Publications by authors named "Masahira Hattori"

298 Publications

Iodidimonas gelatinilytica sp. nov., aerobic iodide-oxidizing bacteria isolated from brine water and surface seawater.

Antonie Van Leeuwenhoek 2021 May 24;114(5):625-631. Epub 2021 Mar 24.

Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, Japan.

Chemo-organotrophic iodide (I)-oxidizing bacterial strains Hi-2 and Mie-1 were isolated from iodide-rich natural gas brine water in Chiba and surface seawater in Mie, Japan, respectively. Cells of strains Hi-2 and Mie-1 were aerobic, Gram-negative and rod-shaped (0.3-0.5 µm width and 1.2-4.4 µm in length). Two isolates grew optimally at 30 °C, pH 7.5 and with 3% NaCl (w/v). Iodide oxidation to form molecular iodine (I) was a biochemically unique trait for strains Hi-2 and Mie-1. The major cellular fatty acids are Cω7c, Cω5c and C 2-OH. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that strains Hi-2 and Mie-1 were located near Iodidimonas muriae C-3 with 99.2% sequence similarity. The calculated digital DNA-DNA hybridization (dDDH) value of 65.7-65.9% between the two isolates and I. muriae C-3 was lower than the threshold of 70%, which was used for prokaryotic species delineation. Strains Hi-2 and Mie-1 differed in the hydrolysis of aesculin, the hydrolysis of gelatin and the major cellular fatty acids composition from I. muriae C-3. Considering these biochemical properties, the major cellular fatty acids composition and dDDH value, a novel species is proposed for strains Hi-2 (= JCM 17844 = LMG 28661) and Mie-1 (= JCM 17845 = LMG 28662), to be named Iodidimonas gelatinilytica.
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http://dx.doi.org/10.1007/s10482-021-01546-2DOI Listing
May 2021

Pancreatic glycoprotein 2 is a first line of defense for mucosal protection in intestinal inflammation.

Nat Commun 2021 02 16;12(1):1067. Epub 2021 Feb 16.

Department of Mucosal Immunology, The University of Tokyo Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.

Increases in adhesive and invasive commensal bacteria, such as Escherichia coli, and subsequent disruption of the epithelial barrier is implicated in the pathogenesis of inflammatory bowel disease (IBD). However, the protective systems against such barrier disruption are not fully understood. Here, we show that secretion of luminal glycoprotein 2 (GP2) from pancreatic acinar cells is induced in a TNF-dependent manner in mice with chemically induced colitis. Fecal GP2 concentration is also increased in Crohn's diease patients. Furthermore, pancreas-specific GP2-deficient colitis mice have more severe intestinal inflammation and a larger mucosal E. coli population than do intact mice, indicating that digestive-tract GP2 binds commensal E. coli, preventing epithelial attachment and penetration. Thus, the pancreas-intestinal barrier axis and pancreatic GP2 are important as a first line of defense against adhesive and invasive commensal bacteria during intestinal inflammation.
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http://dx.doi.org/10.1038/s41467-021-21277-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7887276PMC
February 2021

Alteration of oxidative-stress and related marker levels in mouse colonic tissues and fecal microbiota structures with chronic ethanol administration: Implications for the pathogenesis of ethanol-related colorectal cancer.

PLoS One 2021 12;16(2):e0246580. Epub 2021 Feb 12.

Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan.

Chronic ethanol consumption is a risk factor for colorectal cancer, and ethanol-induced reactive oxygen species have been suggested to play important roles in the pathogenesis of ethanol-related colorectal cancer (ER-CRC). In this study, the effects of 10-week chronic administration of ethanol on the colonic levels of oxidative stress and advance glycation end product (AGE) levels, as well as fecal microbiota structures, were examined in a mouse model. Chronic oral administration of ethanol in mice (1.0 mL of 1.5% or 5.0% ethanol (v/v) per day per mouse, up to 10 weeks) resulted in the elevation of colonic levels of oxidative stress markers (such as 8-hydroxy-2'-deoxyguanosine and 4-hydroxynonenal) compared to control mice, and this was consistently accompanied by elevated levels of inflammation-associated cytokines and immune cells (Th17 and macrophages) and a decreased level of regulatory T (Treg) cells to produce colonic lesions. It also resulted in an alteration of mouse fecal microbiota structures, reminiscent of the alterations observed in human inflammatory bowel disease, and this appeared to be consistent with the proposed sustained generation of oxidative stress in the colonic environment during chronic ethanol consumption. Moreover, the first experimental evidence that chronic ethanol administration results in elevated levels of advanced glycation end products (AGEs) and their receptors (RAGE) in the colonic tissues in mice is also shown, implying enhanced RAGE-mediated signaling with chronic ethanol administration. The RAGE-mediated signaling pathway has thus far been implicated as a link between the accumulation of AGEs and the development of many types of chronic colitis and cancers. Thus, enhancement of this pathway likely exacerbates the ethanol-induced inflammatory states of colonic tissues and might at least partly contribute to the pathogenesis of ER-CRC.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0246580PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7880462PMC
February 2021

Rebamipide ameliorates indomethacin-induced small intestinal damage and proton pump inhibitor-induced exacerbation of this damage by modulation of small intestinal microbiota.

PLoS One 2021 28;16(1):e0245995. Epub 2021 Jan 28.

Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan.

Non-steroidal anti-inflammatory drugs (NSAIDs) induce small intestinal damage. It has been reported that rebamipide, a mucoprotective drug, exerts a protective effect against NSAID-induced small intestinal damage; however, the underlying mechanism remains unknown. In this study, we investigated the significance of the small intestinal microbiota in the protective effect of rebamipide against indomethacin-induced small intestinal damage in mice. A comprehensive analysis of the 16S rRNA gene sequencing revealed an alteration in the composition of the small intestinal microbiota at the species level, modulated by the administration of rebamipide and omeprazole. The transplantation of the small intestinal microbiota of the mice treated with rebamipide suppressed the indomethacin-induced small intestinal damage. Omeprazole, a proton pump inhibitor, exacerbated the indomethacin-induced small intestinal damage, which was accompanied by the alteration of the small intestinal microbiota. We found that the transplantation of the small intestinal microbiota of the rebamipide-treated mice ameliorated indomethacin-induced small intestinal damage and the omeprazole-induced exacerbation of the damage. These results suggest that rebamipide exerts a protective effect against NSAID-induced small intestinal damage via the modulation of the small intestinal microbiota, and that its ameliorating effect extends also to the exacerbation of NSAID-induced small intestinal damage by proton pump inhibitors.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245995PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7842908PMC
January 2021

Complete Genome Sequence of Alistipes indistinctus Strain 2BBH45, Isolated from the Feces of a Healthy Japanese Male.

Microbiol Resour Announc 2021 Jan 14;10(2). Epub 2021 Jan 14.

Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Japan

The genus is one of the members of the human gut microbiota. Here, we report the complete genome sequence of strain 2BBH45, harboring plasmid p2BBH45.
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http://dx.doi.org/10.1128/MRA.01284-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7849707PMC
January 2021

Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria.

Nat Commun 2021 01 4;12(1):27. Epub 2021 Jan 4.

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.

Bacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including as a part of the human microbiomes. Although a few metagenomic studies have focused on oral phages, they relied on short-read sequencing. Here, we conduct a long-read metagenomic study of human saliva using PromethION. Our analyses, which integrate both PromethION and HiSeq data of >30 Gb per sample with low human DNA contamination, identify hundreds of viral contigs; 0-43.8% and 12.5-56.3% of the confidently predicted phages and prophages, respectively, do not cluster with those reported previously. Our analyses demonstrate enhanced scaffolding, and the ability to place a prophage in its host genomic context and enable its taxonomic classification. Our analyses also identify a Streptococcus phage/prophage group and nine jumbo phages/prophages. 86% of the phage/prophage group and 67% of the jumbo phages/prophages contain remote homologs of antimicrobial resistance genes. Pan-genome analysis of the phages/prophages reveals remarkable diversity, identifying 0.3% and 86.4% of the genes as core and singletons, respectively. Furthermore, our study suggests that oral phages present in human saliva are under selective pressure to escape CRISPR immunity. Our study demonstrates the power of long-read metagenomics utilizing PromethION in uncovering bacteriophages and their interaction with host bacteria.
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http://dx.doi.org/10.1038/s41467-020-20199-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782811PMC
January 2021

Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses.

iScience 2020 Dec 23;23(12):101841. Epub 2020 Nov 23.

RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.

Host-microbiota interactions create a unique metabolic milieu that modulates intestinal environments. Integration of 16S ribosomal RNA (rRNA) sequences and mass spectrometry (MS)-based lipidomics has a great potential to reveal the relationship between bacterial composition and the complex metabolic network in the gut. In this study, we conducted untargeted lipidomics followed by a feature-based molecular MS/MS spectral networking to characterize gut bacteria-dependent lipid subclasses in mice. An estimated 24.8% of lipid molecules in feces were microbiota-dependent, as judged by > 10-fold decrease in antibiotic-treated mice. Among these, there was a series of unique and microbiota-related lipid structures, including acyl alpha-hydroxyl fatty acid (AAHFA) that was newly identified in this study Based on the integrated analysis of 985 lipid profiles and 16S rRNA sequence data providing 2,494 operational taxonomic units, we could successfully predict the bacterial species responsible for the biosynthesis of these unique lipids, including AAHFA.
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http://dx.doi.org/10.1016/j.isci.2020.101841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7721639PMC
December 2020

Complete Genome Sequence of sp. Strain 8CFCBH1, a Potent Producer of Equol, Isolated from Healthy Japanese Feces.

Microbiol Resour Announc 2020 Dec 3;9(49). Epub 2020 Dec 3.

Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan

Here, we report the complete genome sequence of sp. strain 8CFCBH1, which was isolated from a Japanese fecal sample. The genome analysis revealed that the 8CFCBH1 strain potentially produces ()-equol.
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http://dx.doi.org/10.1128/MRA.01240-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7714862PMC
December 2020

Long-term persistence of gastric dysbiosis after eradication of Helicobacter pylori in patients who underwent endoscopic submucosal dissection for early gastric cancer.

Gastric Cancer 2020 Nov 17. Epub 2020 Nov 17.

Department of Gastroenterology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi Abeno-ku, Osaka, Japan.

Background: Gastric microbiome, other than Helicobacter pylori, plays a role in the tumorigenesis of gastric cancer (GC). Patients who undergo endoscopic submucosal dissection for early GC have a high risk of developing metachronous GC even after successful eradication of H. pylori. Thus, we investigated the microbial profiles and associated changes in such patients after the eradication of H. pylori.

Methods: A total of 19 H. pylori-infected patients with early GC who were or to be treated by endoscopic resection, with paired biopsy samples at pre- and post-eradication therapy, were retrospectively enrolled. Ten H. pylori-negative patients were enrolled as controls. Biopsy samples were analyzed using 16S rRNA sequencing.

Results: H. pylori-positive patients exhibited low richness and evenness of bacteria with the deletion of several genera, including Blautia, Ralstonia, Faecalibacterium, Methylobacterium, and Megamonas. H. pylori eradication partially restored microbial diversity, as assessed during a median follow-up at 13 months after eradication therapy. However, post-eradication patients had less diversity than that in the controls and possessed a lower abundance of the five genera mentioned above. The eradication of H. pylori also altered the bacterial composition, but not to the same extent as that in controls. The microbial communities could be clustered into three separate groups: H. pylori-negative, pre-eradication, and post-eradication.

Conclusion: Changes in dysbiosis may persist long after the eradication of H. pylori in patients with a history of GC. Dysbiosis may be involved in the development of both primary and metachronous GC after the eradication of H. pylori in such patients.
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http://dx.doi.org/10.1007/s10120-020-01141-wDOI Listing
November 2020

The influences of low protein diet on the intestinal microbiota of mice.

Sci Rep 2020 10 13;10(1):17077. Epub 2020 Oct 13.

Department of Veterinary Medical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.

Recent research suggests that protein deficiency symptoms are influenced by the intestinal microbiota. We investigated the influence of low protein diet on composition of the intestinal microbiota through animal experiments. Specific pathogen-free (SPF) mice were fed one of four diets (3, 6, 9, or 12% protein) for 4 weeks (n = 5 per diet). Mice fed the 3% protein diet showed protein deficiency symptoms such as weight loss and low level of blood urea nitrogen concentration in their serum. The intestinal microbiota of mice in the 3% and 12% protein diet groups at day 0, 7, 14, 21 and 28 were investigated by 16S rRNA gene sequencing, which revealed differences in the microbiota. In the 3% protein diet group, a greater abundance of urease producing bacterial species was detected across the duration of the study. In the 12% diet protein group, increases of abundance of Streptococcaceae and Clostridiales families was detected. These results suggest that protein deficiency may be associated with shifts in intestinal microbiota.
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http://dx.doi.org/10.1038/s41598-020-74122-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7555506PMC
October 2020

Gut microbiota composition in obese and non-obese adult relatives from the highlands of Papua New Guinea.

FEMS Microbiol Lett 2020 Oct;367(19)

Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan.

Obesity is a condition that results from an imbalance between energy intake and expenditure. Recently, obesity has been linked to differences in the composition of gut microbiota. To examine this association in Papua New Guinea (PNG) highlanders, fecal samples were collected from 18 adults; nine obese participants were paired with their non-obese relative. Amplification of the 16S rRNA gene targeting the V1-V2 region was performed on DNA extracts for each participant, with high-quality sequences selected and used for operational taxonomic unit clustering. The data showed Firmicutes and Bacteroidetes were the two dominant phyla, while at genus level Prevotella was the most dominant genus in all of the samples. Nonetheless, statistical evaluation of potential association between nutritional status and bacterial abundance at both phyla and genus levels showed no significant difference. Further studies, ideally in both rural and urban areas, are needed to evaluate the role of the gut microbiome in the occurrence of obesity in PNG and other resource-limited settings.
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http://dx.doi.org/10.1093/femsle/fnaa161DOI Listing
October 2020

Genome Analysis of " Regiella insecticola" Strain TUt, Facultative Bacterial Symbiont of the Pea Aphid .

Microbiol Resour Announc 2020 Oct 1;9(40). Epub 2020 Oct 1.

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan

The genome of " Regiella insecticola" strain TUt, a facultative bacterial symbiont of the pea aphid , was analyzed. We determined a 2.5-Mb draft genome consisting of 14 contigs; this will contribute to the understanding of the symbiont, which underpins various ecologically adaptive traits of the host insect.
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http://dx.doi.org/10.1128/MRA.00598-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7530917PMC
October 2020

Prebiotics protect against acute graft-versus-host disease and preserve the gut microbiota in stem cell transplantation.

Blood Adv 2020 10;4(19):4607-4617

Hematology Division, Tokyo Metropolitan Komagome Hospital, Tokyo, Japan.

Acute graft-versus-host disease (aGVHD) is a major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Therefore, management of aGVHD is important for successful transplantation. Mucosal damage and alteration of the gut microbiota after allo-HSCT are key factors in the development of aGVHD. We conducted a prospective study to evaluate the ability of prebiotics, which can alleviate mucosal damage and manipulate the gut microbiota, to mitigate posttransplantation complications, including aGVHD. Resistant starch (RS) and a commercially available prebiotics mixture, GFO, were administered to allo-HSCT recipients from pretransplantation conditioning to day 28 after allo-HSCT. Prebiotic intake mitigated mucosal injury and reduced the incidence of all aGVHD grades combined and of aGVHD grades 2 to 4. The cumulative incidence of skin aGVHD was markedly decreased by prebiotics intake. Furthermore, the gut microbial diversity was well maintained and butyrate-producing bacterial population were preserved by prebiotics intake. In addition, the posttransplantation fecal butyrate concentration was maintained or increased more frequently in the prebiotics group. These observations indicate that prebiotic intake may be an effective strategy for preventing aGVHD in allo-HSCT, thereby improving treatment outcomes and the clinical utility of stem cell transplantation approaches. This study was registered on the University Hospital Medical Information Network (UMIN) clinical trials registry (https://www.umin.ac.jp/ctr/index.htm) as #UMIN000027563.
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http://dx.doi.org/10.1182/bloodadvances.2020002604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7556149PMC
October 2020

Gut microorganisms act together to exacerbate inflammation in spinal cords.

Nature 2020 09 26;585(7823):102-106. Epub 2020 Aug 26.

RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

Accumulating evidence indicates that gut microorganisms have a pathogenic role in autoimmune diseases, including in multiple sclerosis. Studies of experimental autoimmune encephalomyelitis (an animal model of multiple sclerosis), as well as human studies, have implicated gut microorganisms in the development or severity of multiple sclerosis. However, it remains unclear how gut microorganisms act on the inflammation of extra-intestinal tissues such as the spinal cord. Here we show that two distinct signals from gut microorganisms coordinately activate autoreactive T cells in the small intestine that respond specifically to myelin oligodendrocyte glycoprotein (MOG). After induction of experimental autoimmune encephalomyelitis in mice, MOG-specific CD4 T cells are observed in the small intestine. Experiments using germ-free mice that were monocolonized with microorganisms from the small intestine demonstrated that a newly isolated strain in the family Erysipelotrichaceae acts similarly to an adjuvant to enhance the responses of T helper 17 cells. Shotgun sequencing of the contents of the small intestine revealed a strain of Lactobacillus reuteri that possesses peptides that potentially mimic MOG. Mice that were co-colonized with these two strains showed experimental autoimmune encephalomyelitis symptoms that were more severe than those of germ-free or monocolonized mice. These data suggest that the synergistic effects that result from the presence of these microorganisms should be considered in the pathogenicity of multiple sclerosis, and that further study of these microorganisms may lead to preventive strategies for this disease.
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http://dx.doi.org/10.1038/s41586-020-2634-9DOI Listing
September 2020

Alterations of the gut ecological and functional microenvironment in different stages of multiple sclerosis.

Proc Natl Acad Sci U S A 2020 09 24;117(36):22402-22412. Epub 2020 Aug 24.

Department of Immunology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, 187-8502 Tokyo, Japan;

Multiple sclerosis (MS), an autoimmune disease of the central nervous system, generally starts as the relapsing remitting form (RRMS), but often shifts into secondary progressive MS (SPMS). SPMS represents a more advanced stage of MS, characterized by accumulating disabilities and refractoriness to medications. The aim of this study was to clarify the microbial and functional differences in gut microbiomes of the different stages of MS. Here, we compared gut microbiomes of patients with RRMS, SPMS, and two closely related disorders with healthy controls (HCs) by 16S rRNA gene and whole metagenomic sequencing data from fecal samples and by fecal metabolites. Each patient group had a number of species having significant changes in abundance in comparison with HCs, including short-chain fatty acid (SCFA)-producing bacteria reduced in MS. Changes in some species had close association with clinical severity of the patients. A marked reduction in butyrate and propionate biosynthesis and corresponding metabolic changes were confirmed in RRMS compared with HCs. Although bacterial composition analysis showed limited differences between the patient groups, metagenomic functional data disclosed an increase in microbial genes involved in DNA mismatch repair in SPMS as compared to RRMS. Together with an increased ratio of cysteine persulfide to cysteine in SPMS revealed by sulfur metabolomics, we postulate that excessive DNA oxidation could take place in the gut of SPMS. Thus, gut ecological and functional microenvironments were significantly altered in the different stages of MS. In particular, reduced SCFA biosynthesis in RRMS and elevated oxidative level in SPMS were characteristic.
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http://dx.doi.org/10.1073/pnas.2011703117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7486801PMC
September 2020

TH1 cell-inducing strain identified from the small intestinal mucosa of patients with Crohn's disease.

Gut Microbes 2020 11 20;12(1):1788898. Epub 2020 Jul 20.

Department of Microbiology and Immunology, Keio University School of Medicine , Tokyo, Japan.

Dysbiotic microbiota contributes to the pathogenesis of Crohn's disease (CD) by regulating the immune system. Although pro-inflammatory microbes are probably enriched in the small intestinal (SI) mucosa, most studies have focused on fecal microbiota. This study aimed to examine jejunal and ileal mucosal specimens from patients with CD via double-balloon enteroscopy. Comparative microbiome analysis revealed that the microbiota composition of CD SI mucosa differs from that of non-CD controls, with an increased population of several families, including Enterobacteriaceae, Ruminococcaceae, and Bacteroidaceae. Upon anaerobic culturing of the CD SI mucosa, 80 bacterial strains were isolated, from which 9 strains representing 9 distinct species (, and ) were selected on the basis of their significant association with CD. The colonization of germ-free (GF) mice with the 9 strains enhanced the accumulation of T1 cells and, to a lesser extent, T17 cells in the intestine, among which an strain displayed high potential to induce T1 cells and intestinal inflammation in a strain-specific manner. The present results indicate that the CD SI mucosa harbors unique pro-inflammatory microbiota, including T1 cell-inducing , which could be a potential therapeutic target.
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http://dx.doi.org/10.1080/19490976.2020.1788898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7524366PMC
November 2020

Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation.

Microbiome 2020 06 23;8(1):95. Epub 2020 Jun 23.

Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo, 169-8555, Japan.

Background: The human gut microbiome has been suggested to affect human health and thus has received considerable attention. To clarify the structure of the human gut microbiome, clustering methods are frequently applied to human gut taxonomic profiles. Enterotypes, i.e., clusters of individuals with similar microbiome composition, are well-studied and characterized. However, only a few detailed studies on assemblages, i.e., clusters of co-occurring bacterial taxa, have been conducted. Particularly, the relationship between the enterotype and assemblage is not well-understood.

Results: In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method. We applied LDA to a large-scale human gut metagenome dataset and found that a 4-assemblage LDA model could represent relationships between enterotypes and assemblages with high interpretability. This model indicated that each individual tends to have several assemblages, three of which corresponded to the three classically recognized enterotypes. Conversely, the fourth assemblage corresponded to no enterotypes and emerged in all enterotypes. Interestingly, the dominant genera of this assemblage (Clostridium, Eubacterium, Faecalibacterium, Roseburia, Coprococcus, and Butyrivibrio) included butyrate-producing species such as Faecalibacterium prausnitzii. Indeed, the fourth assemblage significantly positively correlated with three butyrate-producing functions.

Conclusions: We conducted an assemblage analysis on a large-scale human gut metagenome dataset using LDA. The present study revealed that there is an enterotype-independent assemblage. Video Abstract.
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http://dx.doi.org/10.1186/s40168-020-00864-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313204PMC
June 2020

The liver-brain-gut neural arc maintains the T cell niche in the gut.

Nature 2020 09 11;585(7826):591-596. Epub 2020 Jun 11.

Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.

Recent clinical and experimental evidence has evoked the concept of the gut-brain axis to explain mutual interactions between the central nervous system and gut microbiota that are closely associated with the bidirectional effects of inflammatory bowel disease and central nervous system disorders. Despite recent advances in our understanding of neuroimmune interactions, it remains unclear how the gut and brain communicate to maintain gut immune homeostasis, including in the induction and maintenance of peripheral regulatory T cells (pT cells), and what environmental cues prompt the host to protect itself from development of inflammatory bowel diseases. Here we report a liver-brain-gut neural arc that ensures the proper differentiation and maintenance of pT cells in the gut. The hepatic vagal sensory afferent nerves are responsible for indirectly sensing the gut microenvironment and relaying the sensory inputs to the nucleus tractus solitarius of the brainstem, and ultimately to the vagal parasympathetic nerves and enteric neurons. Surgical and chemical perturbation of the vagal sensory afferents at the hepatic afferent level reduced the abundance of colonic pT cells; this was attributed to decreased aldehyde dehydrogenase (ALDH) expression and retinoic acid synthesis by intestinal antigen-presenting cells. Activation of muscarinic acetylcholine receptors directly induced ALDH gene expression in both human and mouse colonic antigen-presenting cells, whereas genetic ablation of these receptors abolished the stimulation of antigen-presenting cells in vitro. Disruption of left vagal sensory afferents from the liver to the brainstem in mouse models of colitis reduced the colonic pT cell pool, resulting in increased susceptibility to colitis. These results demonstrate that the novel vago-vagal liver-brain-gut reflex arc controls the number of pT cells and maintains gut homeostasis. Intervention in this autonomic feedback feedforward system could help in the development of therapeutic strategies to treat or prevent immunological disorders of the gut.
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http://dx.doi.org/10.1038/s41586-020-2425-3DOI Listing
September 2020

Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan.

PLoS One 2020 4;15(3):e0226654. Epub 2020 Mar 4.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th-19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0226654PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7055813PMC
May 2020

Complete Genome Sequence of Akkermansia muciniphila JCM 30893, Isolated from Feces of a Healthy Japanese Male.

Microbiol Resour Announc 2020 Feb 13;9(7). Epub 2020 Feb 13.

Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan

is an anaerobic and mucin-degrading bacterium in the human gut. Here, we report the complete genome sequence of JCM 30893 harboring the plasmid pJ30893.
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http://dx.doi.org/10.1128/MRA.01543-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7019068PMC
February 2020

5-Aminosalicylic acid intolerance is associated with a risk of adverse clinical outcomes and dysbiosis in patients with ulcerative colitis.

Intest Res 2020 Jan 30;18(1):69-78. Epub 2020 Jan 30.

Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.

Background/aims: 5-Aminosalicylic acid (ASA) causes intolerance reactions in some patients. This study was performed to examine the prognosis of patients with ulcerative colitis (UC) and 5-ASA intolerance, and to evaluate the potential interaction between 5-ASA intolerance and the intestinal microbiota.

Methods: We performed a retrospective cohort study of patients with UC who visited participating hospitals. The primary endpoint was to compare the incidence of hospitalization within 12 months between the 5-ASA intolerance group and the 5-ASA tolerance group. The secondary endpoint was to compare the risk of adverse clinical outcomes after the start of biologics between the 2 groups. We also assessed the correlation between 5-ASA intolerance and microbial change in an independently recruited cohort of patients with UC.

Results: Of 793 patients, 59 (7.4%) were assigned to the 5-ASA intolerance group and 734 (92.5%) were assigned to the 5-ASA tolerance group. The admission rate and incidence of corticosteroid use were significantly higher in the intolerance than tolerance group (P< 0.001). In 108 patients undergoing treatment with anti-tumor necrosis factor biologics, 5-ASA intolerance increased the incidence of additional induction therapy after starting biologics (P< 0.001). The 5-ASA intolerance group had a greater abundance of bacteria in the genera Faecalibacterium, Streptococcus, and Clostridium than the 5-ASA tolerance group (P< 0.05).

Conclusions: In patients with UC, 5-ASA intolerance is associated with a risk of adverse clinical outcomes and dysbiosis. Bacterial therapeutic optimization of 5-ASA administration may be important for improving the prognosis of patients with UC.
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http://dx.doi.org/10.5217/ir.2019.00084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000647PMC
January 2020

Altered microbiota composition reflects enhanced communication in 15q11-13 CNV mice.

Neurosci Res 2020 Dec 18;161:59-67. Epub 2019 Dec 18.

RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan; Graduate School of Biomedical and Health Sciences, Hiroshima University, Minami, Hiroshima, 734-8553, Japan; RIKEN Center for Science and Technology Hub, Medical Sciences Innovation Hub Program (MIH), Japan; Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Chuo, Kobe, 650-0017, Japan. Electronic address:

Autism spectrum disorder (ASD) is a complex and heterogeneous neurodevelopmental disorder. In addition to the core symptoms of ASD, many patients with ASD also show comorbid gut dysbiosis, which may lead to various gastrointestinal (GI) problems. Intriguingly, there is evidence that gut microbiota communicate with the central nervous system to modulate behavioral output through the gut-brain axis. To investigate how the microbiota composition is changed in ASD and to identify which microbes are involved in autistic behaviors, we performed a 16S rRNA gene-based metagenomics analysis in an ASD mouse model. Here, we focused on a model with human 15q11-13 duplication (15q dup), the most frequent chromosomal aberration or copy number variation found in ASD. Species diversity of the microbiome was significantly decreased in 15q dup mice. A combination of antibiotics treatment and behavioral analysis showed that neomycin improved social communication in 15q dup mice. Furthermore, comparison of the microbiota composition of mice treated with different antibiotics enabled us to identify beneficial operational taxonomic units (OTUs) for ultrasonic vocalization.
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http://dx.doi.org/10.1016/j.neures.2019.12.010DOI Listing
December 2020

Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis.

Int J Mol Sci 2019 Nov 26;20(23). Epub 2019 Nov 26.

Department of Applied Genomics, Kazusa DNA Research Institute, Chiba 292-0818, Japan.

Data-independent acquisition (DIA)-mass spectrometry (MS)-based proteomic analysis overtop the existing data-dependent acquisition (DDA)-MS-based proteomic analysis to enable deep proteome coverage and precise relative quantitative analysis in single-shot liquid chromatography (LC)-MS/MS. However, DIA-MS-based proteomic analysis has not yet been optimized in terms of system robustness and throughput, particularly for its practical applications. We established a single-shot LC-MS/MS system with an MS measurement time of 90 min for a highly sensitive and deep proteomic analysis by optimizing the conditions of DIA and nanoLC. We identified 7020 and 4068 proteins from 200 ng and 10 ng, respectively, of tryptic floating human embryonic kidney cells 293 (HEK293F) cell digest by performing the constructed LC-MS method with a protein sequence database search. The numbers of identified proteins from 200 ng and 10 ng of tryptic HEK293F increased to 8509 and 5706, respectively, by searching the chromatogram library created by gas-phase fractionated DIA. Moreover, DIA protein quantification was highly reproducible, with median coefficients of variation of 4.3% in eight replicate analyses. We could demonstrate the power of this system by applying the proteomic analysis to detect subtle changes in protein profiles between cerebrums in germ-free and specific pathogen-free mice, which successfully showed that >40 proteins were differentially produced between the cerebrums in the presence or absence of bacteria.
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http://dx.doi.org/10.3390/ijms20235932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6928715PMC
November 2019

Gastric acid inhibitor aggravates indomethacin-induced small intestinal injury via reducing Lactobacillus johnsonii.

Sci Rep 2019 11 25;9(1):17490. Epub 2019 Nov 25.

Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan.

Proton pump inhibitors (PPIs) alter the composition of the intestinal microbiome, exacerbating indomethacin (IND)-induced small intestinal damage. Vonoprazan fumarate inhibits gastric acid secretion using a different mechanism from PPIs. We investigated the effects of both drugs on the intestinal microbiome and IND-induced small intestinal damage. We sought to clarify whether PPI-induced dysbiosis and worsening of the damage were due to a specific drug class effect of PPIs. Rabeprazole administration increased operational taxonomic unit numbers in the small intestines of C57BL/6 J mice, whereas the difference was not significant in the vonoprazan-treated group but exhibited a trend. Permutational multivariate analysis of variance of the unweighted UniFrac distances showed significant differences between vehicle- and vonoprazan- or rabeprazole-treated groups. L. johnsonii was the predominant microbial species, and the population ratio decreased after vonoprazan and rabeprazole administration. The vonoprazan- and rabeprazole-treated groups showed increased IND-induced damage. This high sensitivity to IND-induced damage was evaluated by transplantation with contents from the small intestine of mice treated with either vonoprazan or rabeprazole. Supplementation of L. johnsonii orally in mice treated with rabeprazole and vonoprazan prevented the increase in IND-induced small intestinal damage. In conclusion, both rabeprazole and vonoprazan aggravated NSAID-induced small intestinal injury by reducing the population of L. johnsonii in the small intestine via suppressing gastric acid secretion.
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http://dx.doi.org/10.1038/s41598-019-53559-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6877529PMC
November 2019

sp. nov., sp. nov. and subsp. subsp. nov., isolated from human faeces, and creation of subsp. subsp. nov.

Int J Syst Evol Microbiol 2020 Jan;70(1):473-480

Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan.

Three groups of Gram-stain-negative, obligately anaerobic, rod or coccoid-shaped bacteria, which were phylogenetically assigned in the genus belonging to the family in the phylum , were isolated from the faecal samples of healthy Japanese humans. Group I (strains 5CBH24 and 6CPBBH3) showed highest 16S rRNA gene sequence similarity to '' ph8 (99.73 %). Group II (strain 5CPEGH6) was related to WAL 8301 (96.82 %). Ten strains of group III (3BBH6, 5CPYCFAH4, 5NYCFAH2 and others) were related to DSM 19147 (98.96 %). Group I could be differentiated from other strains by the ability to hydrolyse aesculin and the lack of catalase activity. Strain 5CPEGH6 could be differentiated from JCM 16773 by the inability to hydrolyse aesculin and the lack of catalase activity, and so on. Phenotypic characteristics of group III were similar to those of JCM 16771. Strains 5CBH24, 6CPBBH3 and '' ph8 shared 98.8-98.9 % average nucleotide identity (ANI) with each other. In addition, the DNA-DNA hybridization (DDH) values among three strains were 86.7-89.4 %. Strain 5CPEGH6 showed relatively low values (≤ 84.4 % for ANI ; ≤26.2 % for DDH) with other strains. Three strains in the group III (3BBH6, 5CPYCFAH4 and 5NYCFAH2) shared 97.9-99.9% ANI with each other. These three strains showed 96.9-97.3 % ANI with DSM 19147. The DDH values of strains 3BBH6, 5CPYCFAH4 and 5NYCFAH2 among themselves were 80.5-99.8 %, while those compared to DSM 19147 were 71.0-73.4 %. On the basis of the collected data, three novel species, sp. nov. (5CBH24=JCM 32850=DSM 108979), sp. nov. (5CPEGH6=JCM 32848=DSM 108978) and subsp. subsp. nov. (3BBH6=JCM 32839=DSM 108977), are proposed.
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http://dx.doi.org/10.1099/ijsem.0.003778DOI Listing
January 2020

Effects of storage temperature, storage time, and Cary-Blair transport medium on the stability of the gut microbiota.

Drug Discov Ther 2019 Nov 11;13(5):256-260. Epub 2019 Oct 11.

RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.

How long fecal samples can withstand a period of refrigeration or room temperature, and the appropriate preservative, are largely unknown. Cary-Blair transport medium has been used for many years because it is inexpensive and prevents bacterial overgrowth. However, its effectiveness for metagenomic analyses has never been tested. We found that the microbial compositions using a 16S rRNA sequence of samples left at 4°C for 3 or 7 days or at 25°C for 1, 3, or 7 days differed significantly from samples stored at -80°C in no-preservative method. Whereas samples stored in Cary-Blair medium remained unchanged for longer periods. The relative abundances of phylum Bacteroidetes and Actinobacteria, changed significantly at 25°C, whereas Cary-Blair medium inhibited the reduction in Bacteroidetes and the increase in Actinobacteria. The bacterial survival counts were significantly lower in the RNAlater samples than in the Cary-Blair samples under aerobic and anaerobic culture conditions. In conclusion, storage time and storage temperature significantly affect the gut microbial composition in fecal samples. Given the low cost, inhibitory effect on bacterial changes, and potential utility in bacterial isolation, Cary-Blair medium containers are suitable for large-scale or hospital-based microbiome studies, especially if direct freezing at -80°C is unavailable.
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http://dx.doi.org/10.5582/ddt.2019.01071DOI Listing
November 2019

Draft Genome Sequence of Sporolactobacillus inulinus NBRC 111894, Isolated from Kôso, a Japanese Sugar-Vegetable Fermented Beverage.

Microbiol Resour Announc 2019 Oct 10;8(41). Epub 2019 Oct 10.

ARSOA Research & Development Center, AOB Keioh Group Corporation, Hokuto, Yamanashi, Japan.

NBRC 111894 is a species of endospore-forming lactic acid bacteria isolated from kôso, a Japanese sugar-vegetable fermented beverage. The draft genome sequence of NBRC 111894 is useful for understanding the differences between strains and their conserved characteristics.
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http://dx.doi.org/10.1128/MRA.00751-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6787315PMC
October 2019

Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis.

EBioMedicine 2019 Oct 11;48:513-525. Epub 2019 Sep 11.

Division of Biochemistry, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, Japan; International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan. Electronic address:

Background: The dysbiosis of gut microbiota has been implicated in the pathogenesis of inflammatory bowel diseases; however, the underlying mechanisms have not yet been elucidated. Heavily glycosylated mucin establishes a first-line barrier against pathogens and serves as a niche for microbial growth.

Methods: To elucidate relationships among dysbiosis, abnormal mucin utilisation, and microbial metabolic dysfunction, we analysed short-chain fatty acids (SCFAs) and mucin components in stool samples of 40 healthy subjects, 49 ulcerative colitis (UC) patients, and 44 Crohn's disease (CD) patients from Japan.

Findings: Levels of n-butyrate were significantly lower in stools of both CD and UC patients than in stools of healthy subjects. Correlation analysis identified seven bacterial species positively correlated with n-butyrate levels; the major n-butyrate producer, Faecalibacterium prausnitzii, was particularly underrepresented in CD patients, but not in UC patients. In UC patients, there were inverse correlations between mucin O-glycan levels and the production of SCFAs, such as n-butyrate, suggesting that mucin O-glycans serve as an endogenous fermentation substrate for n-butyrate production. Indeed, mucin-fed rodents exhibited enhanced n-butyrate production, leading to the expansion of RORgtTreg cells and IgA-producing cells in colonic lamina propria. Microbial utilisation of mucin-associated O-glycans was significantly reduced in n-butyrate-deficient UC patients.

Interpretation: Mucin O-glycans facilitate symbiosynthesis of n-butyrate by gut microbiota. Abnormal mucin utilisation may lead to reduced n-butyrate production in UC patients. FUND: Japan Society for the Promotion of Science, Health Labour Sciences Research Grant, AMED-Crest, AMED, Yakult Foundation, Keio Gijuku Academic Development Funds, The Aashi Grass Foundation, and The Canon Foundation.
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http://dx.doi.org/10.1016/j.ebiom.2019.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838389PMC
October 2019

Japanese subgingival microbiota in health vs disease and their roles in predicted functions associated with periodontitis.

Odontology 2020 Apr 9;108(2):280-291. Epub 2019 Sep 9.

Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8549, Japan.

The present study aimed to identify and compare the microbial signatures between periodontally healthy and periodontitis subjects using 454 sequences of 16S rRNA genes. Subgingival plaque samples were collected from ten periodontally healthy subjects and ten matched chronic periodontitis patients. Bacterial DNA was extracted and next-generation sequencing of 16S rRNA genes was performed. The microbial composition differed between healthy subjects and periodontitis patients at all phylogenetic levels. Particularly, 16 species, including Lautropia mirabilis and Neisseria subflava predominated in healthy subjects, whereas nine species, including Porphyromonas gingivalis and Filifactor alocis predominated in periodontitis. UniFrac, a principal coordinate and network analysis, confirmed distinct community profiles in healthy subjects and periodontitis patients. Using predicted function profiling, pathways involved in phenylpropanoid, GPI-anchor biosynthesis, and metabolism of alanine, arginine, aspartate, butanoate, cyanoamino acid, fatty acid, glutamate, methane, proline, and vitamin B6 were significantly over-represented in periodontitis patients. These results highlight the oral microbiota alterations in microbial composition in periodontitis and suggest the genes and metabolic pathways associated with health and periodontitis. Our findings help to further elucidate microbial composition and interactions in health and periodontitis.
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http://dx.doi.org/10.1007/s10266-019-00452-4DOI Listing
April 2020