Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health

Abstract

Parabacteroides distasonis is the type strain for the genus Parabacteroides, a group of gram-negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous species. First isolated in the 1930s from a clinical specimen as Bacteroides distasonis, the strain was re-classified to form the new genus Parabacteroides in 2006. Currently, the genus consists of 15 species, 10 of which are listed as 'validly named' (P. acidifaciens, P. chartae, P. chinchillae, P. chongii, P. distasonis, P. faecis, P. goldsteinii, P. gordonii, P. johnsonii, and P. merdae) and 5 'not validly named' (P. bouchesdurhonensis, P. massiliensis, P. pacaensis, P. provencensis, and P. timonensis) by the List of Prokaryotic names with Standing in Nomenclature. The Parabacteroides genus has been associated with reports of both beneficial and pathogenic effects in human health. Herein, we review the literature on the history, ecology, diseases, antimicrobial resistance, and genetics of this bacterium, illustrating the effects of P. distasonis on human and animal health.

Keywords: Crohn’s disease; Parabacteroides distasonis; antimicrobial activity; gut microbiota; inflammatory bowel disease.

Figure 1.

Correlation of PCR identification vs culture isolation from samples that were detected or undetected via qRT-PCR. Eleven Bacteroides and Parabacteroides species detected via qRT-PCR in 400 human surgical wound infection samples or closed abscesses. Target bacteria were detected from 31 samples (8%) via culture vs. 132 samples (33%) via qRT-PCR (p-value < 0.001). For each species, qRT-PCR detected higher counts than culture; this may reflect the detection of DNA of dead organisms by qRT-PCR. Plot created for this manuscript to illustrate the correlation between qRT-PCR and anerobic culture results for Bacteroides species isolated from wound samples using 132 isolates. a) y-axis corresponds to number of isolates detected by qRT-PCR; x-axis corresponds to number of isolates detected by both qRT-PCR and culture. b) y-axis corresponds to number of isolates detected by qRT-PCR; x-axis corresponds to number of isolates detected by culture. c) y-axis corresponds to number of isolates detected by qRT-PCR. Adapted from using data from Tong et al. with permission. Available from Anaerobe and used with permission from Elsevier

Figure 2.

Protein phylogram of 155 complete genomes of the Bacteroidetes phylum to illustrate the potential functional distinction of Parabacteroides distasonis from other species within the genus. The pipeline for genomic phylograms is described in detail based on information from PATRIC, the Pathosystems Resource Integration Center, https://docs.patricbrc.org. In short, the order-level pre-built trees in PATRIC are constructed by an automated pipeline that begins with amino acid sequence files for each genome. For each order-level tree the genomes from that order are used along with a small set of potential outgroup genomes. Branch values are not bootstrap values, which can be overly optimistic for long genomes. Instead, trees are built from random samples of 50% of the homology groups used for the main tree (gene-wise jackknifing). One hundred of these 50% gene-wise jackknife trees are made using FastTree, and the support values shown indicate the number of times a particular branch was observed in the support trees. As of January 12, 2021, there were 133 P. distasonis genomes available, of which 8 are complete (pie charts).