Microbiota Of Cattle Research Articles

PSLBII-7 Meta-analysis of the whole-body microbiota in cattle

Abstract Distinctive and self-sustainable microbial communities are present along the digestive, respiratory, and reproductive tracts, as well as in the mammary gland, and mucosal surfaces of the eye and hoof in cattle. Although the taxonomic and functional features of each of these communities have been relatively well characterized, this has been largely limited to the microbiome of an individual organ/site. However, recent developments suggest the presence of core taxa shared across the gut, respiratory, and reproductive microbiotas in cattle, and there is a need for a more holistic evaluation of microbial communities in and on cattle. Here, we performed a meta-analysis using all publicly available bovine 16S rRNA gene datasets deposited since 2019 to provide a holistic view of the whole-body microbiota. In total, we retrieved 16S rRNA gene sequences from 6,215 samples (53 studies originating from 29 different anatomical sites within beef and dairy cattle from Africa, Asia, Europe, South America, and North America. The 29 different anatomical sites including gut (ruminal fluid, ruminal tissues, feces, ileum, jejunum, cecum, colon and duodenum), respiratory (nasal cavity, deep nasopharynx, trachea and lung tissue), and reproductive tracts (female: vagina, endometrium and uterus; male: semen and prepuce), as well as the mammary gland (udder, teat apex, teat barrel, teat canal), eye (conjunctiva, ocular fluid and ocular surface swab), blood, hoof, joints and liver. Microbial community structure was distinct among different sample types (PERMANOVA, P < 0.05). Microbial richness differed by sample type (P < 0.0001) with mucosal surfaces (e.g. udder, eye and feet) having the greatest microbial richness followed by the gut. The lungs, liver, joints, semen and prepuce had the least microbial richness. Microbial diversity was greatest in the microbiota of the colon, cecum, teat apex, ruminal tissue and duodenum (Shannon diversity index > 5) while the liver (1.5), joint (2.3), and prepuce microbiota (2.7) were the least diverse. Bacillota had the highest relative abundance among phyla in the majority of microbial communities except for in the blood, prepuce, trachea and nasal cavity (dominated by Pseudomonadota), and liver (dominated by Fusobacteriota). The relatively most abundant genera across all samples were Mycoplasma (12.9%), Prevotella (3.9%), Bacteroides (2.4%), Escherichia (2.1%), Fusobacterium (2.0%), Ruminococcaceae UCG-005 (1.9%), Streptococcus (1.8%), Rikenellaceae RC9 (1.6%), and Corynebacterium (1.4%). However, their relative abundance varied greatly by body site, with the ocular and respiratory system samples dominated by Mycoplasma. Fusobacterium was relatively most abundant in the liver and semen, Corynebacterium in the mammary gland-associated samples, Bacteroides in the gut, and Streptococcus in the lower reproductive tract microbiota. Overall, our meta-analysis provides a comprehensive evaluation of the multiple bacterial communities in and on cattle, which will be useful for harnessing the whole-body microbiome to improve animal health and productivity.

Using Machine Learning and Natural Language Processing for Unveiling Similarities between Microbial Data

Microbiota analysis can provide valuable insights in various fields, including diet and nutrition, understanding health and disease, and in environmental contexts, such as understanding the role of microorganisms in different ecosystems. Based on the results, we can provide targeted therapies, personalized medicine, or detect environmental contaminants. In our research, we examined the gut microbiota of 16 animal taxa, including humans, as well as the microbiota of cattle and pig manure, where we focused on 16S rRNA V3-V4 hypervariable regions. Analyzing these regions is common in microbiome studies but can be challenging since the results are high-dimensional. Thus, we utilized machine learning techniques and demonstrated their applicability in processing microbial sequence data. Moreover, we showed that techniques commonly employed in natural language processing can be adapted for analyzing microbial text vectors. We obtained the latter through frequency analyses and utilized the proposed hierarchical clustering method over them. All steps in this study were gathered in a proposed microbial sequence data processing pipeline. The results demonstrate that we not only found similarities between samples but also sorted groups’ samples into semantically related clusters. We also tested our method against other known algorithms like the Kmeans and Spectral Clustering algorithms using clustering evaluation metrics. The results demonstrate the superiority of the proposed method over them. Moreover, the proposed microbial sequence data pipeline can be utilized for different types of microbiota, such as oral, gut, and skin, demonstrating its reusability and robustness.

Effects of dietary restriction and one-carbon metabolite supplementation during the first 63 days of gestation on the maternal gut, vaginal, and blood microbiota in cattle

BackgroundMaternal diet quality and quantity have significant impacts on both maternal and fetal health and development. The composition and function of the maternal gut microbiome is also significantly influenced by diet; however, little is known about the impact of gestational nutrient restriction on the bovine maternal microbiome during early gestation, which is a critical stage for maternal microbiome-mediated fetal programming to take place. The objective of the present study was to evaluate the impacts of diet restriction and one-carbon metabolite (OCM) supplementation during early gestation on maternal ruminal, vaginal, and blood microbiota in cattle. Thirty-three beef heifers (approx. 14 months old) were used in a 2 × 2 factorial experiment with main factors of target gain (control [CON]; targeted 0.45 kg/d gain vs restricted [RES]; targeted − 0.23 kg/d gain), and OCM supplementation (+ OCM vs − OCM; n = 8/treatment; except n = 9 for RES–OCM). Heifers were individually fed, starting treatment at breeding (d 0) and concluding at d 63 of gestation. Ruminal fluid and vaginal swabs were collected on d − 2, d 35, and d 63 (at necropsy) and whole blood was collected on d 63 (necropsy). Bacterial microbiota was assessed using 16S rRNA gene (V3–V4) sequencing.ResultsOverall ruminal microbiota structure was affected by gain, OCM, time, and their interactions. The RES heifers had greater microbial richness (observed ASVs) but neither Shannon nor Inverse Simpson diversity was significantly influenced by gain or OCM supplementation; however, on d 63, 34 bacterial genera showed differential abundance in the ruminal fluid, with 25 genera enriched in RES heifers as compared to CON heifers. In addition, the overall interaction network structure of the ruminal microbiota changed due to diet restriction. The vaginal microbiota community structure was influenced by gain and time. Overall microbial richness and diversity of the vaginal microbiota steadily increased as pregnancy progressed. The vaginal ecological network structure was distinctive between RES and CON heifers with genera-genera interactions being intensified in RES heifers. A relatively diverse bacterial community was detected in blood samples, and the composition of the blood microbiota differed from that of ruminal and vaginal microbiota.ConclusionRestricted dietary intake during early gestation induced significant alterations in the ruminal microbiota which also extended to the vaginal microbiota. The composition of these two microbial communities was largely unaffected by OCM supplementation. Blood associated microbiota was largely distinctive from the ruminal and vaginal microbiota.

Untargeted metabolomics and metagenomics reveal signatures for intramammary ceftiofur treatment and lactation stage in the cattle hindgut.

The gut microbiota in cattle is essential for protein, energy, and vitamin production and hence, microbiota perturbations can affect cattle performance. This study evaluated the effect of intramammary (IMM) ceftiofur treatment and lactation stage on the functional gut microbiome and metabolome. Forty dairy cows were enrolled at dry-off. Half received IMM ceftiofur and a non-antibiotic teat sealant containing bismuth subnitrate (cases), while the other half received the teat sealant (controls). Fecal samples were collected before treatment at dry off, during the dry period (weeks 1 and 5) and the first week after calving (week 9). Shotgun metagenomic sequencing was applied to predict microbial metabolic pathways whereas untargeted metabolomics was used identify polar and nonpolar metabolites. Compared to controls, long-term changes were observed in the cows given ceftiofur, including a lower abundance of microbial pathways linked to energy production, amino acid biosynthesis, and other vital molecules. The metabolome of treated cows had elevated levels of stachyose, phosphatidylethanolamine diacylglycerol (PE-DAG), and inosine a week after the IMM ceftiofur application, indicating alterations in microbial fermentation, lipid metabolism, energy, and cellular signaling. Differences were also observed by sampling, with cows in late lactation having more diverse metabolic pathways and a unique metabolome containing higher levels of histamine and histamine-producing bacteria. These data illustrate how IMM ceftiofur treatment can alter the functionality of the hindgut metabolome and microbiome. Understanding how antibiotics and lactation stages, which are each characterized by unique diets and physiology, impact the function of resident microbes is critical to define normal gut function in dairy cattle.

Seasonality of the conjunctival microbiota in cattle from a microregion in midwestern Brazil

This study aimed to identify the bacterial and fungal organisms in the conjunctival fornix of healthy cattle in a microregion located in midwestern Brazil. Additionally, we evaluated whether seasonality and cattle category (dairy vs. beef) play a role in our findings. The conjunctival fornix of 74 Holstein x Gyr and 70 Nelore cattle were sampled from February to March (rainy season) and August to September (dry season) of 2017. Bacterial and fungal strains were isolated by classical bacteriological and mycological methods. Some bacterial species were also identified by polymerase chain reaction. From the 144 animals included in the study, a total of 12 bacterial genera were identified, with Bacillus cereus being the most prevalent agent in both seasons and cattle categories. The total number of bacteria was not influenced by seasonality or cattle category (P = 0.25). The number of Moraxella bovoculi identified in dairy (5/74) and beef cattle (7/70) did not differ statistically (P = 0.76). However, seasonality played a role in M. bovoculi identification, being found only during the rainy season in the dairy cattle (P = 0.01), and only during the dry season in the beef cattle (P = 0.04). During the dry season, the number of gram-positive bacteria was significantly higher than the number of gram-negative bacteria in beef cattle (P = 0.009). Fungi were isolated in 20/144 samples. The number of fungi isolated in dairy cattle (16/144) was significantly higher than that isolated in beef cattle (4/144) (P = 0.007). Although a higher number of fungi were isolated in both cattle categories during the rainy season, this finding was not significant (P = 0.53). In this microregion located in midwestern Brazil, Bacillus cereus was the most prevalent and Corynebacterium spp. and Streptococcus spp. the least prevalent bacteria found in the conjunctival fornix of healthy cattle. The prevalence of the conjunctival fungal microbiota (11.8%) was lower than previously reported, with a higher number of isolates found in dairy cattle. Trichosporon spp. (41.2%) and Aspergillus spp. (35.3%) were the most frequent genera, being most commonly isolated in the rainy season.

Effects of Zoovit probiotic on faecal microbiota in cattle

The amount of pathogenic bacteria in feces is an indicator characterizing the health status of animals. This is important to protect the environment and the health of farm workers. The aim of the present study is to determine the effect of probiotic Zoovit on the microbiome of the faecal mass of Holstein cattle. In the experiment, two groups were formed - experimental and control, 30 each. A probiotic was added to the combined feed of the experimental group, but not to the control group. The food ration with the participation of probiotic is placed twice a day. To determine the microbiome in fecal matter in cattle, PCR analyzes were used for the detection of Lactobacillus delbrueckii subsp. bulgaricus, a species-specific PCR assay for the presence of total DNA in L. delbrueckii and L. delbrueckii subsp. bulgaricus and methods for determination of sulfite-reducing colonies. No representatives of Staphulococccua aureus and Clostridium sp were isolated in the faecal mass of the animals from both groups. For Escherichia coli and Coliforms, a significant decrease in the faecal mass of cows fed with feed containing probiotics was found. The presence of L. delbrueckii subsp. bulgaricus in animals receiving a probiotic. Colonies with a colonial characteristic typical of L. delbrueckii subsp. bulgaricus were isolated in the animals receiving probiotic Zoovit and in the control group, no colonies typical of Lactobacillus bulgaricus were found.

The spatial dissimilarities and connections of the microbiota in the upper and lower respiratory tract of beef cattle.

Bovine respiratory disease (BRD) causes morbidity and mortality in cattle. The critical roles of the respiratory microbiota in BRD have been widely studied. The nasopharynx was the most popular sampling niche for BRD pathogen studies. The oral cavity and other niches within the respiratory tract, such as nostrils and lung, are less assessed. In this study, oropharyngeal swabs (OS), nasal swabs (NS), nasopharyngeal swabs (NP), and bronchoalveolar lavage (BAL) were collected from calves located in four countries and analyzed for investigation of the dissimilarities and connections of the respiratory microbiota. The results showed that the microbial diversity, structure, and composition in the upper and lower respiratory tract in beef cattle from China, the USA, Canada, and Italy were significantly different. The microbial taxa for each sampling niche were specific and associated with their local physiology and geography. The signature microbiota for OS, NS, NP, and BAL were identified using the LEfSe algorithm. Although the spatial dissimilarities among the respiratory niches existed, the microbial connections were observed in beef cattle regardless of geography. Notably, the nostril and nasopharynx had more similar microbiomes compared to lung communities. The major bacterial immigration patterns in the bovine respiratory tract were estimated and some of them were associated with geography. In addition, the contribution of oral microbiota to the nasal and lung ecosystems was confirmed. Lastly, microbial interactions were characterized to reveal the correlation between the commercial microbiota and BRD-associated pathogens. In conclusion, shared airway microbiota among niches and geography provides the possibility to investigate the common knowledge for bovine respiratory health and diseases. In spite of the dissimilarities of the respiratory microbiota in cattle, the spatial connections among these sampling niches not only allow us to deeply understand the airway ecosystem but also benefit the research and development of probiotics for BRD.

PSXIV-9 Effects of Dietary Restriction and One-Carbon Metabolite Supplementation During Early Gestation on the Maternal Gut and Vaginal Microbiota in Cattle

Abstract Maternal diet quality and quantity have significant impacts on both maternal and fetal health and development. The composition and function of the maternal gut microbiome is also significantly influenced by diet. However, little is known about the impact of gestational nutrient restriction on the maternal microbiome during early gestation, which is a critical stage for many developmental processes. Here, we evaluated the effects of dietary restriction and one-carbon metabolite (OCM) supplementation on the ruminal and vaginal microbiota of beef heifers during early pregnancy. For this, 32 beef heifers (approximately 14-month-old) were used in a 2 × 2 factorial experiment with main factors including targeted gain (CON; 0.45 kg/d gain vs. RES; -0.23 kg/d gain), and OCM supplementation (OCM vs. noOCM) (n = 8/treatment). OCM heifers received ruminal-protected methionine (20 g/day) and choline (60 g/day) daily via a fine-ground corn carrier, with weekly intramuscular injections of folate (320 mg) and vitamin B12 (20 mg). The noOCM heifers received only corn carrier and saline injections. Heifers were individually fed and began treatment at breeding (d 0) and remained on treatment until d 63 of gestation. Ruminal fluid and vaginal swab samples were collected at d -2, d 35, and d 63 (at necropsy). Microbiota from samples were assessed using 16S rRNA gene (V3-V4) sequencing. Overall community structure of the ruminal microbiota was affected by gain (PERMANOVA: R2 = 0.04, P < 0.0001), OCM (R2 = 0.013, P = 0.03), time (R2 = 0.16, P < 0.0001) and by their interactions (R2 = 0.08, P = 0.004). The greatest difference in ruminal microbial community structure was between RES and CON heifers (R2 ≥ 0.16, P ≤ 0.003) on d 63. Overall microbial richness (total ASVs) was greater in RES (2,900 vs. 2,737; P = 0.005) but was unaffected by OCM (P = 0.25). Analysis via MaAsLin2 revealed that phyla Firmicutes (31% vs. 22%), Actinobacteriota (0.65% vs. 0.36%) and Chloroflexi were enriched (P < 0.05) in RES heifers. Twenty-five of the 34 differentially abundant genera in the rumen microbiota, including Christensellaceae R7 (5.0% vs 2.6%), Lachnobacterium (2.0% vs. 0.46%), and Butyrivibrio were more relatively abundant in RES; whereas 9 genera including Prevotella (16.5% vs. 31.1%), Ruminococcus (1.6% vs. 2.5%) and Saccharofermentans (0.4% vs. 0.5%) were reduced in RES (P < 0.05) on d 63. Overall vaginal microbiota structure was affected by gain (R2 = 0.02, P = 0.023) and time (R2 = 0.34, P < 0.0001) but not OCM (P >0.05). Community structure of RES was distinct from CON (R2 = 0.16, P = 0.032) on d 63, but microbial community richness and diversity were not influenced by OCM (P > 0.05). On d 63, RES heifers had increased Actinobacteriota (30.5% vs. 17.7%), but reduced Proteobacteriota (6.2% vs. 9.4%) and Fusobacteriota (0.02% vs. 0.94%; P < 0.05). In summary, restricted dietary intake during early gestation induced significant alterations in the ruminal microbiota and its impact also extended to the vaginal microbiota. The composition of these two microbial communities remained largely unaffected by OCM supplement.

Dynamic distribution of gut microbiota in cattle at different breeds and health states.

Weining cattle is a precious species with high tolerance to cold, disease, and stress, and accounts for a large proportion of agricultural economic output in Guizhou, China. However, there are gaps in information about the intestinal flora of Weining cattle. In this study, high-throughput sequencing were employed to analyze the intestinal flora of Weining cattle (WN), Angus cattle (An), and diarrheal Angus cattle (DA), and explore the potential bacteria associated with diarrhea. We collected 18 fecal samples from Weining, Guizhou, including Weining cattle, Healthy Angus, and Diarrheal Angus. The results of intestinal microbiota analysis showed there were no significant differences in intestinal flora diversity and richness among groups (p > 0.05). The abundance of beneficial bacteria (Lachnospiraceae, Rikenellaceae, Coprostanoligenes, and Cyanobacteria) in Weining cattle were significantly higher than in Angus cattle (p < 0.05). The potential pathogens including Anaerosporobacter and Campylobacteria were enriched in the DA group. Furthermore, the abundance of Lachnospiraceae was very high in the WN group (p < 0.05), which might explain why Weining cattle are less prone to diarrhea. This is the first report on the intestinal flora of Weining cattle, furthering understanding of the relationship between intestinal flora and health.

Activity- and Enrichment-Based Metaproteomics Insights into Active Urease from the Rumen Microbiota of Cattle.

Regulation of microbial urease activity plays a crucial role in improving the utilization efficiency of urea and reducing nitrogen emissions to the environment for ruminant animals. Dealing with the diversity of microbial urease and identifying highly active urease as the target is the key for future regulation. However, the identification of active urease in the rumen is currently limited due to large numbers of uncultured microorganisms. In the present study, we describe an activity- and enrichment-based metaproteomic analysis as an approach for the discovery of highly active urease from the rumen microbiota of cattle. We conducted an optimization method of protein extraction and purification to obtain higher urease activity protein. Cryomilling was the best choice among the six applied protein extraction methods (ultrasonication, bead beating, cryomilling, high-pressure press, freeze-thawing, and protein extraction kit) for obtaining protein with high urease activity. The extracted protein by cryomilling was further enriched through gel filtration chromatography to obtain the fraction with the highest urease activity. Then, by using SDS-PAGE, the gel band including urease was excised and analyzed using LC-MS/MS, searching against a metagenome-derived protein database. Finally, we identified six microbial active ureases from 2225 rumen proteins, and the identified ureases were homologous to those of Fibrobacter and Treponema. Moreover, by comparing the 3D protein structures of the identified ureases and known ureases, we found that the residues in the β-turn of flap regions were nonconserved, which might be crucial in influencing the flexibility of flap regions and urease activity. In conclusion, the active urease from rumen microbes was identified by the approach of activity- and enrichment-based metaproteomics, which provides the target for designing a novel efficient urease inhibitor to regulate rumen microbial urease activity.

Epidemiology and pathophysiology of hemolytic uremic syndrome associated with shiga toxin (literature review)

Hemolytic uremic syndrome (HUS) associated with shiga toxin E. coli(STEC) is one of the most common causes of acute kidney injury in young children. The share of STEC-HUS among all HUS variants is up to 90%. Not all STECs are pathogenic to humans, and those that cause disease (hemorrhagic colitis, HUS) are referred to as enterohemorrhagic E. coli(EHEC). The main pathogens causing STEC-HUS include the serotype E. coliO157: H7, less often serotypes O26, O80, O103, O121, O145. EHEC exist as normal microbiota in cattle, but can also be found in goats, sheep, pigs, chickens, dogs, and rats. Infection can occur when using undercooked ground beef, unpasteurized milk, water, including tap water and from open ponds and pools, from an infected person and when visiting farms and zoos. The epidemiological history should be carefully assessed in each patient with HUS, taking into account the annual outbreaks of this disease in different regions of the world. In recent years actively discussed the issue of the transfer of shiga toxin (Stx) from the intestine to the blood and from the blood to target organs in the form of microvesicles, the wall of which is the outer shell of E.coliand blood cells. This allows Stx to escape the response of the human immune system. The article describes in detail the mechanisms of infection and expression of pathogenic genes of EHEC, the effect of Stx on endothelial cells, on expression of adhesion molecules and inflammatory chemokines, activation of the alternative complement pathway, which determine the development of HUS.

Unveiling the Bovine Epimural Microbiota Composition and Putative Function.

Numerous studies have used the 16S rRNA gene target in an attempt to characterize the structure and composition of the epimural microbiota in cattle. However, comparisons between studies are challenging, as the results show large variations associated with experimental protocols and bioinformatics methodologies. Here, we present a meta-analysis of the rumen epimural microbiota from 11 publicly available amplicon studies to assess key technical and biological sources of variation between experiments. Using the QIIME2 pipeline, 332 rumen epithelial microbiota samples were analyzed to investigate community structure, composition, and functional potential. Despite having a significant impact on microbial abundance, country of origin, farm, hypervariable region, primer set, animal variability, and biopsy location did not obscure the identification of a core microbiota. The bacterial genera Campylobacter, Christensenellaceae R-7 group, Defluviitaleaceae UCG-011, Lachnospiraceae UCG-010, Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-014, Succiniclasticum, Desulfobulbus, and Comamonas spp. were found in nearly all epithelium samples (>90%). Predictive analysis (PICRUSt) was used to assess the potential functions of the epithelial microbiota. Regularized canonical correlation analysis identified several pathways associated with the biosynthesis of precursor metabolites in Campylobacter, Comamonas, Desulfobulbus, and Ruminococcaceae NK4A214, highlighting key metabolic functions of these microbes within the epithelium.

Meta-analysis of bovine respiratory microbiota: link between respiratory microbiota and bovine respiratory health.

Bovine respiratory microbiota plays a significant role in bovine respiratory health. We conducted a meta-analysis using publicly available 16S rRNA gene datasets from the respiratory tract to characterize respiratory microbiota in feedlot cattle. Our aims were to determine the factors that influence microbiota development and to assess the differences in microbiota composition and diversity between healthy calves and those that developed bovine respiratory disease (BRD). Our results showed that the overall composition and diversity of respiratory microbiota in cattle were significantly affected by study design, 16S rRNA hypervariable region sequenced, health status, time since arrival to the feedlot, sampling sites in the respiratory tract and antibiotic treatment. Assessment of diversity indices showed a statistically significant difference between the BRD-affected cattle and healthy control calves. Using multivariate network analysis and Spearman's correlation analyses, we further distinguished the taxa that were commonly associated with BRD when the day of arrival to the feedlot was added to the model. The probability of being identified as BRD was significantly correlated with days 7, 12 and 14 following the calf's arrival to the feedlot. These findings could help in proposing strategies to further evaluate the link between respiratory microbiota and bovine respiratory health.

Topography of the respiratory tract bacterial microbiota in cattle

BackgroundBacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. The nasopharynx is generally accepted as the primary source of pathogenic bacteria that cause BP. However, it has recently been shown in humans that the oropharynx may act as the primary reservoir for pathogens that reach the lung. The objective was therefore to describe the bacterial microbiota present along the entire cattle respiratory tract to determine which upper respiratory tract (URT) niches may contribute the most to the composition of the lung microbiota.MethodsSeventeen upper and lower respiratory tract locations were sampled from 15 healthy feedlot steer calves. Samples were collected using a combination of swabs, protected specimen brushes, and saline washes. DNA was extracted from each sample and the 16S rRNA gene (V3-V4) was sequenced. Community composition, alpha-diversity, and beta-diversity were compared among sampling locations.ResultsMicrobiota composition differed across sampling locations, with physiologically and anatomically distinct locations showing different relative abundances of 1137 observed sequence variants (SVs). An analysis of similarities showed that the lung was more similar to the nasopharynx (R-statistic = 0.091) than it was to the oropharynx (R-statistic = 0.709) or any other URT sampling location. Five distinct metacommunities were identified across all samples after clustering at the genus level using Dirichlet multinomial mixtures. This included a metacommunity found primarily in the lung and nasopharynx that was dominated by Mycoplasma. Further clustering at the SV level showed a shared metacommunity between the lung and nasopharynx that was dominated by Mycoplasma dispar. Other metacommunities found in the nostrils, tonsils, and oral microbiotas were dominated by Moraxella, Fusobacterium, and Streptococcus, respectively.ConclusionsThe nasopharyngeal bacterial microbiota is most similar to the lung bacterial microbiota in healthy cattle and therefore may serve as the primary source of bacteria to the lung. This finding indicates that the nasopharynx is likely the most important location that should be targeted when doing bovine respiratory microbiota research.4oDYTht3cF8JKr3LU-_s_YVideo abstract.

The composition of the perinatal intestinal microbiota in cattle

Recent research suggests that the microbial colonization of the mammalian intestine may begin before birth, but the observations are controversial due to challenges in the reliable sampling and analysis of low-abundance microbiota. We studied the perinatal microbiota of calves by sampling them immediately at birth and during the first postnatal week. The large size of the bovine newborns allows sampling directly from rectum using contamination-shielded swabs. Our 16S rDNA data, purged of potential contaminant sequences shared with negative controls, indicates the existence of a diverse low-abundance microbiota in the newborn rectal meconium and mucosa. The newborn rectal microbiota was composed of Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. The microbial profile resembled dam oral rather than fecal or vaginal vestibular microbiota, but included typical intestinal taxa. During the first postnatal day, the rectum was invaded by Escherichia/Shigella and Clostridia, and the diversity collapsed. By 7 days, diversity was again increasing. In terms of relative abundance, Proteobacteria were replaced by Firmicutes, Bacteroidetes and Actinobacteria, including Faecalibacterium, Bacteroides, Lactobacillus, Butyricicoccus and Bifidobacterium. Our observations suggest that mammals are seeded before birth with a diverse microbiota, but the microbiota changes rapidly in the early postnatal life.

Complete Genome Sequence of a New Zealand Isolate of the Bovine Pathogen Streptococcus uberis.

ABSTRACTStreptococcus uberis forms part of the native microbiota of cattle and is able to opportunistically infect the mammary gland; as such, it is a leading cause of bovine mastitis globally. Here, we report the complete genome sequence of S. uberis NZ01, isolated in New Zealand from a cow with a clinical case of bovine mastitis.

Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves

BackgroundThe microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community composition of the upper and lower respiratory tracts in calves.ResultsThe microbiota of the upper (nasal swab [NS]) and the lower (trans-tracheal aspiration [TTA]) respiratory tracts of 19 post-weaned Piedmontese calves with (8/19) and without (11/19) clinical signs of respiratory disease, coming from six different farms, was characterized by 16S rRNA gene metabarcoding. A total of 29 phyla (29 in NS, 21 in TTA) and 305 genera (289 in NS, 182 in TTA) were identified. Mycoplasma (60.8%) was the most abundant genus identified in both the NS (27.3%) and TTA (76.7%) samples, followed by Moraxella (16.6%) in the NS and Pasteurella (7.3%) in the TTA samples. Pasteurella multocida (7.3% of total operational taxonomic units [OTUs]) was the most abundant species in the TTA and Psychrobacter sanguinis (1.1% of total OTUs) in the NS samples. Statistically significant differences between the NS and the TTA samples were found for both alpha (Shannon index, observed species, Chao1 index, and Simpson index; P = 0.001) and beta (Adonis; P = 0.001) diversity. Comparison of the NS and TTA samples by farm origin and clinical signs revealed no statistical difference (P > 0.05), except for farm origin for the NS samples when compared by the unweighted UniFrac metric (P = 0.05).ConclusionsUsing 16S rRNA gene sequencing, we characterized the microbiota of the upper and lower respiratory tracts of calves, both healthy individuals and those with clinical signs of respiratory disease. Our results suggest that environmental factors may influence the composition of the upper airway microbiota in cattle. While the two microbial communities (upper and lower airways) differed in microbial composition, they shared several OTUs, suggesting that the lung microbiota may be a self-sustaining, more homogeneous ecosystem, influenced by the upper respiratory tract microbiota.

Weaned beef calves fed selenium-biofortified alfalfa hay have an enriched nasal microbiota compared with healthy controls.

Selenium (Se) is an essential trace mineral important for immune function and overall health of cattle. The nasopharyngeal microbiota in cattle plays an important role in overall respiratory health, especially when stresses associated with weaning, transport, and adaptation to a feedlot affect the normal respiratory defenses. Recent evidence suggests that cattle diagnosed with bovine respiratory disease complex have significantly less bacterial diversity. The objective of this study was to determine whether feeding weaned beef calves Se-enriched alfalfa (Medicago sativa) hay for 9 weeks in a preconditioning program prior to entering the feedlot alters nasal microbiota. Recently weaned beef calves (n = 45) were blocked by sex and body weight, randomly assigned to 3 treatment groups with 3 pens of 5 calves per treatment group, and fed an alfalfa hay based diet for 9 weeks. Alfalfa hay was harvested from fields fertilized with sodium selenate at a rate of 0, 45.0 or 89.9 g Se/ha. Blood samples were collected biweekly and analyzed for whole-blood Se concentrations. Nasal swabs were collected during week 9 from one or two calves from each pen (total n = 16). Calculated Se intake from dietary sources was 3.0, 15.6, and 32.2 mg Se/head/day for calves consuming alfalfa hay with Se concentrations of 0.34 to 2.42 and 5.17 mg Se/kg dry matter, respectively. Whole-blood Se concentrations after 8 weeks of feeding Se-fertilized alfalfa hay were dependent upon Se-application rates (0, 45.0, or 89.9 g Se/ha) and were 155, 345, and 504 ng/mL (PLinear < 0.0001). Microbial DNA was extracted from nasal swabs and amplified and sequenced. Alpha rarefaction curves comparing the species richness (observed OTUs) and overall diversity (Chao1, Observed OTU, and Shannon index) between calves fed selenium-biofortified alfalfa hay compared with control calves showed that Se-supplementation tended to be associated with an enriched nasal microbiota. ANOSIM of unweighted UniFrac distances showed that calves fed high Se-biofortified alfalfa hay clustered separately when compared with control calves in the PCoA plot (R = 0.216, P = 0.04). The bacterial orders Lactobacillales and Flavobacteriales were increased in healthy control calves compared with Clostridiales and Bacteroidales being increased in calves fed Se-biofortified alfalfa hay. Although there were strong trends, no significant differences were noted for any of the bacterial taxa. Based upon these findings, we suggest that weaned beef calves fed Se-biofortified hay tend to have an enriched nasal microbiota. Feeding Se-biofortified alfalfa hay to weaned beef calves prior to entering the feedlot is a strategy for increasing nasopharyngeal microbial diversity.

Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis.

Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better comprehension of bovine physiology and reproductive health being of great economic interest. Up to date, studies involving cattle microbiota are focused on the gastrointestinal tract, and little is known about the vaginal microbiota. This study aimed to investigate the vaginal microbiome in Nellore cattle, heifers and cows, pregnant and non-pregnant, using a culture independent approach. The main bacterial phyla found were Firmicutes (~40–50%), Bacteroidetes (~15–25%) and Proteobacteria (~5–25%), in addition to ~10–20% of non-classified bacteria. 45–55% of the samples were represented by only ten OTUs: Aeribacillus, Bacteroides, Clostridium, Ruminococcus, Rikenella, Alistipes, Bacillus, Eubacterium, Prevotella and non-classified bacteria. Interestingly, microbiota from all 20 animals could be grouped according to the respiratory metabolism of the main OTUs found, creating three groups of vaginal microbiota in cattle. Archaeal samples were dominated by the Methanobrevibacter genus (Euryarchaeota, ~55–70%). Ascomycota was the main fungal phylum (~80–95%) and Mycosphaerella the most abundant genus (~70–85%). Hormonal influence was not clear, but a tendency for the reduction of bacterial and increase of archaeal populations in pregnant animals was observed. Eukaryotes did not vary significantly between pregnant and non-pregnant animals, but tended to be more abundant on cows than on heifers. The present work describes a great microbial variability in the vaginal community among the evaluated animals and groups (heifers and cows, pregnant and non-pregnant), which is significantly different from the findings previously reported using culture dependent methods, pointing out the need for further studies on this issue. The microbiome found also indicates that the vaginal colonization appears to be influenced by the gastrointestinal community.

The nasopharyngeal microbiota of feedlot cattle.

The bovine nasopharyngeal tract plays an important role in animal health and welfare by acting as a site for the carriage of pathogens causing bovine respiratory disease, a condition which results in significant morbidity and mortality in feedlot cattle. We characterized the bacterial nasopharyngeal microbiota in cattle at feedlot entry (day 0) and day 60 using 454 pyrosequencing. We also identified the most frequently isolated aerobic bacteria from nasopharyngeal swabs after plating onto three types of media. The cattle nasopharyngeal microbiota was composed primarily of Proteobacteria (68.9%) and Firmicutes (19.2%). At the genus-level, there was more inter-individual variability and a total of 55 genera were identified. The genera Pseudomonas (23.7%), Shewanella (23.5%), Acinetobacter (17.5%), and Carnobacterium (12.2%) were most prevalent at entry, while after 60 days in the feedlot, Staphylococcus (20.8%), Mycoplasma (14.9%), Mannheimia (10.4%), and Moraxella (9.4%) were dominant. The nasopharyngeal microbiota also became more homogenous after 60 days in the feedlot and differed in structure at day 0 and 60. Using culture-based methods, the most frequently isolated bacteria from nasopharyngeal swabs were Bacillus, Staphylococcus, Moraxella, Pasteurella, and Mannheimia. These results provide insight into the nasopharyngeal microbiota of cattle and demonstrate that specific changes take place during feedlot production.