3.
Enterotypes in the landscape of gut microbial community composition.
Costea PI,
Hildebrand F,
Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F,
Sunagawa S, Wang J, Weinstock GM, Wu GD,
Zeller G, Zhao L,
Raes J, Knight R,
Bork P Nat Microbiol.
2018 Jan; 3(1): 8-16. PubMed:
29255284.
Abstract + PDF
Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
2.
Publisher Correction: Enterotypes in the landscape of gut microbial community composition.
Costea PI,
Hildebrand F,
Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F,
Sunagawa S, Wang J, Weinstock GM, Wu GD,
Zeller G, Zhao L,
Raes J, Knight R,
Bork P Nat Microbiol.
2018 Mar 13; 3(3): 388. PubMed:
29440750.
Abstract + PDF
In the version of this Perspective originally published, the first and last name of co-author Manimozhiyan Arumugam were switched. This has now been corrected in all versions of the Perspective.
1.
Recovery of gut microbiota of healthy adults following antibiotic exposure.
Palleja A, Mikkelsen KH,
Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT,
Coelho LP, Yang H, Wang J, Typas A, Nielsen MF, Nielsen HB,
Bork P, Wang J, Vilsbøll T, Hansen T, Knop FK,
Arumugam M, Pedersen O
Nat Microbiol.
2018 Nov 22; 3(11): 1255-1265. PubMed:
30349083.
Abstract + PDF
To minimize the impact of antibiotics, gut microorganisms harbour and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing-based metagenomics, we analysed the partial eradication and subsequent regrowth of the gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin. Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and the depletion of Bifidobacterium species and butyrate producers. The gut microbiota of the subjects recovered to near-baseline composition within 1.5 months, although 9 common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days. Species that harbour β-lactam resistance genes were positively selected for during and after the intervention. Harbouring glycopeptide or aminoglycoside resistance genes increased the odds of de novo colonization, however, the former also decreased the odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention and their antibiotics resistance gene carriage modulates their recovery processes.