title: Nitrogen fixation and nifH diversity in human gut microbiota.
abstract: It has been hypothesized that nitrogen fixation occurs in the human gut. However, whether the gut microbiota truly has this potential remains unclear. We investigated the nitrogen-fixing activity and diversity of the nitrogenase reductase (NifH) genes in the faecal microbiota of humans, focusing on Papua New Guinean and Japanese individuals with low to high habitual nitrogen intake. A (15)N2 incorporation assay showed significant enrichment of (15)N in all faecal samples, irrespective of the host nitrogen intake, which was also supported by an acetylene reduction assay. The fixed nitrogen corresponded to 0.01% of the standard nitrogen requirement for humans, although our data implied that the contribution in the gut in vivo might be higher than this value. The nifH genes recovered in cloning and metagenomic analyses were classified in two clusters: one comprising sequences almost identical to Klebsiella sequences and the other related to sequences of Clostridiales members. These results are consistent with an analysis of databases of faecal metagenomes from other human populations. Collectively, the human gut microbiota has a potential for nitrogen fixation, which may be attributable to Klebsiella and Clostridiales strains, although no evidence was found that the nitrogen-fixing activity substantially contributes to the host nitrogen balance.
authors.affiliation: Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.|Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.|Department of International Health, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.
authors.forename: Katsura
authors.initials: K
authors.lastname: Igai
authors.affiliation: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan.
authors.forename: Manabu
authors.initials: M
authors.lastname: Itakura
authors.affiliation: Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
authors.forename: Suguru
authors.initials: S
authors.lastname: Nishijima
authors.affiliation: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan.
authors.forename: Hirohito
authors.initials: H
authors.lastname: Tsurumaru
authors.affiliation: Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Suda
authors.affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
authors.forename: Takumi
authors.initials: T
authors.lastname: Tsutaya
authors.affiliation: Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
authors.forename: Eriko
authors.initials: E
authors.lastname: Tomitsuka
authors.affiliation: Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Tadokoro
authors.affiliation: Department of Sociological Studies, Faculty of Human Sciences, Wako University, Tokyo, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Baba
authors.affiliation: Faculty of Letters, Chiba University, Chiba, Japan.
authors.forename: Shingo
authors.initials: S
authors.lastname: Odani
authors.affiliation: The Japanese Red Cross Akita College of Nursing, Akita, Japan.
authors.forename: Kazumi
authors.initials: K
authors.lastname: Natsuhara
authors.affiliation: Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
authors.forename: Ayako
authors.initials: A
authors.lastname: Morita
authors.affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
authors.forename: Minoru
authors.initials: M
authors.lastname: Yoneda
authors.affiliation: Papua New Guinea Institute of Medical Research, Eastern Highlands Province, Papua New Guinea.|School of Applied and Biomedical Sciences, Federation University Australia, Victoria, Australia.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Greenhill
authors.affiliation: Papua New Guinea Institute of Medical Research, Eastern Highlands Province, Papua New Guinea.
authors.forename: Paul F
authors.initials: PF
authors.lastname: Horwood
authors.affiliation: Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan.
authors.forename: Jun-Ichi
authors.initials: J
authors.lastname: Inoue
authors.affiliation: Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan.
authors.forename: Moriya
authors.initials: M
authors.lastname: Ohkuma
authors.affiliation: Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Hongoh
authors.affiliation: Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.|Department of International Health, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.
authors.forename: Taro
authors.initials: T
authors.lastname: Yamamoto
authors.affiliation: Papua New Guinea Institute of Medical Research, Eastern Highlands Province, Papua New Guinea.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Siba
authors.affiliation: Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
authors.forename: Masahira
authors.initials: M
authors.lastname: Hattori
authors.affiliation: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan.
authors.forename: Kiwamu
authors.initials: K
authors.lastname: Minamisawa
authors.affiliation: Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Umezaki
mesh_terms: D000114:Acetylene / Q000737:chemistry / Q000378:metabolism; D000328:Adult; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D000068016:Eubacteriales / Q000201:enzymology / Q000235:genetics / Q000302:isolation & purification; D016208:Databases, Factual; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome; D006801:Humans; D007709:Klebsiella / Q000201:enzymology / Q000235:genetics / Q000302:isolation & purification; D008297:Male; D056186:Metagenomics; D009584:Nitrogen / Q000737:chemistry / Q000378:metabolism*; D009586:Nitrogen Fixation; D009587:Nitrogen Isotopes / Q000378:metabolism; D010088:Oxidoreductases / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny; D012329:RNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D017422:Sequence Analysis, DNA; D055815:Young Adult
chemical_list: D001426:Bacterial Proteins; D009587:Nitrogen Isotopes; C000615243:Nitrogen-15; D012329:RNA, Bacterial; D010088:Oxidoreductases; C029130:nitrogenase reductase; D009584:Nitrogen; D000114:Acetylene