Publications

Below are some recent papers that have been published by BCMM members.

2020

A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria

JE Bisanz, P Soto-Perez, C Noecker, AA Aksenov, KN Lam, GE Kenney, EN Bess, HJ Haiser, TS Kyaw, FB Yu, VM Rekdal, CWY Ha, S Devkota, EP Balskus, PC Dorrestein, E Allen-Vercoe, PJ Turnbaugh. Cell Host and Microbe, 2020

 

Phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.

P.H. Bradley, K.S. Pollard. Bioinformatics, 2020

 

Viable bacterial colonization is highly limited in the human intestine in utero.

Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Nature Medicine, 2020
 

Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria.

Bess EN, Bisanz JE, Yarza F, Bustion A, Rich BE, Li X, Kitamura S, Waligurski E, Ang QY, Alba DL, Spanogiannopoulos P, Nayfach S, Koliwad SK, Wolan DW, Franke AA, Turnbaugh PJ. Nature Microbiology, 2020
 

2019

Toxin-Triggered Interleukin-1 Receptor Signaling Enables Early-Life Discrimination of Pathogenic versus Commensal Skin Bacteria.

Leech JM, Dhariwala MO, Lowe MM, Chu K, Merana GR, Cornuot C, Weckel A, Ma JM, Leitner EG, Gonzalez JR, Vasquez KS, Diep BA, Scharschmidt TC. Cell Host & Microbe, 2019
 

Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance.

Levan, S.R., Stamnes, K.A., Lin, D.L., Panzer A.R., Fukui E., McCauley K, Fujimura KE, McKean M, Ownby DR, Zoratti EM, Boushey HA, Cabana MD, Johnson CC, Lynch SV. Nature Microbiology, 2019

Population Genetics in the Human Microbiome

N.G. Garud and K.S. Pollard. Trends in Genetics, 2019
 

A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome

A. Almeida, S. Nayfach, M. Boland, F. Strozzi, M. Beracochea, Z.J. Shi, K.S. Pollard, D.H. Parks, P. Hugenholtz, N. Segata, N.C. Kyrpides, R.D. Finn. BioRxiv, 2019
 

Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

M. Roodgar, B.H. Good, N.R. Garud, S. Martis, M. Avula, W. Zhou, S. Lancaster, H. Lee, A. Babveyh, S. Nesamoney, K.S. Pollard, M.P. Snyder. BioRxiv, 2019
 

Cooking shapes the structure and function of the gut microbiome 

Carmody RN, Bisanz JE, Bowen BP, Maurice CF, Lyalina S, Louie KB, Treen D, Chadaideh KS, Maini Rekdal V, Bess EN, Spanogiannopoulos P, Ang QY, Bauer KC, Balon TW, Pollard KS, Northen TR, Turnbaugh PJ. Nature Microbiology, 2019
 

CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog 

Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ. Cell Host Microbe, 2019
 

Recirculating Intestinal IgA-Producing Cells Regulate Neuroinflammation via IL-10.

Rojas OL, Pröbstel AK, Porfilio EA, Wang AA, Charabati M, Sun T, Lee DSW, Galicia G, Ramaglia V, Ward LA, Leung LYT, Najafi G, Khaleghi K, Garcillán B, Li A, Besla R, Naouar I, Cao EY, Chiaranunt P, Burrows K, Robinson HG, Allanach JR, Yam J, Luck H, Campbell DJ, Allman D, Brooks DG, Tomura M, Baumann R, Zamvil SS, Bar-Or A, Horwitz MS, Winer DA, Mortha A, Mackay F, Prat A, Osborne LC, Robbins C, Baranzini SE, Gommerman JL. Cell, 2019