Capturing One of the Human Gut Microbiome's Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data.
The role of the microbiome in health and disease is attracting great attention, yet we still know little about some of the most prevalent microorganisms inside our bodies. Several years ago, Human Microbiome Project (HMP) researchers generated a list of "most wanted" taxa: bacteria both prevalent among healthy volunteers and distantly related to any sequenced organisms. Unfortunately, the challenge of assembling high-quality genomes from a tangle of metagenomic reads has slowed progress in learning about these uncultured bacteria. Here, we describe how recent advances in sequencing and analysis allowed us to assemble "most wanted" genomes from metagenomic data collected from four stool samples. Using a combination of both de novo and guided assembly methods, we assembled and binned over 100 genomes from an initial data set of over 1,300 Gbp. One of these genome bins, which met HMP's criteria for a "most wanted" taxa, contained three essentially complete genomes belonging to a previously uncultivated species. This species is most closely related to Eubacterium desmolans and the clostridial cluster IV/Clostridium leptum subgroup species Butyricicoccus pullicaecorum (71-76% average nucleotide identity). Gene function analysis indicates that the species is an obligate anaerobe, forms spores, and produces the anti-inflammatory short-chain fatty acids acetate and butyrate. It also appears to take up metabolically costly molecules such as cobalamin, methionine, and branch-chained amino acids from the environment, and to lack virulence genes. Thus, the evidence is consistent with a secondary degrader that occupies a host-dependent, nutrient-scavenging niche within the gut; its ability to produce butyrate, which is thought to play an anti-inflammatory role, makes it intriguing for the study of diseases such as colon cancer and inflammatory bowel disease. In conclusion, we have assembled essentially complete genomes from stool metagenomic data, yielding valuable information about uncultured organisms' metabolic and ecologic niches, factors that may be required to successfully culture these bacteria, and their role in maintaining health and causing disease.
Microbiome Program, Center for Individualized Medicine, Mayo Clinic, RochesterMN, USA; Department of Surgery, Mayo Clinic, RochesterMN, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA.
Patricio
P
Jeraldo
Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana IL, USA.
Alvaro
A
Hernandez
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark.
Henrik B
HB
Nielsen
Department of Health Sciences Research, Mayo Clinic, Rochester MN, USA.
Xianfeng
X
Chen
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, UrbanaIL, USA.
Bryan A
BA
White
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL, USA; Department of Physics, University of Illinois at Urbana-Champaign, UrbanaIL, USA.
Nigel
N
Goldenfeld
Microbiome Program, Center for Individualized Medicine, Mayo Clinic, RochesterMN, USA; Department of Surgery, Mayo Clinic, RochesterMN, USA.
Heidi
H
Nelson
Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester MN, USA.
David
D
Alhquist
Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester MN, USA.
Lisa
L
Boardman
Division of Gastroenterology and Hepatology, Mayo Clinic, RochesterMN, USA; Division of Gastroenterology and Hepatology, Mayo Clinic, RochesterMN, USA; Division of Gastroenterology and Hepatology, Mayo Clinic, RochesterMN, USA.
Nicholas
N
Chia
Butyricicoccus; binning; genome assembly; metagenomics; microbiome