What are all these microbes that we often identify by sequence analysis alone? Below are papers we have written to delve into the biology of the lesser known members of the microbiota. We can infer some of their biology through genome analysis, ecological distributions, patterns of distribution with other microbes, and sometimes culturing. Here are some of our favorite beasts:


Christensenella minuta and Methanobrevibacter smithii

Liu X, Sutter JS, de la Cuesta-Zuluaga J, Waters JL, Youngblut ND, Ley RE. Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb.nov. based on whole genome analysis. Int. J. Syst. Evol. Microbiol. 71:004774 (2021)

Ruaud A, Esquivel-Elizondo S, de la Cuesta-Zuluaga J, Waters JL, Angenent LT, Youngblut ND and Ley RE. Syntrophy via Interspecies H2 transfer between Christensenella and Methanobrevibacter underlies their global co-occurrence in the human gut. mBio 11 (1) e03235-19 (2020)

Waters JL and Ley RE. The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health. BMC Biology 17: 83 (2019)


Methanomassiliicoccales (trimethylamine using methanogens):

de la Cuesta-Zuluaga J, Spector TD, Youngblut ND, Ley RE. Genomic insights into adaptations of TMA-utilizing methanogens to diverse habitats including the human gut. bioRxiv 2020.09.17.302828; doi: (2020)



Welter DK, Ruaud A, Henseler ZM, de Jong HN, van Coerverden de Groot P, Michaux J, Goermezano L, Waters JL, Youngbluy ND, Ley RE. Free-living psychrophilic bacteria of the genus Psychrobacter are descendents of pathobionts. mSystems (6): 00258-21 (2021)


The Bacteroidetes:

Johnson EL, Heaver SL, Walters WA and Ley RE. Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes. Journal of Molecular Medicine (Berl) 95: 1-8 (2017)

Ley RE. Prevotella in the gut: choose carefully. Nature reviews: Gastroenterology & Hepatology (2016)


Dark Cyanos (Melainabacteria)

DiRienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF and Ley RE. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife 2:e01102 (2013)


The virome

Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector T, Bell JT, Youngblut ND, Hewson I, Reyes A and Ley RE. Virome diversity correlates with intestinal microbiome diversity in adult monozygotic twins. (2019). Cell Host & Microbe 25: 261-272 (2019)