Below are some recent papers that have been published by our community (BCMM members shown in bold). View a complete list of all publications by BCMM members on Dimensions.
2022
Sustained effect of LACTIN-V (Lactobacillus crispatus CTV-05) on genital immunology following standard bacterial vaginosis treatment: results from a randomised, placebo-controlled trial
Eric Armstrong, Anke Hemmerling, Steve Miller, Kerianne E Burke, Sara J Newmann, Sheldon R Morris, Hilary Reno, Sanja Huibner, Maria Kulikova, Nico Nagelkerke, Bryan Coburn, Craig R Cohen, and Rupert Kaul. Lancet Microbe. April 21, 2022.
Microbial signals, MyD88, and lymphotoxin drive TNF-independent intestinal epithelial tissue damage
Iulia Rusu, Elvira Mennillo, Jared L. Bain, Zhongmei Li, Xiaofei Sun, Kimberly M. Ly, Yenny Y. Rosli, Mohammad Naser, Zunqiu Wang, Rommel Advincula, Philip Achacoso, Ling Shao, Bahram Razani, Ophir D. Klein, Alexander Marson, Jessie A. Turnbaugh, Peter J. Turnbaugh, Barbara A. Malynn, Averil Ma, and Michael G. Kattah. J Clin Invest. 2022;132(5):e154993.
MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome‐metabolome data
Cecilia Noecker, Alexander Eng, Efrat Muller, Elhanan Borenstein. Bioinformatics, January 06, 2022.
DART takes aim at community editing
Connie W. Y. Ha & Suzanne Devkota, Nature Microbiology, 2022; volume 7, pages 8–9.
2021
Moraxella-dominated pediatric nasopharyngeal microbiota associate with upper respiratory infection and sinusitis
Kathryn E. McCauley, Gregory DeMuri, Kole Lynch, Douglas W. Fadrosh, Clark Santee, Nabeetha N. Nagalingam, Ellen R, Wald, Susan V. Lynch. PLOS One, December 28, 2021.
The impact of environmental mycobiomes on geographic variation in COVID-19 mortality
Joshua Ladau, Katrina Abuabara, Angelica M. Walker, Marcin P. Joachimiak, Ishan Bansal, Yulun Wu, Elijah B. Hoffman, Chaincy Kuo, Nicola Falco, Jared Streich, Mark J. van der Laan, Haruko M. Wainwright, Eoin L. Brodie, Matthias Hess, Daniel Jacobson, and James B. Brown. MedRXiv (preprint), December 26, 2021.
Fast and accurate metagenotyping of the human gut microbiome with GT-Pro
Zhou Jason Shi, Boris Dimitrov, Chunyu Zhao, Stephen Nayfach & Katherine S. Pollard. Nature Biotechnology, December 23, 2021.
Periodontal Disease: The Good, The Bad, and The Unknown
Lea M. Sedghi, Margot Bacino and Yvonne Lorraine Kapila.. Front. Cell. Infect. Microbiol., 07 December 2021.
The oralome and its dysbiosis: New insights into oral microbiome-host interactions
Allan Radaic, Yvonne L.Kapila. Computational and Structural Biotechnology Journal, Volume 19, 2021, Pages 1335-1360.
Baby’s skin bacteria: first impressions are long-lasting
Miqdad O.Dhariwala, Tiffany C.Scharschmidt, Trends in Immunology, Volume 42, Issue 12, December 2021, Pages 1088-1099.
Human gut bacterial metabolism drives Th17 activation and colitis
Margaret Alexander, Qi Yan Ang, Renuka R.Nayak, Annamarie E.Bustion, Moriah Sandy, Bing Zhang, Vaibhav Upadhyay, Katherine S.Pollard, Susan V. Lynch, Peter J.Turnbaugh. Cell Host & Microbe, November 24, 2021.
Black In Immuno: harnessing social media and digital platforms to connect the dots
Joel Babdor, Amy C. Fan, Madina Wane, Berenice Mbiribindi, Alexis S. Mobley, Justine C. Noel & Elaine Kouame. Nature Reviews Immunology, 2021; Volume 21, pages 756–757.
Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome
Kathy N. Lam, Peter Spanogiannopoulos, Paola Soto-Perez, Allison M. Weakley, Feiqiao B. Yu, Peter J. Turnbaugh. Cell Reports, November 2, 2021; Volume 37, Issue 5, 109930.
The oral microbiome: Role of key organisms and complex networks in oral health and disease
Lea Sedghi, Vincent DiMassa, Anthony Harrington, Susan V. Lynch, Yvonne L. Kapila. Periodontology 2000, October 2021; Volume 87, Issue 1: 107-131.
Maternal gut microbiome regulates immunity to RSV infection in offspring
Wendy Fonseca, Carrie-Anne Malinczak, Kei Fujimura, Danny Li, Kathryn McCauley, Jia L , Shannon K.K. Best, Diana Zhu, Andrew J. Rasky, Christine C. Johnson, Jennifer Bermick, Edward M. Zoratti, Dennis Ownby, Susan V. Lynch, Nicholas W. Lukacs, Catherine Ptaschinski. J Exp Med, 2021; 218 (11): e20210235.
Lung immune tone via gut-lung axis: gut-derived LPS and short-chain fatty acids’ immunometabolic regulation of lung IL-1β, FFAR2, and FFAR3 expression
Qing Liu, Xiaoli Tian, Daisuke Maruyama, Mehrdad Arjomandi, and Arun Prakash. Am J Physiol Lung Cell Mol Physiol, 2021; 321: L65–L78.
Caloric restriction disrupts the microbiota and colonization resistance
Reiner Jumpertz von Schwartzenberg, Jordan E. Bisanz, Svetlana Lyalina, Peter Spanogiannopoulos, Qi Yan Ang, Jingwei Cai, Sophia Dickmann, Marie Friedrich, Su-Yang Liu, Stephanie L. Collins, Danielle Ingebrigtsen, Steve Miller, Jessie A. Turnbaugh, Andrew D. Patterson, Katherine S. Pollard, Knut Mai, Joachim Spranger & Peter J. Turnbaugh. Nature, 2021; volume 595, pages 272–277
Intestinal changes associated with fluoride exposure in rats: Integrative morphological, proteomic and microbiome analyses
Aline Dionizio, Dawud Abduweli Uyghurturk, Carina Guimarães Souza Melo, Isabela Tomazini Sabino-Arias, Tamara Teodoro Araujo, Talita Mendes Silva Ventura, Juliana Vanessa Colombo Martins Perles, Jacqueline Nelisis Zanoni, Pamela Den Besten, Marília Afonso Rabelo Buzalaf. Chemosphere, 2021.
Hair of the mouse: A skin bacteria “cocktail” gets follicles back on their feet
Jeanmarie R. Gonzalez, Geil R. Merana, Tiffany C. Scharschmidt. Cell Host and Microbe, 2021 May 12; 29(5):742-744.
The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury
Matt S Zinter, Caroline A Lindemans, Birgitta A Versluys, Madeline Y Mayday, Sara Sunshine, Gustavo Reyes, Marina Sirota, Anil Sapru, Michael A Matthay, Sandhya Kharbanda, Christopher C Dvorak, Jaap J Boelens, Joseph L DeRisi. Blood, 2021 Mar 25;137(12):1679-1689
The oralome and its dysbiosis: New insights into oral microbiome-host interactions
Allan Radaic and Yvonne L. Kapila. Computational and Structural Biotechnology Journal, 2021; 19:1335-1360.
Microbiota, Epigenetics, and Trained Immunity. Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood
Susan V. Lynch and Donata Vercelli. American Journal of Respiratory and Critical Care Medicine, 2021; 203(7).
2020
Gut microbiota-specific IgA+ B cells traffic to the CNS in active multiple sclerosis
AK Pröbstel, X Zhou, R Baumann, S Wischnewski, M Kutza, OL Rojas, K Sellrie, A Bischof, K Kim, A Ramesh, R Dandekar, AL Greenfield, RD Schubert, JE Bisanz, S Vistnes, K Khaleghi, J Landefeld, G Kirkish, F Liesche-Starnecker, V Ramaglia, S Singh, EB Tran, P Barba, K Zorn, J Oechtering, K Forsberg, LR Shiow, RG Henry, J Graves, BAC Cree, SL Hauser, J Kuhle, JM Gelfand, PM Andersen, J Schlege, PJ Turnbaugh, PH Seeberger, JL Gommerman, MR Wilson, L Schirmer, SE Baranzini. Science Immunology, 2020.
Periodontal pathogens promote cancer aggressivity via TLR/MyD88 triggered activation of Integrin/FAK signaling that is therapeutically reversible by a probiotic bacteriocin
P Kamarajan, I Ateia, JM Shin, JC Fenno, C Le, L Zhan, A Chang, R Darveau, YL Kapila. PLOS Pathogens, 2020. Read press release.
Modulation of pathogenic oral biofilms towards health with nisin probiotic
Radaic A, Ye C, Parks B, Gao L, Kuraji R, Malone E, Kamarajan P, Zhan L, Kapila YL. J Oral Microbiol. 2020 Aug 24;12(1):1809302.
Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions
Margaret Alexander, Peter J.Turnbaugh. Immunity, 2020 Aug 18; 53(2).
Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis
The iMSMS Consortium (SE Baranzini). Multiple Sclerosis Journal, 2020.
Polymicrobial periodontal disease triggers a wide radius of effect and unique virome
Li Gao, Misun Kang, Martin Jinye Zhang, M. Reza Sailani, Ryutaro Kuraji, April Martinez, Changchang Ye, Pachiyappan Kamarajan, Charles Le, Ling Zhan, Hélène Rangé, Sunita P. Ho & Yvonne L. Kapila. npj Biofilms and Microbiomes, 2020
Probing the tumor micro(b)environment
Chloe E. Atreya, Peter J. Turnbaugh. Science, 2020
Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells
Qi Yan Ang, Margaret Alexander, John C. Newman, Yuan Tian, Jingwei Cai, Vaibhav Upadhyay, Jessie A.Turnbaugh, Eric Verdin, Kevin D. Hall, Rudolph L.Leibel, Eric Ravussin, Michael Rosenbaum, Andrew D.Patterson, Peter J.Turnbaugh. Cell, 2020
Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives
Ling Zou, Peter Spanogiannopoulos, Lindsey M. Pieper, Huan-Chieh Chien, Wenlong Cai, Natalia Khuri, Joshua Pottel, Bianca Vora, Zhanglin Ni, Eleftheria Tsakalozou, Wenjun Zhang, Brian K. Shoichet, Kathleen M. Giacomini, and Peter J. Turnbaugh. Proceedings of the National Academy of Sciences, 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
