PMID- 30355340 OWN - NLM STAT- MEDLINE DCOM- 20190705 LR - 20240103 IS - 1471-2180 (Electronic) IS - 1471-2180 (Linking) VI - 18 IP - 1 DP - 2018 Oct 24 TI - Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing. PG - 157 LID - 10.1186/s12866-018-1304-7 [doi] LID - 157 AB - BACKGROUND: Most studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene. RESULTS: Using culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p < 0.02). We isolated fewer aero-intolerant species in the upper gut: 37 from the stomach and 150 from the left colon (p < 0.004). Using metagenomics, 1,021 species were identified. The upper gut microbiota was revealed to be less rich than the lower gut microbiota, with 37,622 reads from the stomach, 28,390 from the duodenum, and 79,047 from the left colon (p < 0.009). There were fewer reads for aero-intolerant species in the upper gut (8,656 in the stomach, 5,188 in the duodenum and 72,262 in the left colon, p < 0.02). Patients taking proton pump inhibitors (PPI) were then revealed to have a higher stomach pH and a greater diversity of species in the upper digestive tract than patients not receiving treatment (p < 0.001). CONCLUSION: Significant modifications in bacterial composition and diversity exist throughout the gastrointestinal tract. We suggest that the upper gut may be key to understanding the relationship between the gut microbiota and health. FAU - Mailhe, Morgane AU - Mailhe M AD - Aix Marseille Univ, IRD, MEPHI, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. FAU - Ricaboni, Davide AU - Ricaboni D AD - Aix Marseille Univ, IRD, MEPHI, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. AD - Department of Clinical and Biomedical Sciences Luigi Sacco, III Division of Infectious Diseases, University of Milano, Via GB Grassi, 74, 20157, Milan, Italy. FAU - Vitton, Veronique AU - Vitton V AD - Service de Gastroenterologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, 13915, Marseille, France. FAU - Gonzalez, Jean-Michel AU - Gonzalez JM AD - Service de Gastroenterologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, 13915, Marseille, France. FAU - Bachar, Dipankar AU - Bachar D AD - Aix Marseille Univ, IRD, MEPHI, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. FAU - Dubourg, Gregory AU - Dubourg G AD - Aix Marseille Univ, IRD, MEPHI, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. FAU - Cadoret, Frederic AU - Cadoret F AD - Aix Marseille Univ, IRD, MEPHI, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. FAU - Robert, Catherine AU - Robert C AD - Aix Marseille Univ, IRD, VITROME, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseillle, France. FAU - Delerce, Jeremy AU - Delerce J AD - Aix Marseille Univ, IRD, MEPHI, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. FAU - Levasseur, Anthony AU - Levasseur A AD - Aix Marseille Univ, IRD, MEPHI, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. FAU - Fournier, Pierre-Edouard AU - Fournier PE AD - Aix Marseille Univ, IRD, VITROME, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseillle, France. FAU - Angelakis, Emmanouil AU - Angelakis E AD - Aix Marseille Univ, IRD, VITROME, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseillle, France. FAU - Lagier, Jean-Christophe AU - Lagier JC AD - Aix Marseille Univ, IRD, MEPHI, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. FAU - Raoult, Didier AU - Raoult D AD - Aix Marseille Univ, IRD, MEPHI, IHU - Mediterranee Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. didier.raoult@gmail.com. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Retracted Publication DEP - 20181024 PL - England TA - BMC Microbiol JT - BMC microbiology JID - 100966981 RN - 0 (DNA, Bacterial) RN - 0 (Proton Pump Inhibitors) RN - 0 (RNA, Ribosomal, 16S) SB - IM RIN - BMC Microbiol. 2024 Jan 3;24(1):10. PMID: 38172679 MH - Adult MH - Aged MH - Aged, 80 and over MH - Bacteria/*classification/isolation & purification MH - Colon/*microbiology MH - Colonoscopy MH - Colony Count, Microbial MH - DNA, Bacterial/genetics MH - Endoscopy, Digestive System MH - Female MH - *Gastrointestinal Microbiome MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Hydrogen-Ion Concentration MH - Male MH - *Metagenomics MH - Middle Aged MH - Proton Pump Inhibitors/administration & dosage MH - RNA, Ribosomal, 16S/genetics MH - Sequence Analysis, DNA MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Stomach/*microbiology MH - Young Adult PMC - PMC6201554 OTO - NOTNLM OT - Culturomics OT - Gut microbiota OT - Metagenomics OT - New species COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Patients gave their signed informed consent and the study was validated by the ethics committee of the Institut Hospitalo-Universitaire (IHU) Mediterranee Infection under number 2016-010. CONSENT FOR PUBLICATION: Not applicable. COMPETING INTERESTS: The authors have no competing interests or other interests that might be perceived to influence the results and discussion reported in this paper. The authors have no personal or financial conflict of interest. PUBLISHER'S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EDAT- 2018/10/26 06:00 MHDA- 2019/07/06 06:00 PMCR- 2018/10/24 CRDT- 2018/10/26 06:00 PHST- 2018/05/24 00:00 [received] PHST- 2018/10/04 00:00 [accepted] PHST- 2018/10/26 06:00 [entrez] PHST- 2018/10/26 06:00 [pubmed] PHST- 2019/07/06 06:00 [medline] PHST- 2018/10/24 00:00 [pmc-release] AID - 10.1186/s12866-018-1304-7 [pii] AID - 1304 [pii] AID - 10.1186/s12866-018-1304-7 [doi] PST - epublish SO - BMC Microbiol. 2018 Oct 24;18(1):157. doi: 10.1186/s12866-018-1304-7.