Dataset Information

Comparative Analyses of the Digestive Tract Microbiota of New Guinean Passerine Birds.

ABSTRACT: The digestive tract microbiota (DTM) plays a plethora of functions that enable hosts to exploit novel niches. However, our understanding of the DTM of birds, particularly passerines, and the turnover of microbial communities along the digestive tract are limited. To better understand how passerine DTMs are assembled, and how the composition changes along the digestive tract, we investigated the DTM of seven different compartments along the digestive tract of nine New Guinean passerine bird species using Illumina MiSeq sequencing of the V4 region of the 16S rRNA. Overall, passerine DTMs were dominated by the phyla Firmicutes and Proteobacteria. We found bird species-specific DTM assemblages and the DTM of different compartments from the same species tended to cluster together. We also found a notable relationship between gut community similarity and feeding guilds (insectivores vs. omnivores). The dominant bacterial genera tended to differ between insectivores and omnivores, with insectivores mainly having lactic acid bacteria that may contribute to the breakdown of carbohydrates. Omnivorous DTMs were more diverse than insectivores and dominated by the bacterial phyla Proteobacteria and Tenericutes. These bacteria may contribute to nitrogen metabolism, and the diverse omnivorous DTMs may allow for more flexibility with varying food availability as these species have wider feeding niches. In well-sampled omnivorous species, the dominant bacterial genera changed along the digestive tracts, which was less prominent for insectivores. In conclusion, the DTMs of New Guinean passerines seem to be species specific and, at least in part, be shaped by bird diet. The sampling of DTM along the digestive tract improved capturing of a more complete set of members, with implications for our understanding of the interactions between symbiont and gut compartment functions.

SUBMITTER: Bodawatta KH

PROVIDER: S-EPMC6097311 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Comparative Analyses of the Digestive Tract Microbiota of New Guinean Passerine Birds.

Bodawatta Kasun H KH Sam Katerina K Jønsson Knud A KA Poulsen Michael M

Frontiers in microbiology 20180810

The digestive tract microbiota (DTM) plays a plethora of functions that enable hosts to exploit novel niches. However, our understanding of the DTM of birds, particularly passerines, and the turnover of microbial communities along the digestive tract are limited. To better understand how passerine DTMs are assembled, and how the composition changes along the digestive tract, we investigated the DTM of seven different compartments along the digestive tract of nine New Guinean passerine bird speci ...[more]

PMID: 30147680

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Project description:BackgroundThe gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed "selective decontamination of the digestive tract" (SDD), is used in some countries where it improves clinical outcome in ICU patients. Yet, the impact of ICU hospitalization and SDD on the gut microbiota remains largely unknown. Here, we characterize the composition of the gut microbiota and its antimicrobial resistance genes ("the resistome") of ICU patients during SDD and of healthy subjects.ResultsFrom ten patients that were acutely admitted to the ICU, 30 fecal samples were collected during ICU stay. Additionally, feces were collected from five of these patients after transfer to a medium-care ward and cessation of SDD. Feces from ten healthy subjects were collected twice, with a 1-year interval. Gut microbiota and resistome composition were determined using 16S rRNA gene phylogenetic profiling and nanolitre-scale quantitative PCRs. The microbiota of the ICU patients differed from the microbiota of healthy subjects and was characterized by lower microbial diversity, decreased levels of Escherichia coli and of anaerobic Gram-positive, butyrate-producing bacteria of the Clostridium clusters IV and XIVa, and an increased abundance of Bacteroidetes and enterococci. Four resistance genes (aac(6')-Ii, ermC, qacA, tetQ), providing resistance to aminoglycosides, macrolides, disinfectants, and tetracyclines, respectively, were significantly more abundant among ICU patients than in healthy subjects, while a chloramphenicol resistance gene (catA) and a tetracycline resistance gene (tetW) were more abundant in healthy subjects.ConclusionsThe gut microbiota of SDD-treated ICU patients deviated strongly from the gut microbiota of healthy subjects. The negative effects on the resistome were limited to selection for four resistance genes. While it was not possible to disentangle the effects of SDD from confounding variables in the patient cohort, our data suggest that the risks associated with ICU hospitalization and SDD on selection for antibiotic resistance are limited. However, we found evidence indicating that recolonization of the gut by antibiotic-resistant bacteria may occur upon ICU discharge and cessation of SDD.

Dataset Information

Comparative Analyses of the Digestive Tract Microbiota of New Guinean Passerine Birds.

Publications

Comparative Analyses of the Digestive Tract Microbiota of New Guinean Passerine Birds.

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