Data on gut metagenomes of the patients with alcoholic dependence syndrome and alcoholic liver cirrhosis

Alcoholism is associated with significant changes in gut microbiota composition. Metagenomic sequencing allows to assess the altered abundance levels of bacterial taxa and genes in a culture-independent way. We collected 99 stool samples from the patients with alcoholic dependence syndrome (n=72) and alcoholic liver cirrhosis (n=27). Each of the samples was surveyed using “shotgun” (whole-genome) sequencing on SOLiD platform. The reads are deposited in the ENA (project ID: PRJEB18041).

using "shotgun" (whole-genome) sequencing on SOLiD platform. The reads are deposited in the ENA (project ID: PRJEB18041

Value of the data
The data describes the human gut microbiota composition in two cohorts of the patients with alcoholism manifesting distinct degrees of liver dysfunctions: patients with alcoholic dependence syndrome (ADS; alcoholics without advanced liver disease) and patients with alcoholic liver cirrhosis (ALC; alcoholics with advanced liver disease).
The data can be used for identifying the changes of gut microbiota associated with alcoholism as well as with the associated liver damage at the levels of community structure (taxonomic composition) and gene potential (functional composition).
The data can be used for validating the universality of potential biomarkers of alcoholismassociated dysbiosis via the meta-analysis together with the published gut metagenomes of the world populations.
The data can be used in phylogeographic analyses of human microbiota to assess the genomic variations of the gut microbial species typical for Russian population as compared with the other world populations.

Data
The data represent 99 "shotgun" metagenomes of stool samples collected from the patients with ADS and ALC in 3 clinical centers from 3 Russian cities -Moscow, Kazan and Saint-Petersburg. The datasets include 25.8 716.1 mln of 50 bp reads per sample (mean7 s.d., 127.5 Gbp in total). The description of the data is listed in Table 1.

Cohorts assembly
The study was approved by the ethical committee of the Federal Research Clinical Centre of Physical-Chemical Medicine. Each patient signed an informed consent before the start of the study. The patients were enrolled in Moscow Clinical Scientific Center (Moscow), Narcology Dispensary of Republic of Tatarstan (Kazan) and Saint-Petersburg Bekhterev Psychoneurological Research Institute (Saint-Petersburg). The cohort included 2 groups: 72 patients with the diagnosis "alcoholic dependence syndrome" and 27 -with "alcoholic liver cirrhosis".

Patients inclusion and exclusion criteria
General exclusion criteria: non-alcoholic liver diseases, decompensated diseases of other organs, intake of probiotics and/or prebiotics, medications (non-steroidal anti-inflammatory drugs, antibiotics and proton pump inhibitors) less than 1 month prior to the sample collection, abdominal surgery less than 3 months prior to the sample collection. Additional inclusion criteria for the ALC group: alcoholic liver cirrhosis, age over 18 years and alcohol abuse history; the exclusion criteria were the stool changes and bowel movement frequency. Additional inclusion criteria for the ADS group: alcoholic dependence syndrome, alcohol abuse history of Z 8 years. Additional exclusion criteria specific for the ADS cohort: decrease of thrombocytes, albumin and/or prothrombin, increase of INR (international normalized ratio).

Sample collection and metagenomic sequencing
Stool samples were collected from the subjects, stored and subject to DNA extraction as described before [1]. "Shotgun" metagenomic libraries preparation and sequencing using SOLiD 5500xl platform (Life Technology, USA) was performed according to the recommendations of the manufacturer using the following reagent kits: 5500 SOLiD Fragment Library Core Kit, SOLiD Fragment Library Barcoding Kit, SOLiD FlowChip Kit, SOLiD FWD SR S50 Kit, SOLiD Run Cycle Buffer Kit. Barcoded fragment (nonpaired) read libraries were created from 5 μg of total DNA for each of the samples. The resulting read length was 50 bp.