changes of the fecal bacterial community in dairy cows during early lactation

The dynamics of the community structure and composition of the dairy cow fecal bacterial communities during early lactation is unclear, therefore this study was conducted to characterize the fecal bacterial communities in dairy cows during early lactation using 16S rRNA gene sequencing. Feces were sampled from 20 healthy fresh Holstein dairy cows on day 1 (Fresh1d group) and day 14 (Fresh14d group) after calving. After calving, cows were fed the same fresh diet. The dominant phyla Firmicutes and Proteobacteria were decreased (P ≤ 0.01) with lactating progress and phyla Bacteroidetes were increased (P = 0.008) with lactating progress and dietary transition. At family level, the predominant families were Ruminococcaceae (35.23%), Lachnospiraceae (11.46%), Rikenellaceae (10.44%) and Prevotellaceae (6.89%). A total of 14 genera were different between fecal samples from Fresh1d and Fresh14d, included the predominant genera, such as Ruminococcaceae_UCG-005 (P = 0.008), Rikenellaceae_RC9_gut_group (P = 0.043) and Christensenellaceae_R-7_group (P = 0.008). All fecal bacterial communities shared members of the genera Ruminococcaceae_UCG-005, Bacteroides and Rikenellaceae_RC9_gut_group. These findings help to improve our understanding of the composition and structure of the fecal microbial community in fresh cows and may provide insight into bacterial adaptation time and dietary in lactating cows.

An Overview of the Elusive Passenger in the Gastrointestinal Tract of Cattle: The Shiga Toxin Producing Escherichia coli

For approximately 10,000 years, cattle have been our major source of meat and dairy. However, cattle are also a major reservoir for dangerous foodborne pathogens that belong to the Shiga toxin-producing Escherichia coli (STEC) group. Even though STEC infections in humans are rare, they are often lethal, as treatment options are limited. In cattle, STEC infections are typically asymptomatic and STEC is able to survive and persist in the cattle GIT by escaping the immune defenses of the host. Interactions with members of the native gut microbiota can favor or inhibit its persistence in cattle, but research in this direction is still in its infancy. Diet, temperature and season but also industrialized animal husbandry practices have a profound effect on STEC prevalence and the native gut microbiota composition. Thus, exploring the native cattle gut microbiota in depth, its interactions with STEC and the factors that affect them could offer viable solutions against STEC carriage in cattle.

A meta-analysis of the bovine gastrointestinal tract microbiota

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

Detection of Flea-Borne Pathogens from Cats and Fleas in a Maltese Shelter

In a sanctuary located on the island of Malta, 23 clinically healthy cats randomly selected were sampled for blood and fleas. Only fleas were collected from 35 cats. All fleas were identified as Ctenocephalides felis, except for one specimen of Ctenocephalides canis. To the best of the authors' knowledge, this may be the first time to establish the occurrence of Bartonella koehlerae and B. clarridgeiae, as well as of Candidatus Mycoplasma haemominutum in the blood samples of 11 cats (47.82% [95% CI: 29.33-67.04]) with conventional PCR assays. One or more pathogens were found in 54 (96.42% [95% CI: 86.74-99.70]) out of 56 pooled flea samples, the most prevalent was Rickettsia felis. The DNA of Bartonella henselae, the commonest etiological agent of cat scratch disease, was detected first time in a pooled flea sample of a cat.

Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau

The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000–5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different forage growth stages. This indicates that microbial changes in the rumen depend on changes in the forage nutritional composition. These findings provide evidence on the rumen microbial diversity of yaks in the QTP.

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.

Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda

The red panda (Ailurus fulgens) is a herbivorous carnivore that is protected worldwide. The gastrointestinal tract (GIT) microbial community has widely acknowledged its vital role in host health, especially in diet digestion; However, no study to date has revealed the GIT microbiota in the red panda. Here, we characterized the microbial biogeographical characteristics in the GIT of a red panda using high-throughput sequencing technology. Significant differences were observed among GIT segments by beta diversity of microbiota, which were divided into four distinct groups: the stomach, small intestine, large intestine, and feces. The stomach and duodenum showed less bacterial diversity, but contained higher bacterial abundance and the most unclassified tags. The number of species in the stomach and small intestine samples was higher than that of the large intestine and fecal samples. A total of 133 core operational taxonomic units were obtained from the GIT samples with 97% sequence identity. Proteobacteria (52.16%), Firmicutes (10.09%), and Bacteroidetes (7.90%) were the predominant phyla in the GIT of the red panda. Interestingly, Escherichia-Shigella were largely abundant in the stomach, small intestine, and feces whereas the abundance of Bacteroides in the large intestine was high. Overall, our study provides a deeper understanding of the gut biogeography of the red panda microbial population. Future research will be important to investigate the microbial culture, metagenomics and metabolism of red panda GIT, especially in Escherichia-Shigella.