Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing

Multi-omics strategy reveals potential role of antimicrobial resistance and virulence factor genes responsible for Simmental diarrheic calves caused by Escherichia coli

Escherichia coli (E. coli) is reported to be an important pathogen associated with calf diarrhea. Antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) pose a considerable threat to both animal and human health. However, little is known about the characterization of ARGs and VFGs presented in the gut microbiota of diarrheic calves caused by E. coli. In this study, we used multi-omics strategy to analyze the ARG and VFG profiles of Simmental calves with diarrhea caused by E. coli K99. We found that gut bacterial composition and their microbiome metabolic functions varied greatly in diarrheic calves compared to healthy calves. In total, 175 ARGs were identified, and diarrheal calves showed a significantly higher diversity and abundance of ARGs than healthy calves. Simmental calves with diarrhea showed higher association of VFGs with pili function, curli assembly, and ferrienterobactin transport of E. coli. Co-occurrence patterns based on Pearson correlation analysis revealed that E. coli had a highly significant (P < 0.0001) correlation coefficient (>0.8) with 16 ARGs and 7 VFGs. Metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Phylotype analysis of E. coli genomes showed that the predominant phylogroup B1 in diarrheic Simmental calves was associated with 10 ARGs and 3 VFGs. These findings provide an overview of the diversity and abundance of the gut microbiota in diarrheic calves caused by E. coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the calves affected with diarrhea.IMPORTANCESimmental is a well-recognized beef cattle breed worldwide. They also suffer significant economic losses due to diarrhea. In this study, fecal metagenomic analysis was applied to characterize the antibiotic resistance gene (ARG) and virulence factor gene (VFG) profiles of diarrheic Simmental calves. We identified key ARGs and VFGs correlated with Escherichia coli isolated from Simmental calves. Additionally, metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Our findings provide an insight into the diversity and abundance of the gut microbiota in diarrheic calves caused by Escherichia coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the diarrheal calves from cattle hosts.

Fecal and vaginal microbiota of vaccinated and non-vaccinated pregnant elk challenged with Brucella abortus

Introduction

Brucella abortus is the causative agent of brucellosis in cattle and in humans, resulting in economic losses in the agricultural sector and representing a major threat to public health. Elk populations in the American Northwest are reservoirs for this bacterium and transmit the agent to domestic cattle herds. One potential strategy to mitigate the transmission of brucellosis by elk is vaccination of elk populations against B. abortus; however, elk appear to be immunologically distinct from cattle in their responses to current vaccination strategies. The differences in host response to B. abortus between cattle and elk could be attributed to differences between the cattle and elk innate and adaptive immune responses. Because species-specific interactions between the host microbiome and the immune system are also known to affect immunity, we sought to investigate interactions between the elk microbiome and B. abortus infection and vaccination.

Methods

We analyzed the fecal and vaginal microbial communities of B. abortus-vaccinated and unvaccinated elk which were challenged with B. abortus during the periparturient period.

Results

We observed that the elk fecal and vaginal microbiota are similar to those of other ruminants, and these microbial communities were affected both by time of sampling and by vaccination status. Notably, we observed that taxa representing ruminant reproductive tract pathogens tended to increase in abundance in the elk vaginal microbiome following parturition. Furthermore, many of these taxa differed significantly in abundance depending on vaccination status, indicating that vaccination against B. abortus affects the elk vaginal microbiota with potential implications for animal reproductive health.

Discussion

This study is the first to analyze the vaginal microbiota of any species of the genus Cervus and is also the first to assess the effects of B. abortus vaccination and challenge on the vaginal microbiome.

Unlocking gut microbiota potential of dairy cows in varied environmental conditions using shotgun metagenomic approach

Food security and environmental pollution are major concerns for the expanding world population, where farm animals are the largest source of dietary proteins and are responsible for producing anthropogenic gases, including methane, especially by cows. We sampled the fecal microbiomes of cows from varying environmental regions of Pakistan to determine the better-performing microbiomes for higher yields and lower methane emissions by applying the shotgun metagenomic approach. We selected managed dairy farms in the Chakwal, Salt Range, and Patoki regions of Pakistan, and also incorporated animals from local farmers. Milk yield and milk fat, and protein contents were measured and correlated with microbiome diversity and function. The average milk protein content from the Salt Range farms was 2.68%, with an average peak milk yield of 45 litters/head/day, compared to 3.68% in Patoki farms with an average peak milk yield of 18 litters/head/day. Salt-range dairy cows prefer S-adenosyl-L-methionine (SAMe) to S-adenosyl-L-homocysteine (SAH) conversion reactions and are responsible for low milk protein content. It is linked to Bacteroides fragilles which account for 10% of the total Bacteroides, compared to 3% in the Patoki region. The solid Non-Fat in the salt range was 8.29%, whereas that in patoki was 6.34%. Moreover, Lactobacillus plantarum high abundance in Salt Range provided propionate as alternate sink to [H], and overcoming a Methanobrevibacter ruminantium high methane emissions in the Salt Range. Furthermore, our results identified ruminant fecal microbiomes that can be used as fecal microbiota transplants (FMT) to high-methane emitters and low-performing herds to increase farm output and reduce the environmental damage caused by anthropogenic gases emitted by dairy cows.

Effect of a High-Starch or a High-Fat Diet on the Milk Performance, Apparent Nutrient Digestibility, Hindgut Fermentation Parameters and Microbiota of Lactating Cows

In this study, changes in milk performance, nutrient digestibility, hindgut fermentation parameters and microflora were observed by inducing milk fat depression (MFD) in dairy cows fed with a high-starch or a high-fat diet. Eight Holstein cows were paired in a completely randomized cross-over design within two 35 d periods (18 d control period and 17d induction period). During the control period, all cows were fed the low-starch and low-fat diet (CON), and at the induction period, four of the cows were fed a high-starch diet with crushed wheat (IS), and the other cows were fed a high-fat diet with sunflower fat (IO). The results showed that, compared to when the cows were fed the CON diet, when cows were fed the IS or IO diet, they had lower milk fat concentrations, energy corrected milk, 3.5% fat-corrected milk yield, feed efficiency and apparent digestibility of NDF and ADF. However, cows fed the IO diet had a lower apparent digestibility of ether extracts. In addition, we observed that when cows were fed the high-starch (IS) or high-fat (IO) diet, they had a higher fecal concentration of propionate and acetate, and a lower NH3-N. Compared to when the cows were fed the CON diet, cows fed the IS diet had a lower pH, and cows fed the IO diet had a lower concentration of valerate in feces. In the hindgut microbiota, the relative abundance of Oscillospiraceae_UCG-005 was increased, while the Verrucomicrobiota and Lachnospiraceae_AC2044_group were decreased when cows were fed the IO diet. The relative abundance of Prevotellaceae_UCG-003 was increased, while the Alistipes and Verrucomicrobiota decreased, and the Treponema, Spirochaetota and Lachnospiraceae_AC2044_group showed a decreasing trend when cows were fed the IS diet. In summary, this study suggested that high-starch or high-fat feeding could induce MFD in dairy cows, and the high-fat diet had the greatest effect on milk fat; the high-starch or high-fat diet affected hindgut fermentation and apparent fiber digestibility. The changes in hindgut flora suggested that hindgut microbiota may be associated with MFD in cows.

Longitudinal Changes in Milk Microorganisms in the First Two Months of Lactation of Primiparous and Multiparous Cows

The present experiment was carried out to analyze the longitudinal changes in milk microorganisms. For this purpose, milk samples were collected from 12 healthy cows (n = 96; six primiparous cows and six multiparous cows) at eight different time points. The characteristics and variations in microbial composition were analyzed by 16S rRNA gene high-throughput sequencing. In the primiparous group, higher and more stable alpha diversity was observed in transitional and mature milk compared with the colostrum, with no significant difference in alpha diversity at each time point in the multiparous group. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota were the most dominant phyla, and Pseudomonas, UCG-005, Acinetobacter, Vibrio, Lactobacillus, Bacteroides, Serratia, Staphylococcus, and Glutamicibacter were the most dominant genera in both primiparous and multiparous cow milk. Some typically gut-associated microbes, such as Bacteroides, UCG-005, and Rikenellaceae_RC9_gut_group, etc., were enriched in the two groups. Biomarker taxa with the day in time (DIM) were identified by a random forest algorithm, with Staphylococcus showing the highest degree of interpretation, and the difference in milk microbiota between the two groups was mainly reflected in 0 d-15 d. Additionally, network analysis suggested that there were bacteria associated with the total protein content in milk. Collectively, our results disclosed the longitudinal changes in the milk microbiota of primiparous and multiparous cows, providing further evidence in dairy microbiology.

Characterization of the archaeal community in foods: The neglected part of the food microbiota

Despite the large number of studies conducted on archaea associated with extreme environments, the archaeal community composition in food products is still poorly known. Here, we investigated a new insight into exploring the archaeal community in several food matrices, with a particular focus on determining whether living archaea were present. A total of 71 samples of milk, cheese and its derived brine, honey, hamburger, clam, and trout were analyzed by high-throughput 16S rRNA sequencing. Archaea were detected in all the samples, ranging from 0.62 % of microbial communities in trout to 37.71 % in brine. Methanogens dominated 47.28 % of the archaeal communities, except for brine, which was dominated by halophilic taxa affiliated with the genus Haloquadratum (52.45 %). Clams were found to be a food with high richness and diversity of archaea and were targeted for culturing living archaea under different incubation time and temperature conditions. A subset of 16 communities derived from culture-dependent and culture-independent communities were assessed. Among the homogenates and living archaeal communities, the predominant taxa were distributed in the genera Nitrosopumilus (47.61 %) and Halorussus (78.78 %), respectively. A comparison of the 28 total taxa obtained by culture-dependent and culture-independent methods enabled their categorization into different groups, including detectable (8 out of 28), cultivable (8 out of 28), and detectable-cultivable (12 out of 28) taxa. Furthermore, using the culture method, the majority (14 out of 20) of living taxa grew at lower temperatures of 22 and 4 °C during long-term incubation, and few taxa (2 out of 20) were found at 37 °C during the initial days of incubation. Our results demonstrated the distribution of archaea in all analyzed food matrices, which opens new perspectives to expand our knowledge on archaea in foods and their beneficial and detrimental effects.

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.

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

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

Gut Microbiota Profiles in Dairy Cattle from Highland and Coastal Regions Using Shotgun Metagenomic Approach

There is significant difference in milk production of highland and coastal regions in Indonesia of which the latter is critically low. The recent studies indicate a possibility of improving the milk yield and quality by manipulating the gut microbiota, for which profiling and abundance of gut microbiota in these divergent regions need to be addressed. The present study was the first of its kind to explore the dairy cattle gut microbiota diversity, abundance, and functional annotation of the two divergent Indonesian regions, the highland and coastal regions, by shotgun metagenomic approach. Unfavorable environmental conditions such as type of forage grass in coastal regions and high temperature remain a limiting factor; however, the improvement through manipulating the gut microbiota was not considered until recently to improve the quality and quantity of coastal region dairy cattle. The application of recent advance technologies can help achieve this goal on sustainable basis. The results show Bacteroidetes in higher abundance in coastal region (FPP) than in highland (Salatiga) while Firmicutes were higher in Salatiga. Furthermore, a collective physiology of the community was found by annotating the sequences against KEGG, eggNOG, and CAZy databases. To identify the role in pathways, an mPATH analysis was performed to have insight into the microbiota community in different metabolic pathways. The identified targets can be used as prebiotic and/or probiotic to improve the average milk yield of coastal region dairy cattle by manipulating the dairy feed with desired microbes.

Exploration and comparison of bacterial communities present in bovine faeces, milk and blood using 16S rRNA metagenomic sequencing

Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most abundant phyla overall. A total of 58 genus-level taxa occurred concurrently between the body sites. The important taxa could be categorized into four potentially pathogenic clusters i.e. arthropod-borne; food-borne and zoonotic; mastitogenic; and metritic and abortigenic. A number of taxa were significantly differentially abundant (DA) between sites based on the Wald test implemented in DESeq2 package. Majority of the DA taxa (i.e. Romboutsia, Paeniclostridium, Monoglobus, Akkermansia, Turicibacter, Bacteroides, Candidatus_Saccharimonas, UCG-005 and Prevotellaceae_UCG-004) were significantly enriched in faeces in comparison to milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the largest microbial genus in the entire analysis. This study provides insights into the microbial community composition of the sampled body sites and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the community of Waaihoek in KwaZulu-Natal, Republic of South Africa pertaining to their unsanitary practices associated with the use of cattle by-products.

Fecal Microbiome Features Associated with Extended-Spectrum β-Lactamase-Producing Enterobacterales Carriage in Dairy Heifers

Extended-spectrum β-lactamases (ESBLs) are a growing public health threat, and one key human exposure point is through livestock and the food supply. Understanding microbiome factors associated with fecal ESBL carriage can help detect and ideally assist with controlling and preventing ESBL dissemination among livestock. The objective of this study was to investigate the diversity and composition of the heifer fecal microbiota in ESBL-producing Enterobacterales (ESBL-PE) carriers and noncarriers. A total of 59 fecal samples were collected from replacement heifers between 12 and 18 months old from eight dairy farms in central Israel. Genomic DNA was extracted, and 16S rRNA amplicon sequencing was performed (Illumina short reads), focusing on a comparison between 33 ESBL-PE carriers (55.9%) and 26 (44.1%) noncarriers. Samples were analyzed and compared using QIIME2 (DADA2 pipeline and taxonomic assignment with SILVA database) and associated R packages for alpha and beta diversity and taxonomic abundances. Alpha diversity (Shannon diversity) and beta diversity (unweighted UniFrac) showed no significant difference between ESBL-PE carriers and noncarriers. Heifers from farms feeding calves with pooled colostrum had higher ESBL-PE carriage rates than heifers from farms feeding with individual mother colostrum (p < 0.001). Taxonomical abundance analysis revealed that the most common bacterial phyla were Bacteroidetes (44%) and Firmicutes (38%). There was no significant difference in taxonomic composition between ESBL-PE carriers and noncarriers at the phylum and genus levels. However, LEfSe biomarker discovery analysis identified several genera which were significantly different between carriers and noncarriers. For example, Prevotellacaea, Bacteroides, Rikenellaceae, and uncultured Bacteroidales were more abundant in ESBL carriers than noncarriers. Some aspects of microbiota composition differ between ESBL carriers and noncarriers in dairy heifers, specifically the abundance of certain genera. Feeding with pooled colostrum may play a role in that assembly. These could potentially serve as markers of ESBL-PE carriage. However, further research is needed to determine whether these observed differences have a significant impact on colonization with ESBL-PE.

Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk

Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.

Characterization of Microbiome on Feces, Blood and Milk in Dairy Cows with Different Milk Leucocyte Pattern

Simple Summary

Mastitis is an inflammation of the mammary gland caused by microorganisms and associated with an altered immune response. Recently, several studies hypothesized that a translocation of some bacteria from the gastrointestinal tract to the mammary gland can occur and that this bacterial crossing could be the cause of certain mastitis. The aim of this research is to investigate the bacteria translocation from the gut to the mammary gland, the so-called entero-mammary pathway, through the study of the fecal, blood and milk microbiome. Cows were recruited on the basis of their mammary gland health status and classified as healthy, at risk of mastitis and with mastitis. The microbial composition of feces, blood and milk were analyzed through high-throughput sequencing technique and the results were checked through a quantitative real-time PCR analysis. Although small differences were found in the microbiome of these three specimens between the groups of animals, beta biodiversity, that is, the ratio between whole and individual species diversity, highlighted a microbial community change in the milk of cows with different udder health conditions. The three matrices shared a high number of taxa; however, our results do not confirm a bacterial crossing from gut to milk, that still remains hypothetical.

Abstract

Mastitis is an inflammatory disease of the mammary gland, caused by the invasion of microorganism on this site, associated with an altered immune response. Recent studies in this field hypothesize that the origin of these pathogens can also be from the gastrointestinal tract, through the entero-mammary pathway in relation to an increase in gut permeability. In this study, we wanted to investigate if inflammatory status of the mammary gland is related to an alteration of gut permeability. The microbiome of feces, blood and milk of lactating cows, recruited on the basis of the total somatic cell count and of the percentage of polymorphonuclear neutrophils and lymphocytes, was studied. Cows were divided into healthy (G), at risk of mastitis (Y) and with mastitis (R) classifications. The bacterial DNA was extracted and the V3 and V4 regions of 16S rRNA sequenced. Moreover, the quantification of total bacteria was performed with quantitative real-time PCR. A non-parametric Kruskal–Wallis test was applied at the phylum, family and genera levels and beta biodiversity was evaluated with the unweighted UniFrac distance metric. Significant differences between groups were found for the microbial composition of feces (Clostridiaceae, Turicibacteriaceae for family level and Clostridium, Dorea, SMB53 and Turicibacter for genus level), blood (Tenericutes for phylum level and Mycoplasma for genus level) and milk (OD1 and Proteobacteria for phylum level, Enterobacteriaceae and Moraxallaceae for family level and Olsenella and Rhodococcus for genus level). The beta biodiversity of feces and blood did not change between groups. Significant differences (p < 0.05) were observed between the beta diversity in milk of G group and Y group and between Y group and R group. The number of taxa in common between feces, blood and milk were 8 at a phylum, 19 at a family and 15 at a genus level. From these results, the bacterial crossing from gut to milk in cows was not confirmed but remained hypothetical and deserves further investigation.