Digestive Tract Microbiome Research Articles

The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.

Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae “clade I” strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills’ metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.

Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using Deep 16sRNA Pyrosequencing.

Effects of vertebrate-associated microbiota on physiology and health are of significant interest in current biological research. Most previous studies have focused on host-microbiota interactions in captive-bred mammalian models. These interactions and their outcomes are still relatively understudied, however, in wild populations and non-mammalian taxa. Using deep pyrosequencing, we described the cloacal microbiome (CM) composition in free living barn swallows Hirundo rustica, a long-distance migratory passerine bird. Barn swallow CM was dominated by bacteria of the Actinobacteria, Proteobacteria and Firmicutes phyla. Bacteroidetes, which represent an important proportion of the digestive tract microbiome in many vertebrate species, was relatively rare in barn swallow CM (< 5%). CM composition did not differ between males and females. A significant correlation of CM within breeding pair members is consistent with the hypothesis that cloacal contact during within-pair copulation may promote transfer of bacterial assemblages. This effect on CM composition had a relatively low effect size, however, possibly due to the species’ high level of sexual promiscuity.

Beta-diversity metrics of the upper digestive tract microbiome are associated with body mass index.

Studies of the fecal microbiome have implicated the gut microbiota in obesity, but few studies have examined the microbial diversity at other sites. The association between obesity and the upper gastrointestinal (UGI) microbial diversity was explored. The UGI microbiome of 659 healthy Chinese adults with a measured body mass index (BMI) range of 15.0 to 35.7 was characterized using the 16S rRNA gene DNA microarray (HOMIM). In multivariate-adjusted models, alpha diversity was not associated with BMI. However, beta diversity, assessed by principal coordinate vectors generated from an unweighted UniFrac distance matrix of pairwise comparisons, was associated with BMI (third and fourth vectors, P = 0.01 and P = 0.03, respectively). Moreover, beta diversity, assessed by cluster membership (three clusters), was also associated with BMI; individuals in the first cluster [median BMI 22.35, odds ratio (OR) = 0.48, 95% confidence interval (CI) = 0.05-4.34] and second cluster [median BMI 22.55, OR = 0.26, 95% CI = 0.09-0.75] were significantly less likely to be obese (BMI ≥ 27.5) than those in the third cluster (median BMI 23.59). A beta-diversity metric of the UGI microbiome is associated with a four fold difference in obesity risk in this Asian population. Future studies should address whether the UGI microbiome plays a causal role in obesity.

Alteration of digestive tract microbiome in neonatal Holstein bull calves by bacitracin methylene disalicylate treatment and scours1

The effects of bacitracin methylene disalicylate (BMD) and scours on the fecal microbiome, animal performance, and health were studied in Holstein bull calves. Holstein bull calves (n = 150) were obtained from a single source at 12 to 24 h of age. Bull calves were randomly assigned to 1 of 2 treatments including CON (no BMD; n = 75 calves) and BMD (n = 75 calves). Starting 3 d after arrival, BMD was added into milk replacer (0.5 g/feeding; twice daily) and fed to the calves for 10 consecutive d. No differences (P > 0.10) were observed in ADG for d 0 to 28 and d 0 to 56, DMI for d 0 to 28, d 29 to 56, and d 0 to 56, or G:F for d 0 to 28, d 29 to 56, and d 0 to 56; ADG for d 29 to 56 tended to increase (P < 0.10) for BMD-treated calves compared with controls. Fecal samples were collected from 15 scouring calves and 10 cohorts (nonscouring calves received on the same day and administered the same treatment as the scouring calves). Animal morbidity and fecal score did not vary between the 2 treatments. Mortality was not influenced by the treatments in the BMD administration period or throughout the experiment. Fecal samples were subjected to pyrotagged 454 FLX pyrosequencing of 16S rRNA gene amplicon to examine compositional dynamics of fecal microbes. Escherichia, Enterococcus, and Shigella had greater (P < 0.05) populations in the BMD group whereas Dorea, Roseburia, Fecalibacterium, Papillibacter, Collinsella, Eubacterium, Peptostreptococcus, and Prevotella were decreased (P < 0.05) by BMD treatment. Genus populations were also compared between scouring and nonscouring calves. Streptococcus was the only genus that had notable increase (P < 0.05) in fecal samples from scouring calves whereas populations of Bacteroides, Roseburia, and Eubacterium were markedly (P < 0.05) greater in nonscouring calves. These results show that BMD has the ability to alter the composition of the fecal microbiome but failed to improve performance in Holstein bull calves. Discrepancy of microorganism profiles between scouring and nonscouring calves might be associated with the occurrence of scours and bacterial genera identified might be potential target of treating diarrhea.

Abstract PR8: Beta-diversity metrics of the upper digestive tract microbiome are associated with body mass index.

Abstract Recent studies implicate the gut microbiome in the etiology of obesity. However, the contribution of the microbiome remains uncertain due to conflicting results. Previous studies have examined different populations and ages, but most have focused on the fecal microbiome, while few studies have examined the role of microbial diversity at other body sites. To explore the association between obesity and the microbial diversity of the upper digestive tract, we studied in cross-section a cohort of 659 healthy Chinese adults (ages 34 to 67 years) with a measured body mass index range of 15.0 to 35.7. We characterized the upper gastrointestinal tract microbiome using the HOMIM DNA microarray, which tests for the presence of approximately 300 species/strains of bacteria. We characterized alpha-diversity using taxa counts, and we created beta-diversity metrics using an unweighted unifrac distance matrix of pairwise comparisons of the whole cohort. We performed unsupervised clustering in this matrix and found support for three clusters, and we generated principal coordinate vectors from the matrix. Body mass index was examined as a continuous variable on the log scale in regression models adjusted for age, sex, tobacco smoking, alcohol drinking, antibiotic use, sample collection device, and the number of decayed, missing, and filled teeth. We found that alpha-diversity (numbers of strains, species, genera, families, orders, classes, or phyla) was not associated with body mass index. The presence or absence of each individual species/strain of bacteria on the HOMIM DNA microarray was not associated with body mass index after Bonferroni correction for multiple comparisons. However, beta-diversity, as assessed by cluster membership (first cluster compared with third cluster, p=0.0121; second cluster compared with third cluster, p=0.0002) and principal coordinate vectors, scaled to their interquartile ranges (p-values for the third and fourth vectors were p=0.0132 and p=0.0280, respectively), were associated with body mass index. Moreover, in adjusted models with multiple microbial diversity metrics, cluster membership remained independently associated with body mass index, while the vector associations were attenuated. Individuals in the first (median body mass index 22.35, interquartile range 19.17-23.31) and second (median body mass index 22.55, interquartile range 20.50-24.38) clusters had lower median body mass indexes that fall within the optimum Asian BMI range than the median body mass index in the third cluster (23.59, interquartile range 21.50-25.32), which is considered to fall in the range of increased risk for obesity-related diseases in Asian populations. Our results demonstrate for the first time that beta-diversity in the upper digestive tract microbiome is associated with body mass index. Future longitudinal, prospective studies should address whether the upper digestive tract microbiome plays a causal role for obesity. This proffered talk is also presented as Poster 56. Citation Format: Shih-Wen Lin, Neal D. Freedman, Jianxin Shi, Mitchell H. Gail, Guoqin Yu, Vanja Klepac-Ceraj, Bruce J. Paster, Bruce A. Dye, Wen-Qiang Wei, Jin-Hu Fan, You-Lin Qiao, Sanford M. Dawsey, Christian C. Abnet. Beta-diversity metrics of the upper digestive tract microbiome are associated with body mass index. [abstract]. In: Proceedings of the AACR Special Conference on Post-GWAS Horizons in Molecular Epidemiology: Digging Deeper into the Environment; 2012 Nov 11-14; Hollywood, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(11 Suppl):Abstract nr PR8.