Literature DB >> 28138508

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

Alexander V Tyakht1, Veronika B Dubinkina1, Vera Y Odintsova2, Konstantin S Yarygin3, Boris A Kovarsky2, Alexander V Pavlenko3, Dmitry S Ischenko3, Anna S Popenko2, Dmitry G Alexeev3, Anastasiya Y Taraskina4, Regina F Nasyrova4, Evgeny M Krupitski4, Nino V Shalikiani5, Igor G Bakulin5, Petr L Shcherbakov5, Lyubov O Skorodumova2, Andrei K Larin2, Elena S Kostryukova3, Rustam A Abdulkhakov6, Sayar R Abdulkhakov7, Sergey Y Malanin8, Ruzilya K Ismagilova8, Tatiana V Grigoryeva8, Elena N Ilina2, Vadim M Govorun1.   

Abstract

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).

Entities:  

Keywords:  Alcohol dependence syndrome; Alcoholic liver cirrhosis; Alcoholism; Dysbiosis; Gut microbiota; Metagenome; “Shotgun” metagenomics

Year:  2017        PMID： 28138508      PMCID： PMC5257029          DOI： 10.1016/j.dib.2017.01.008

Source DB:  PubMed          Journal:  Data Brief        ISSN： 2352-3409


Specifications Table 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 alcoholism-associated 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±16.1 mln of 50 bp reads per sample (mean±s.d., 127.5 Gbp in total). The description of the data is listed in Table 1.
Table 1

Information about the datasets, samples and subjects. Abbreviations: ADS - alcohol dependence syndrome, ALC - alcoholic liver cirrhosis, BMI – body-mass index, ENA – European Nucleotide Archive, NA – not available.

Sample IDENA sample accessionENA experiment IDGroupCollection siteAge, yearsGenderBMI
ADS_1ERS1454656ERR1748966ADSSaint-PetersburgN/AM21.67
ADS_10ERS1454657ERR1748967ADSSaint-Petersburg39M20.13
ADS_11ERS1454658ERR1748968ADSSaint-Petersburg60MNA
ADS_12ERS1454659ERR1748969ADSSaint-Petersburg41M20.46
ADS_13ERS1454660ERR1748970ADSSaint-Petersburg55M19.86
ADS_14ERS1454661ERR1748971ADSSaint-Petersburg29M23.5
ADS_15ERS1454662ERR1748972ADSSaint-Petersburg47M24.76
ADS_16ERS1454663ERR1748973ADSSaint-Petersburg43M20.45
ADS_17ERS1454664ERR1748974ADSSaint-Petersburg52M19.35
ADS_18ERS1454665ERR1748975ADSSaint-Petersburg41M21.59
ADS_19ERS1454666ERR1748976ADSSaint-Petersburg36M19.23
ADS_2ERS1454667ERR1748977ADSSaint-Petersburg50M21.52
ADS_20ERS1454668ERR1748978ADSSaint-Petersburg29M26.8
ADS_21ERS1454669ERR1748979ADSSaint-Petersburg45M24.23
ADS_22ERS1454670ERR1748980ADSSaint-Petersburg49M23.04
ADS_23ERS1454671ERR1748981ADSSaint-Petersburg26M23.69
ADS_24ERS1454672ERR1748982ADSSaint-Petersburg45MNA
ADS_25ERS1454673ERR1748983ADSSaint-Petersburg50M19.46
ADS_26ERS1454674ERR1748984ADSSaint-Petersburg40M24.26
ADS_27ERS1454675ERR1748985ADSSaint-Petersburg29MNA
ADS_28ERS1454676ERR1748986ADSSaint-Petersburg52MNA
ADS_29ERS1454677ERR1748987ADSSaint-Petersburg44M23.6
ADS_3ERS1454678ERR1748988ADSSaint-Petersburg37M21.41
ADS_30ERS1454679ERR1748989ADSSaint-Petersburg54MNA
ADS_31ERS1454680ERR1748990ADSSaint-Petersburg31M22.6
ADS_32ERS1454681ERR1748991ADSSaint-Petersburg49MNA
ADS_33ERS1454682ERR1748992ADSSaint-Petersburg40M16.58
ADS_34ERS1454683ERR1748993ADSSaint-Petersburg25M19.7
ADS_35ERS1454684ERR1748994ADSSaint-Petersburg38M21.69
ADS_36ERS1454685ERR1748995ADSSaint-Petersburg54MNA
ADS_37ERS1454686ERR1748996ADSSaint-Petersburg32M17.25
ADS_38ERS1454687ERR1748997ADSSaint-Petersburg43MNA
ADS_39ERS1454688ERR1748998ADSKazan20MNA
ADS_4ERS1454689ERR1748999ADSSaint-Petersburg53M23.23
ADS_40ERS1454690ERR1749000ADSKazan30M21.97
ADS_41ERS1454691ERR1749001ADSKazan40M19.66
ADS_42ERS1454692ERR1749002ADSKazan59F30.76
ADS_43ERS1454693ERR1749003ADSKazan31M20.98
ADS_44ERS1454694ERR1749004ADSKazan60M25.62
ADS_45ERS1454695ERR1749005ADSKazan53M20.72
ADS_46ERS1454696ERR1749006ADSKazan48M22.49
ADS_47ERS1454697ERR1749007ADSKazan55M27.89
ADS_48ERS1454698ERR1749008ADSKazan45M21.26
ADS_49ERS1454699ERR1749009ADSKazan54M28.33
ADS_5ERS1454700ERR1749010ADSSaint-Petersburg33M19.1
ADS_50ERS1454701ERR1749011ADSKazan36M21.14
ADS_51ERS1454702ERR1749012ADSKazan41M18.26
ADS_52ERS1454703ERR1749013ADSKazan32M23.6
ADS_53ERS1454704ERR1749014ADSKazan41M22.53
ADS_54ERS1454705ERR1749015ADSKazan34M28
ADS_55ERS1454706ERR1749016ADSKazan30M23.24
ADS_56ERS1454707ERR1749017ADSKazan59M24.69
ADS_57ERS1454708ERR1749018ADSKazan55M26.99
ADS_58ERS1454709ERR1749019ADSKazan31M23.46
ADS_59ERS1454710ERR1749020ADSKazan38M23.33
ADS_6ERS1454711ERR1749021ADSSaint-Petersburg44MNA
ADS_60ERS1454712ERR1749022ADSKazan56F36.85
ADS_61ERS1454713ERR1749023ADSKazan53F29.74
ADS_62ERS1454714ERR1749024ADSKazan44M20.05
ADS_63ERS1454715ERR1749025ADSKazan52M23.94
ADS_64ERS1454716ERR1749026ADSKazan43M25.98
ADS_65ERS1454717ERR1749027ADSKazan47M24.54
ADS_66ERS1454718ERR1749028ADSKazan57M22.72
ADS_67ERS1454719ERR1749029ADSKazan57M26.78
ADS_68ERS1454720ERR1749030ADSKazan51M29.75
ADS_69ERS1454721ERR1749031ADSKazan33M25.47
ADS_7ERS1454722ERR1749032ADSSaint-Petersburg37M21.46
ADS_70ERS1454723ERR1749033ADSKazan32M19.25
ADS_71ERS1454724ERR1749034ADSKazan60F35.49
ADS_72ERS1454725ERR1749035ADSKazan41M25.66
ADS_8ERS1454726ERR1749036ADSSaint-Petersburg56M20.17
ADS_9ERS1454727ERR1749037ADSSaint-Petersburg56M21.19
ALC_1ERS1454728ERR1749038ALCMoscow46M33.33
ALC_10ERS1454729ERR1749039ALCMoscow58F25.08
ALC_11ERS1454730ERR1749040ALCMoscow55M24.49
ALC_12ERS1454731ERR1749041ALCMoscow37M28.53
ALC_13ERS1454732ERR1749042ALCMoscow32M37.65
ALC_14ERS1454733ERR1749043ALCMoscow39F23.44
ALC_15ERS1454734ERR1749044ALCMoscow50F27.34
ALC_16ERS1454735ERR1749045ALCMoscow53M26.78
ALC_17ERS1454736ERR1749046ALCMoscow54M30.45
ALC_18ERS1454737ERR1749047ALCMoscow40M23.89
ALC_19ERS1454738ERR1749048ALCMoscow50M30.02
ALC_2ERS1454739ERR1749049ALCMoscow41M23.93
ALC_20ERS1454740ERR1749050ALCMoscow52M20.05
ALC_21ERS1454741ERR1749051ALCMoscow52M22.83
ALC_22ERS1454742ERR1749052ALCMoscow52M28.39
ALC_23ERS1454743ERR1749053ALCMoscow52M24.9
ALC_24ERS1454744ERR1749054ALCMoscow54M26.59
ALC_25ERS1454745ERR1749055ALCMoscow44M30.25
ALC_26ERS1454746ERR1749056ALCMoscow55M33.91
ALC_27ERS1454747ERR1749057ALCMoscow47M25.99
ALC_3ERS1454748ERR1749058ALCMoscow57M25
ALC_4ERS1454749ERR1749059ALCMoscow52F22.77
ALC_5ERS1454750ERR1749060ALCMoscow58M30.93
ALC_6ERS1454751ERR1749061ALCMoscow49F27.06
ALC_7ERS1454752ERR1749062ALCMoscow42M31.83
ALC_8ERS1454753ERR1749063ALCMoscow57M24.07
ALC_9ERS1454754ERR1749064ALCMoscow44M30.72

Experimental design, materials and methods

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 ≥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 (non-paired) read libraries were created from 5 μg of total DNA for each of the samples. The resulting read length was 50 bp.
Subject areaBiology
More specific subject areaBacterial metagenomics
Type of dataText files: sequences
How data was acquiredDNA sequencing using SOLiD 5500xl platform
Data formatRaw
Experimental factorsDNA extracted from stool samples
Experimental featuresBarcoded fragment (non-paired) read libraries were created from 5 μg of total DNA for each of the samples. The sequencing was performed using the SOLiD 5500xl platform according to the recommendations of the manufacturer.
Data source locationKazan, Russian Federation; Moscow, Russian Federation; Saint-Petersburg, Russian Federation
Data accessibilityThe datasets are deposited in the ENA (project ID: PRJEB18041, URL: http://www.ebi.ac.uk/ena/data/view/PRJEB18041)
  1 in total

1.  Human gut microbiota community structures in urban and rural populations in Russia.

Authors:  Alexander V Tyakht; Elena S Kostryukova; Anna S Popenko; Maxim S Belenikin; Alexander V Pavlenko; Andrey K Larin; Irina Y Karpova; Oksana V Selezneva; Tatyana A Semashko; Elena A Ospanova; Vladislav V Babenko; Igor V Maev; Sergey V Cheremushkin; Yuriy A Kucheryavyy; Petr L Shcherbakov; Vladimir B Grinevich; Oleg I Efimov; Evgenii I Sas; Rustam A Abdulkhakov; Sayar R Abdulkhakov; Elena A Lyalyukova; Maria A Livzan; Valentin V Vlassov; Renad Z Sagdeev; Vladislav V Tsukanov; Marina F Osipenko; Irina V Kozlova; Alexander V Tkachev; Valery I Sergienko; Dmitry G Alexeev; Vadim M Govorun
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919
  1 in total
  3 in total

1.  Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease.

Authors:  Veronika B Dubinkina; Alexander V Tyakht; Vera Y Odintsova; Konstantin S Yarygin; Boris A Kovarsky; Alexander V Pavlenko; Dmitry S Ischenko; Anna S Popenko; Dmitry G Alexeev; Anastasiya Y Taraskina; Regina F Nasyrova; Evgeny M Krupitsky; Nino V Shalikiani; Igor G Bakulin; Petr L Shcherbakov; Lyubov O Skorodumova; Andrei K Larin; Elena S Kostryukova; Rustam A Abdulkhakov; Sayar R Abdulkhakov; Sergey Y Malanin; Ruzilya K Ismagilova; Tatiana V Grigoryeva; Elena N Ilina; Vadim M Govorun
Journal:  Microbiome       Date:  2017-10-17       Impact factor: 14.650

2.  Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies.

Authors:  Mohadeseh Naseri; Fahimeh Palizban; Abbas Yadegar; Mohsen Khodarahmi; Hamid Asadzadeh Aghdaei; Hamidreza Houri; Javad Zahiri
Journal:  Gut Pathog       Date:  2022-02-15       Impact factor: 4.181

3.  Integrated Analyses of the Gut Microbiota, Intestinal Permeability, and Serum Metabolome Phenotype in Rats with Alcohol Withdrawal Syndrome.

Authors:  Fan Yang; Jidong Wei; Mengke Shen; Yating Ding; Yufan Lu; Hafiz Muhammad Ishaq; Duan Li; Dong Yan; Qi Wang; Ruiling Zhang
Journal:  Appl Environ Microbiol       Date:  2021-08-26       Impact factor: 4.792
  3 in total

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