Human Stomach Microbiome

Updated July 2016. Feel free to leave suggestions for more in the comments below.

Research papers

Comparison of Gastric Microbiota Between Gastric Juice and Mucosa by Next Generation Sequencing Method – Jihee Sung – Journal of Cancer Prevention – April 2016

Identification of low abundance microbiome in clinical samples using whole genome sequencing – Chao Zhang – Genome Biology – November 2015

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome – DeAnna E. Beasley, Amanda M. Koltz, Joanna E. Lambert, Noah Fierer, Rob R. Dunn – PLOS ONE – July 2015

Comparisons of stomach acidity across trophic groups in mammal and bird taxa show that scavengers and carnivores have significantly higher stomach acidities compared to herbivores or carnivores feeding on phylogenetically distant prey such as insects or fish.

Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett’s Esophagus Cohort – Alevtina Gall, Jutta Fero, Connor McCoy, Brian C. Claywell, Carissa A. Sanchez, Patricia L. Blount, Xiaohong Li, Thomas L. Vaughan, Frederick A. Matsen, Brian J. Reid, Nina R. Salama – PLOS ONE – June 2015

The bacterial composition in the upper GI tract was characterized in a subset of participants (n=12) of the Seattle Barrett’s Esophagus Research cohort using broad-range 16S PCR and pyrosequencing of biopsy and brush samples collected from squamous esophagus, Barrett’s esophagus, stomach corpus and stomach antrum.

Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia – Dariush Nasrollahzadeh, Reza Malekzadeh, Alexander Ploner, Ramin Shakeri, Masoud Sotoudeh, Saman Fahimi, Siavosh Nasseri-Moghaddam, Farin Kamangar, Christian C. Abnet, Björn Winckler, Farhad Islami, Paolo Boffetta, Paul Brennan, Sanford M. Dawsey & Weimin Ye – Scientific Reports – 2015

DNA was extracted from snap-frozen gastric corpus tissues and 16S rRNA was sequenced on GS-FLX Titanium. After noise removal, an average of 3004 reads per sample was obtained from 93 subjects.

Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer – Francisco Aviles-Jimenez, Flor Vazquez-Jimenez, Rafael Medrano-Guzman, Alejandra Mantilla & Javier Torres – Scientific Reports – February 2014

Study included five patients each of non-atrophic gastritis (NAG), intestinal metaplasia (IM) and intestinal-type gastric cancer (GC). Gastric tissue was obtained and DNA extracted for microbiota analyses using the microarray G3 PhyloChip.

Characterization of bacterial biota in the distal esophagus of Japanese patients with reflux esophagitis and Barrett’s esophagus – Ning Liu, Takafumi Ando*, Kazuhiro Ishiguro, Osamu Maeda, Osamu Watanabe, Kohei Funasaka, Masanao Nakamura, Ryoji Miyahara, Naoki Ohmiya and Hidemi Goto – BMC Infectious Diseases – 2013

Two biopsy specimens were obtained from the distal esophagus at 1 cm above the gastroesophageal junction under endoscopic examination in 18 patients (6 each with normal esophagus, reflux esophagitis, and Barrett’s esophagus) and used for histological examination and DNA extraction.

The role of the gastrointestinal microbiome in Helicobacter pylori pathogenesis – A. Sheh – Gut Microbes – November 2013

Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota – Erik C von Rosenvinge et al.- The ISME Journal – March 2013

Gastric fluid was collected from 25 patients undergoing clinically indicated upper endoscopy. DNA isolates were used for PCR amplification of bacterial 16S ribosomal RNA (rRNA) genes and fungal internal transcribed spacers (ITS).

Probiotics-Containing Yogurts Suppress Helicobacter pylori Load and Modify Immune Response and Intestinal Microbiota in the Helicobacter pylori-Infected Children – Yao-Jong Yang – Helicobacter – August 2012

Structure of the human gastric bacterial community in relation to Helicobacter pylori status – Ana Goldman et al.- The ISME Journal – 2010

We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively).

Bacterial Microbiota Profiling in Gastritis without Helicobacter pylori Infection or Non-Steroidal Anti-Inflammatory Drug Use – Xiao-Xing Li et al. – PLOS ONE – 2009

In this study, cloning and sequencing of the 16S rRNA was used to profile the stomach microbiota from normal and gastritis patients. One hundred and thirty three phylotypes from eight bacterial phyla were identified.

Molecular analysis of the bacterial microbiota in the human stomach – Elisabeth M. Bik et al. – PNAS – January 2006

We characterized bacterial diversity within the human gastric mucosa by using a small subunit 16S rDNA clone library approach and analyzed 1,833 sequences generated by broad-range bacterial PCR from 23 gastric endoscopic biopsy samples.

Review papers

The esophageal microbiota in health and disease – Vincenzo Di Pilato – Annals of the New York Academy of Sciences – July 2016

The stomach in health and disease – R H Hunt – Gut – September 2015

Gastric Microbiota – Gianluca Ianiro – Helicobacter – September 2015

Effect of Helicobacter pylori Infection on the Composition of Gastric Microbiota in the Development of Gastric Cancer – Lei Cao – Gastrointestinal Tumors – April 2015

H. pylori and its modulation of gastrointestinal microbiota – Christian Schulz – Journal of Digestive Diseases – March 2015

The human gastric microbiota: Is it time to rethink the pathogenesis of stomach diseases?– Gerardo Nardone – United European Gastroenterology – January 2015

Gastric and Enterohepatic Helicobacters other than Helicobacter pylori – Armelle Ménard – Helicobacter – August 2014

Human gut microbiota: does diet matter? – Johanna Maukonen – Winter Meeting of the Nutrition Society – Proceedings of the Nutrition Society – August 2014

Gastric Microbiome and Gastric Cancer – Brawner, Kyle M. – The Cancer Journal – May 2014

Microbiome in Reflux Disorders and Esophageal Adenocarcinoma – Yang, Liying – The Cancer Journal – May 2014

Role of childhood infection in the sequelae of H. pylori disease – Paul R. Harris – Gut Microbes – November 2013

Survival in hostile territory: the microbiota of the stomach – Ines Yang – FEMS Microbiology Reviews