scholarly journals Effect of hay type on cecal and fecal microbiome and fermentation parameters in horses

2020 ◽  
Author(s):  
Rachel J Sorensen ◽  
James S Drouillard ◽  
Teresa L Douthit ◽  
Qinghong Ran ◽  
Douglas G Marthaler ◽  
...  
Keyword(s):  
Fixed Effects ◽  
Volatile Fatty Acids ◽  
Random Effect ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Fecal Microbiome ◽  
Β Diversity ◽  
Fermentation Parameters

Abstract The effect of hay type on the microbiome of the equine gastrointestinal tract is relatively unexplored. Our objective was to characterize the cecal and fecal microbiome of mature horses consuming alfalfa or Smooth Bromegrass (brome) hay. Six cecally cannulated horses were used in a split plot design run as a crossover in 2 periods. Whole plot treatment was ad libitum access to brome or alfalfa hay fed over two 21-d acclimation periods with subplots of sampling location (cecum and rectum) and sampling hour. Each acclimation period was followed by a 24-h collection period where cecal and fecal samples were collected every 3 h for analysis of pH and volatile fatty acids (VFA). Fecal and cecal samples were pooled and sent to a commercial lab (MR DNA, Shallowater, TX) for amplification of the V4 region of the 16S rRNA gene and sequenced using Illumina HiSeq. Main effects of hay on VFA, pH, and taxonomic abundances were analyzed using the MIXED procedure of SAS 9.4 with fixed effects of hay, hour, location, period, all possible interactions and random effect of horse. Alpha and β diversity were analyzed using the R Dame package. Horses fed alfalfa had greater fecal than cecal pH (P ≤ 0.05) whereas horses fed brome had greater cecal than fecal pH (P ≤ 0.05). Regardless of hay type, total volatile fatty acid (VFA) concentrations were greater (P ≤ 0.05) in the cecum than in feces, and alfalfa resulted in greater (P ≤ 0.05) VFA concentrations than brome in both sampling locations. Alpha diversity was greater (P ≤ 0.05) in fecal compared to cecal samples. Microbial community structure within each sampling location and hay type differed from one another (P ≤ 0.05). Bacteroidetes were greater (P ≤ 0.05) in the cecum compared to the rectum, regardless of hay type. Firmicutes and Firmicutes:Bacteroidetes were greater (P ≤ 0.05) in the feces compared to cecal samples of alfalfa-fed horses. In all, fermentation parameters and bacterial abundances were impacted by hay type and sampling location in the hindgut.

PSV-B-18 Characterization of the fecal microbiome of healthy adult beagle dogs supplemented with graded levels of bacillus coagulans GBI-30, 6086

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 337-338
Author(s):  
Heather L Acuff ◽  
Tara N Gaire ◽  
Tyler Doerksen ◽  
Andrea Lu ◽  
Michael P Hays ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Fixed Effects ◽  
Mixed Model ◽  
Healthy Adult ◽  
Random Effect ◽  
Bacillus Coagulans ◽  
Community Diversity ◽  
Rrna Gene ◽  
Beagle Dogs ◽  
Fecal Microbiome

Abstract This study aimed to evaluate the effect of Bacillus coagulans GBI-30, 6086 on the fecal microbiome of healthy adult dogs. Extruded diets containing graded levels of probiotic applied either to the base ration before extrusion or as a topical coating post-extrusion were randomly assigned to ten individually-housed Beagle dogs (7 castrated males, 3 spayed females) of similar age (5.75 ± 0.23 yr) and body weight (12.3 ± 1.5 kg) in a 5 x 5 replicated Latin square with 16-d adaptation and 5-d total fecal collection for each period. Five dietary treatments were formulated to deliver a dose of 0-, 6-, 7-, 8-, or 9-log10 CFU·dog-1·d-1. Fresh fecal samples (n=50) were analyzed by 16S rRNA gene pyrosequencing. Community diversity was evaluated in R (v4.0.3, R Core Team, 2019). Relative abundance data were analyzed using a mixed model (v9.4, SAS Institute, Inc., Cary, NC) with treatment and period as fixed effects and dog as a random effect. Results were considered significant at P < 0.05. Predominant phyla were Firmicutes (mean 81.2% ± 5), Actinobacteria (mean 9.9% ± 4.4), Bacteroidetes (mean 4.5% ± 1.7), Proteobacteria (mean 1.3% ± 0.7), and Fusobacteria (mean 1.1% ± 0.6). No evidence of shifts in predominant phyla, class, family, or genus taxonomic levels were observed except for the Bacillus genus, which had a greater relative abundance (P = 0.0189) in the low probiotic coating and high probiotic coating treatment groups compared to the extruded probiotic group. Alpha-diversity indices (Richness, Chao1, ACE, Shannon, Simpson, Inverse Simpson, and Fisher) and beta-diversity metrics (principal coordinate analysis and multi-dimensional scaling) were similar for all treatments. This data indicates that supplementation with Bacillus coagulans GBI-30, 6086 at a dose of up to 9 log10 CFU·d-1 did not alter the overall diversity of the fecal microbiome of healthy adult dogs over a 21-d period.

scholarly journals PSI-34 The Impact of Varying Protein Sources on Feedlot Goat Fecal Microbiome

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 256-256
Author(s):  
Allianna Mitchell ◽  
Cassandra K Jones
Keyword(s):  
Soybean Meal ◽  
Pcr Amplification ◽  
Alpha Diversity ◽  
Protein Source ◽  
Illumina Hiseq ◽  
Fecal Microbiome ◽  
Protein Sources ◽  
Β Diversity ◽  
Α Diversity ◽  
The Impact

Abstract The effect of protein sources with different RUP values on feedlot goat fecal microbiome has not been studied. This experiment evaluated the impact of varying protein sources on feedlot goat fecal microbiome. Fourty-five Boer-influenced goats (23.53 kg ± 1.07; approximately 75 d of age) were blocked by body weight and randomly allocated to 1 of 3 treatment diets (15 goats/treatment) with ad libitum feed and water for 42 d. Diets were formulated to be isocaloric and isonitrogenous, with varying primary protein source: 1) 18.7% solvent-extracted soybean meal (SBM), 2) 22.0% expelled soybean meal (SoyPlus), or 3) 34.4% distillers’ dried grains with solubles (DDGS). On d 42, fecal pellets were collected from each goat and stored at -80°C until microbiome sequencing. Samples underwent PCR amplification of the V4 region of the 16S gene and sequencing on Illumina HiSeq 2500 (Illumina Inc., San Diego, CA) by a commercial lab (MR DNA, Shallowater, TX). Data were analyzed using the GLIMMIX procedure of SAS with Turkey’s test for post hoc comparisons. Beta and alpha diversity were analyzed using Qiime with Kruskal-Wallis pairwise comparisons and ANOSIM. Genera, with individual abundance greater than 1%, that were higher (P ≤ 0.05) in SBM-fed goats compared to goats fed DDGS and SoyPlus include Clostridium, Paludibacter, Tannerella, and Methanobrevibacter. At the phylum level, Bacteroidetes was greater in SBM-fed goats compared to DDGS-fed goats (P = 0.04) and Euryarchaeota was more abundant in goats fed SBM compared to DDGS (P = 0.003) and SoyPlus (P = 0.0001). Protein source did not affect β-diversity (r ≈ 0) or α-diversity (P > 0.10). In summary, altering protein source in finishing goat diets created shifts in some phyla and genera, however the diversity within and between microbial communities across treatments were uninfluenced.

scholarly journals 89 Effects of Saccharomyces cerevisiae fermentation product on fecal microbiota populations of dogs subjected to exercise challenge

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 63-63
Author(s):  
Patrícia M Oba ◽  
Meredith Carroll ◽  
Tammi Epp ◽  
Christine Warzecha ◽  
Jessica L Varney ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Fixed Effects ◽  
Immune Cell ◽  
Random Effect ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Exercise Challenge ◽  
Fermentation Product ◽  
Relative Abundances ◽  
Saccharomyces Cerevisiae Fermentation Product

Abstract Previously, a Saccharomyces cerevisiae fermentation product (SCFP) was demonstrated to positively alter fecal microbiota, fecal metabolites, and circulating immune cell functionality in adult dogs. The objective of this study was to determine the fecal characteristics, microbiota, and metabolites of trained dogs subjected to an exercise challenge. All procedures were approved by the Four Rivers Kennel IACUC prior to experimentation. Thirty-six adult dogs (mean age: 7.1 y; mean BCS: 4.9) were used. Dogs were randomly assigned to control or SCFP-supplemented (250 mg/d) diets, trained, and fed for a few mo prior to exercise challenge. Fresh fecal samples were collected for the measurement of fecal characteristics, microbiota, and metabolites before and after an exercise challenge (10 mile run). Fecal microbiota data were evaluated using QIIME2. All other data were analyzed using the Mixed Models procedure of SAS, with treatment and exercise as fixed effects, dog as random effect, and P < 0.05 considered significant. For both treatments, fecal scores and butyrate and propionate concentrations were lower and fecal pH and ammonia, isobutyrate, isovalerate, and total BCFA concentrations were higher after exercise challenge. SCFP did not affect fecal scores, pH, dry matter, or fermentative end-product concentrations after exercise challenge. Alpha-diversity or beta-diversity (unweighted PCoA plot) were not affected by SCFP before or after exercise challenge. The weighted PCoA plot, however, showed clustering of dogs before exercise and after exercise, regardless of treatment. Fecal Collinsella, Slackia, Turicibacter, Blautia, Dorea, Ruminococcus, Faecalibacterium, Catenibacterium, Clostridium (Erysipelotrichaceae family), and Eubacterium relative abundances were higher, while fecal Bacteroides, Parabacteroides, Prevotella (Prevotellaceae family), Phascolarctobacterium, Fusobacterium, Suttella and Anaerobiospirillum relative abundances were lower after exercise challenge. SCFP increased fecal Lactobacillus compared to controls. Our data demonstrate that exercise and SCFP alter fecal microbiota in dogs. Higher SCFP dosages may provide greater changes and may be of interest in future studies.

scholarly journals 2576. The Microbiome of Recurrent Bacterial Vaginosis Compared with Asymptomatic Controls

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S895-S895
Author(s):  
Elizabeth O Shay ◽  
Oluwatosin Goje ◽  
Roshan Padmanabhan ◽  
Charis Eng
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Vaginosis ◽  
Alpha Diversity ◽  
Dna Probe ◽  
Gardnerella Vaginalis ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Β Diversity ◽  
Probe Test

Abstract Background Bacterial vaginosis (BV) affects nearly 1 in 3 women in the United States and is poorly understood. The study of the vaginal microbiome, using 16S rRNA-gene amplicon sequencing, has increased our knowledge of BV. We aimed to characterize the vaginal microbiome of women with recurrent BV firstly in comparison to controls, and secondly in comparison to a sub-population of our asymptomatic controls, positive for Gardnerella vaginalis via a vaginal pathogens DNA direct probe test (DNA probe). Methods Women aged 18–40 years, with recurrent BV, and asymptomatic controls were prospectively enrolled. Vaginal samples were collected from each participant. DNA was extracted, amplified using primers targeting the V3-V4 variable region of the 16S rRNA-gene, and then sequenced and processed through a hybrid Qiime MICCA bioinformatics pipeline. We also tested for G. vaginalis using the DNA probe. Results Seventeen recurrent BV patients and 46 controls were enrolled. Β diversity (P = 0.045), but not alpha diversity (P = 0.076) differed between groups. The genera Gardnerella and Prevotella were relatively more abundant, while Lactobacillus was relatively less abundant in recurrent BV vs. control groups. Of the patients for whom results of the DNA probe for Gardnerella vaginalis were available, 11 (69%) recurrent BV patients and 14 (35%) controls were positive. Control patients, negative by the DNA probe test, showed decreased alpha diversity (P = 0.0001) and significantly different β diversity (P = 0.001) compared with recurrent BV patients. Neither alpha (P = 0.31) nor β (P = 0.096) diversity differed between recurrent BV patients and controls that were G. vaginalis positive. Conclusion The microbiome of recurrent BV patients is distinct from that of asymptomatic controls; recurrent BV patients exhibit different β diversity, less Lactobacillus and more Gardnerella and Prevotella. Asymptomatic Gardnerella vaginalis-colonized controls demonstrate similar microbiome profiles to those of recurrent BV patients. These findings suggest that individual factors may influence whether or not a patient with a BV microbiomic profile experiences symptoms. Further investigation into these mechanisms could yield insights into the treatment of recurrent BV. Disclosures All authors: No reported disclosures.

scholarly journals Response of Root-Associated Bacterial Communities to Different Degrees of Soft Rot Damage in Amorphophallus konjac Under a Robinia pseudoacacia Plantation

2021 ◽  
Vol 12 ◽  
Author(s):  
Fei He
Keyword(s):  
Community Composition ◽  
Bacterial Communities ◽  
Disease Incidence ◽  
Robinia Pseudoacacia ◽  
Alpha Diversity ◽  
Soft Rot ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Amorphophallus Konjac ◽  
Damage Degree

Bacterial soft rot is a destructive disease that restricts the development of the konjac (Amorphophallus konjac K. Koch ex N.E.Br) industry. The objective of this study was to investigate how soft rot disease affects bacterial communities associated with the roots of konjac plants growing under a pure Robinia pseudoacacia plantation. Three sampling sites affected by different degrees of soft rot damage were selected based on the disease incidence [0%, non-diseased (ND); 4.2%, moderately diseased (MD); and 18.6%, highly diseased (HD)]. The variation in soil and root bacterial diversity and community composition among the sampling sites was determined by Illumina HiSeq sequencing of the V3–V4 hypervariable regions of the bacterial 16S rRNA gene. The results showed that the contents of soil organic matter and available nutrients (N, P, and K) increased with increasing damage degree, whereas higher damage degree resulted in lower soil pH and enzymatic activity (sucrase, urease, catalase, and polyphenol oxidase). The composition of root-associated bacterial communities differed among the three sampling sites. Proteobacteria was the most dominant bacterial phylum in all soil and root samples. Pseudomonas, Bacillus, Rhizobium, and Streptomyces were the most abundant in all samples from the ND sites, whereas Pectobacterium carotovorum and Serratia were predominant in the samples from the MD and HD sites. The abundance and alpha diversity of root-associated bacteria were significantly higher (p < 0.05) in the ND sites than in the diseased sites. The results suggested pronounced differences in the abundance, alpha diversity, and community composition of bacteria associated with the roots of konjac plants affected by different degrees of soft rot damage. Such differences in bacterial community structure were related to dynamic changes in soil variables, especially soil available potassium content, sucrase activity, and urease activity. Analysis of the dominant root-associated bacterial taxa offers an approach to predict the damage degree due to soft rot in konjac and provides evidence for the prevention of this soil-borne disease via microecological regulation.

scholarly journals Cecal versus fecal microbiota in Ossabaw swine and implications for obesity

2018 ◽  
Vol 50 (5) ◽  
pp. 355-368 ◽  
Author(s):  
Matthew R. Panasevich ◽  
Umesh D. Wankhade ◽  
Sree V. Chintapalli ◽  
Kartik Shankar ◽  
R. Scott Rector
Keyword(s):  
Control Diet ◽  
Critical Role ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Metabolic Capacity ◽  
Fecal Samples ◽  
Fecal Microbiome ◽  
The Metabolic Syndrome ◽  
High Fructose

The gut microbiome plays a critical role in the onset and progression of obesity and the metabolic syndrome. However, it is not well documented whether the cecal vs. the fecal microbiome is more relevant when assessing their contributions to these diseases. Here, we amplified the V4 region of the 16S rRNA gene from cecal and fecal samples of female Ossabaw swine fed a low-fat control diet (10.5% fat, n = 4) or Western diet (43.0% fat, 17.8% high fructose corn syrup, 2% cholesterol; n = 3) for 36 wk. Obesity significantly lowered alpha-diversity ( P < 0.05), and there was clear separation in beta-diversity between lean and obese pigs, as well as between cecal and fecal samples ( P < 0.05). Obesity dramatically increased ( P < 0.05) the Firmicutes:Bacteroidetes ratio in fecal samples, and Actinobacteria was higher ( P < 0.05) in fecal vs. cecal samples in obese pigs. Cyanobacteria, Proteobacteria, and Fusobacteria were increased ( P < 0.05), while Spirochaetes, Tenericutes, and Verrucomicrobia were decreased ( P < 0.05) in obese vs. lean pigs. Prevotellaceae was reduced ( P < 0.05) in obese fecal vs. cecal samples. Moreover, cecal samples in obese had greater ( P < 0.05) predicted metabolic capacity for glycan biosynthesis and metabolism and LPS biosynthesis compared with fecal. Obese pigs also had greater ( P < 0.05) capacity for carbohydrate metabolism, which was driven by obese fecal rather than cecal samples and was opposite in lean pigs ( P < 0.05). The observed differences in pro-inflammatory microbiota and their metabolic capacity in cecal vs. fecal samples of obese pigs provide new insight into evaluating the microbiome in the pathogenesis of obesity and metabolic disease.

scholarly journals Topography of the respiratory tract bacterial microbiota in cattle

2020 ◽  
Author(s):  
Christopher McMullen ◽  
Trevor W. Alexander ◽  
Renaud Léguillette ◽  
Matthew Workentine ◽  
Edouard Timsit
Keyword(s):  
Respiratory Tract ◽  
Pathogenic Bacteria ◽  
Primary Source ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Bacterial Microbiota ◽  
Sampling Locations

Abstract Background Bacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. While the bacterial composition of the bovine upper respiratory tract (URT) has not been studied in detail, 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 URT niches may contribute the most to the composition of the lung microbiota. Methods Seventeen 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. Results Microbiota composition differed across sampling locations, with physiologically and anatomically distinct locations showing different relative abundances of 1,137 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. Conclusions The nasopharyngeal bacterial microbiota is most similar to the lung bacterial microbiota and therefore may serve as the primary source of bacteria to the lung. This finding confirms that the nasopharyngeal microbiota should be the focus of research as it relates to the role of the URT microbiota in BP. As well, this microbiota should be the main target for future interventions and pharmaceuticals aimed at controlling and preventing BP.

scholarly journals Gut Microbiome Composition and Metabolomic Profiles of Wild and Captive Chinese Monals (Lophophorus Lhuysii)

2020 ◽  
Author(s):  
Dandan Jiang ◽  
Xin He ◽  
Marc Valitutto ◽  
Li Chen ◽  
Qin Xu ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Bacterial Species ◽  
Bird Species ◽  
Alpha Diversity ◽  
Integrated Approach ◽  
Rrna Gene ◽  
Metabolomic Profile ◽  
Liquid Chromatograph ◽  
Fecal Microbiome ◽  
Microbiome Composition

Abstract Background：The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains of southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolomics of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal rRNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatograph (UHPLC) based metabolomics were used to examine the fecal microbiome composition and the metabolomic profile of Chinese monals. Results: The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial species in the two groups showed remarkable differences at all levels. Metabolomic profiling revealed a concurrent difference, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, these metabolites in difference are have a strong correlation with the main microbe in genus level.Conclusions: Various factors related to diet and environmental conditions played a crucial role in shaping the gut microbiome composition and metabolomic profile. Through this study, we have established a baseline for a normal gut microbiome and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive specimens has an impact on their overall health and reproduction.

scholarly journals PSVIII-10 Effects of Folia Betulae and Méntha piperíta extracts on microbiological and enzymatic characteristics of cattle rumen

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 257-258
Author(s):  
Ajna Makaeva ◽  
Kseniya Atlanderova ◽  
Galimzhan Duskaev ◽  
Baer Nurzhanov ◽  
Albert Rysaev
Keyword(s):  
Volatile Fatty Acids ◽  
16S Rrna Gene Sequencing ◽  
Barley Grain ◽  
Mentha Piperita ◽  
Rrna Gene ◽  
Methane Formation ◽  
Dry Matter Digestibility ◽  
Medicinal Substances ◽  
Rrna Gene Sequencing ◽  
Fermentation Parameters

Abstract Refusal of antibiotics and a decrease in the greenhouse effect allows active study of the effectiveness of medicinal plants in order to increase the productivity of cattle. The aim of this study was to evaluate the effect of Folia Betulae (FB) and Méntha piperíta (MP) extracts (0.5 ml/kg body weight) on rumenal microbiota and fermentation characteristics against the background of control (C). They were added separately as a substrate to the diets of bulls with rumen fistula (dairy breed, 12-month, diet - 60% hay, 40% barley grain within 10 days). Fermentation parameters (CH4, volatile fatty acids, grain dry matter digestibility (DM) were analyzed daily, and microbiota of archaea and bacteria were analyzed using highly efficient 16S rRNA gene sequencing. FB and MP were prepared by grinding, extraction in a water bath (30 min, 70°C) and filtration. The results of this study showed that the formation of propionate and digestibility of DM did not differ compared to C. Methanobacteria in MP had lower values (P ≤ 0.05) compared with FB and C (less than CH4). Bacterial communities differed: Bacteroidetes predominated more in MP (P ≤ 0.05) and further in FB (P ≤ 0.05) compared with C. At the family level, Prevotellaceae dominated in MP (P ≤ 0.05), Bacteroidales in FB (P ≤ 0.05)) and Porphyromonadaceae in MP and FB (P ≤ 0.05). Firmicutes had lower values (P ≤ 0.05) in all cases compared to C, Clostridia class was lower by 6.0–8.4% (P ≤ 0.05) (due to Clostridiales and Lachnospiraceae families). This study emphasizes the potential use of herbal medicinal substances as a natural feed supplement, which can play a role in reducing methane formation and the development of gram-positive bacteria, without adverse effect to ruminal microbiota. This research was performed with financial support from the RSF (16-16-10048) and project 0761-2019-0005.

scholarly journals Topography of the respiratory tract bacterial microbiota in cattle

2020 ◽  
Author(s):  
Christopher McMullen ◽  
Trevor W. Alexander ◽  
Renaud Léguillette ◽  
Matthew Workentine ◽  
Edouard Timsit
Keyword(s):  
Respiratory Tract ◽  
Pathogenic Bacteria ◽  
Primary Source ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Bacterial Microbiota ◽  
Sampling Locations ◽  
Healthy Cattle

Abstract Background Bacterial 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. Methods Seventeen 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. Results Microbiota composition differed across sampling locations, with physiologically and anatomically distinct locations showing different relative abundances of 1,137 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. Conclusions The 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.

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