Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2020 Jun 9:11:906.
doi: 10.3389/fimmu.2020.00906. eCollection 2020.

The Genus Alistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health

Affiliations
Review

The Genus Alistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health

Bianca J Parker et al. Front Immunol. .

Abstract

Alistipes is a relatively new genus of bacteria isolated primarily from medical clinical samples, although at a low rate compared to other genus members of the Bacteroidetes phylum, which are highly relevant in dysbiosis and disease. According to the taxonomy database at The National Center for Biotechnology Information, the genus consists of 13 species: Alistipes finegoldii, Alistipes putredinis, Alistipes onderdonkii, Alistipes shahii, Alistipes indistinctus, Alistipes senegalensis, Alistipes timonensis, Alistipes obesi, Alistipes ihumii, Alistipes inops, Alistipes megaguti, Alistipes provencensis, and Alistipes massiliensis. Alistipes communis and A. dispar, and the subspecies A. Onderdonkii subspecies vulgaris (vs. onderdonkii subsp.) are the newest strains featured outside that list. Although typically isolated from the human gut microbiome various species of this genus have been isolated from patients suffering from appendicitis, and abdominal and rectal abscess. It is possible that as Alistipes spp. emerge, their identification in clinical samples may be underrepresented as novel MS-TOF methods may not be fully capable to discriminate distinct species as separate since it will require the upgrading of MS-TOF identification databases. In terms of pathogenicity, there is contrasting evidence indicating that Alistipes may have protective effects against some diseases, including liver fibrosis, colitis, cancer immunotherapy, and cardiovascular disease. In contrast, other studies indicate Alistipes is pathogenic in colorectal cancer and is associated with mental signs of depression. Gut dysbiosis seems to play a role in determining the compositional abundance of Alistipes in the feces (e.g., in non-alcoholic steatohepatitis, hepatic encephalopathy, and liver fibrosis). Since Alistipes is a relatively recent sub-branch genus of the Bacteroidetes phylum, and since Bacteroidetes are commonly associated with chronic intestinal inflammation, this narrative review illustrates emerging immunological and mechanistic implications by which Alistipes spp. correlate with human health.

Keywords: A. indistinctus; A. onderdonkii; A. putredinis; A. senegalensis; A. shahii; A. timonensis; Alistipes finegoldii; inflammatory bowel diseases.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Nucleotide and phylogram of 16S rRNA gene DNA sequences from thirteen strains described in the genus Alistipes. (A) Alsitipes megaguti complete 16S rRNA gene sequences derived from PATRIC complete genome illustrates slight differences between three gene copies contained within three operons in a single genome. Only the most divergent parts of the genes are shown. (B) Overview of complete alignment for the 13 strains. Notice the A. obesi insertion at around 1,100 bp position. (C) Detail of sequence insertion in the A. obesi starting at position 1,137 bp position. (D) Overview of the distance tree with 10,000 bootstrap branch values depicted if value >90%. Branching set at 60% threshold. Notice that differences may occur in part due to uneven partial gene sequences. Analysis conducted with CLC genomics viewer. Notice position of T. massiliensis vs. A. inops and A. putredinis.
Figure 2
Figure 2
Protein phylogram of 155 complete genomes of the Bacteroidetes phylum to illustrate the potential functional distinction of the genus Alistipes within the group. The pipeline for genomic phylograms is described in detail as follow by 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 May 19, 2020, there were 140 Alistipes genomes available (11287 unique contigs), of which 10 are complete.

References

    1. Goodrich JK, Davenport ER, Clark AG, Ley RE. The relationship between the human genome and microbiome comes into view. Annu Rev Genet. (2017) 51:413–33. 10.1146/annurev-genet-110711-155532 - DOI - PMC - PubMed
    1. Lynch SV, Pedersen O. The human intestinal microbiome in health and disease. N Engl J Med. (2016) 375:2369–79. 10.1056/NEJMra1600266 - DOI - PubMed
    1. Vivarelli S, Salemi R, Candido S, Falzone L, Santagati M, Stefani S, et al. . Gut microbiota and cancer: from pathogenesis to therapy. Cancers. (2019) 11:38. 10.3390/cancers11010038 - DOI - PMC - PubMed
    1. Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, et al. . Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol. (2017) 2:17004. 10.1038/nmicrobiol.2017.4 - DOI - PMC - PubMed
    1. Yoshida N, Yamashita T, Hirata KI. Gut microbiome and cardiovascular diseases. Diseases. (2018) 6:56. 10.3390/diseases6030056 - DOI - PMC - PubMed

Publication types

LinkOut - more resources