Probiotic treatment vs empiric oral antibiotics for managing dysbiosis in short bowel syndrome: Impact on the mucosal and stool microbiota, short-chain fatty acids, and adaptation.

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Abstract

Infants and children with short bowel syndrome (SBS) are presumed to be at risk of gut microbial dysbiosis with potential sequelae of bacterial overgrowth that include sepsis, d-lactic acidosis, mucosal inflammation, and malabsorption. In neonatal piglets with SBS, we compared intestinal microbial composition, short-chain fatty acids (SCFAs), and adaptation given probiotic (PRO) treatment (Lactobacillus and Bifidobacterium spp) vs oral metronidazole (MET).

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DADA2: High resolution sample inference from Illumina amplicon data

Benjamin J. Callahan, Paul McMurdie, Michael Rosen … (2016)

We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.

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Proteobacteria: microbial signature of dysbiosis in gut microbiota.

Na-Ri Shin, Tae Whon, Jin-Woo Bae (2015)

Recent advances in sequencing techniques, applied to the study of microbial communities, have provided compelling evidence that the mammalian intestinal tract harbors a complex microbial community whose composition is a critical determinant of host health in the context of metabolism and inflammation. Given that an imbalanced gut microbiota often arises from a sustained increase in abundance of the phylum Proteobacteria, the natural human gut flora normally contains only a minor proportion of this phylum. Here, we review studies that explored the association between an abnormal expansion of Proteobacteria and a compromised ability to maintain a balanced gut microbial community. We also propose that an increased prevalence of Proteobacteria is a potential diagnostic signature of dysbiosis and risk of disease.