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. 2017 Jan 17;11:98–102. doi: 10.1016/j.dib.2017.01.008

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

Alexander V Tyakht a,⁎, Veronika B Dubinkina a, Vera Y Odintsova b, Konstantin S Yarygin a,b, Boris A Kovarsky b, Alexander V Pavlenko a,b, Dmitry S Ischenko a,b, Anna S Popenko b, Dmitry G Alexeev a,b, Anastasiya Y Taraskina c, Regina F Nasyrova c, Evgeny M Krupitski c, Nino V Shalikiani d, Igor G Bakulin d, Petr L Shcherbakov d, Lyubov O Skorodumova b, Andrei K Larin b, Elena S Kostryukova a,b, Rustam A Abdulkhakov e, Sayar R Abdulkhakov e,f, Sergey Y Malanin f, Ruzilya K Ismagilova f, Tatiana V Grigoryeva f, Elena N Ilina b, Vadim M Govorun a
PMCID: PMC5257029  PMID: 28138508

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).

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

Specifications Table

Subject area Biology
More specific subject area Bacterial metagenomics
Type of data Text files: sequences
How data was acquired DNA sequencing using SOLiD 5500xl platform
Data format Raw
Experimental factors DNA extracted from stool samples
Experimental features Barcoded 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 location Kazan, Russian Federation; Moscow, Russian Federation; Saint-Petersburg, Russian Federation
Data accessibility The datasets are deposited in the ENA (project ID: PRJEB18041, URL: http://www.ebi.ac.uk/ena/data/view/PRJEB18041)
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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.

1. 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 ID ENA sample accession ENA experiment ID Group Collection site Age, years Gender BMI
ADS_1 ERS1454656 ERR1748966 ADS Saint-Petersburg N/A M 21.67
ADS_10 ERS1454657 ERR1748967 ADS Saint-Petersburg 39 M 20.13
ADS_11 ERS1454658 ERR1748968 ADS Saint-Petersburg 60 M NA
ADS_12 ERS1454659 ERR1748969 ADS Saint-Petersburg 41 M 20.46
ADS_13 ERS1454660 ERR1748970 ADS Saint-Petersburg 55 M 19.86
ADS_14 ERS1454661 ERR1748971 ADS Saint-Petersburg 29 M 23.5
ADS_15 ERS1454662 ERR1748972 ADS Saint-Petersburg 47 M 24.76
ADS_16 ERS1454663 ERR1748973 ADS Saint-Petersburg 43 M 20.45
ADS_17 ERS1454664 ERR1748974 ADS Saint-Petersburg 52 M 19.35
ADS_18 ERS1454665 ERR1748975 ADS Saint-Petersburg 41 M 21.59
ADS_19 ERS1454666 ERR1748976 ADS Saint-Petersburg 36 M 19.23
ADS_2 ERS1454667 ERR1748977 ADS Saint-Petersburg 50 M 21.52
ADS_20 ERS1454668 ERR1748978 ADS Saint-Petersburg 29 M 26.8
ADS_21 ERS1454669 ERR1748979 ADS Saint-Petersburg 45 M 24.23
ADS_22 ERS1454670 ERR1748980 ADS Saint-Petersburg 49 M 23.04
ADS_23 ERS1454671 ERR1748981 ADS Saint-Petersburg 26 M 23.69
ADS_24 ERS1454672 ERR1748982 ADS Saint-Petersburg 45 M NA
ADS_25 ERS1454673 ERR1748983 ADS Saint-Petersburg 50 M 19.46
ADS_26 ERS1454674 ERR1748984 ADS Saint-Petersburg 40 M 24.26
ADS_27 ERS1454675 ERR1748985 ADS Saint-Petersburg 29 M NA
ADS_28 ERS1454676 ERR1748986 ADS Saint-Petersburg 52 M NA
ADS_29 ERS1454677 ERR1748987 ADS Saint-Petersburg 44 M 23.6
ADS_3 ERS1454678 ERR1748988 ADS Saint-Petersburg 37 M 21.41
ADS_30 ERS1454679 ERR1748989 ADS Saint-Petersburg 54 M NA
ADS_31 ERS1454680 ERR1748990 ADS Saint-Petersburg 31 M 22.6
ADS_32 ERS1454681 ERR1748991 ADS Saint-Petersburg 49 M NA
ADS_33 ERS1454682 ERR1748992 ADS Saint-Petersburg 40 M 16.58
ADS_34 ERS1454683 ERR1748993 ADS Saint-Petersburg 25 M 19.7
ADS_35 ERS1454684 ERR1748994 ADS Saint-Petersburg 38 M 21.69
ADS_36 ERS1454685 ERR1748995 ADS Saint-Petersburg 54 M NA
ADS_37 ERS1454686 ERR1748996 ADS Saint-Petersburg 32 M 17.25
ADS_38 ERS1454687 ERR1748997 ADS Saint-Petersburg 43 M NA
ADS_39 ERS1454688 ERR1748998 ADS Kazan 20 M NA
ADS_4 ERS1454689 ERR1748999 ADS Saint-Petersburg 53 M 23.23
ADS_40 ERS1454690 ERR1749000 ADS Kazan 30 M 21.97
ADS_41 ERS1454691 ERR1749001 ADS Kazan 40 M 19.66
ADS_42 ERS1454692 ERR1749002 ADS Kazan 59 F 30.76
ADS_43 ERS1454693 ERR1749003 ADS Kazan 31 M 20.98
ADS_44 ERS1454694 ERR1749004 ADS Kazan 60 M 25.62
ADS_45 ERS1454695 ERR1749005 ADS Kazan 53 M 20.72
ADS_46 ERS1454696 ERR1749006 ADS Kazan 48 M 22.49
ADS_47 ERS1454697 ERR1749007 ADS Kazan 55 M 27.89
ADS_48 ERS1454698 ERR1749008 ADS Kazan 45 M 21.26
ADS_49 ERS1454699 ERR1749009 ADS Kazan 54 M 28.33
ADS_5 ERS1454700 ERR1749010 ADS Saint-Petersburg 33 M 19.1
ADS_50 ERS1454701 ERR1749011 ADS Kazan 36 M 21.14
ADS_51 ERS1454702 ERR1749012 ADS Kazan 41 M 18.26
ADS_52 ERS1454703 ERR1749013 ADS Kazan 32 M 23.6
ADS_53 ERS1454704 ERR1749014 ADS Kazan 41 M 22.53
ADS_54 ERS1454705 ERR1749015 ADS Kazan 34 M 28
ADS_55 ERS1454706 ERR1749016 ADS Kazan 30 M 23.24
ADS_56 ERS1454707 ERR1749017 ADS Kazan 59 M 24.69
ADS_57 ERS1454708 ERR1749018 ADS Kazan 55 M 26.99
ADS_58 ERS1454709 ERR1749019 ADS Kazan 31 M 23.46
ADS_59 ERS1454710 ERR1749020 ADS Kazan 38 M 23.33
ADS_6 ERS1454711 ERR1749021 ADS Saint-Petersburg 44 M NA
ADS_60 ERS1454712 ERR1749022 ADS Kazan 56 F 36.85
ADS_61 ERS1454713 ERR1749023 ADS Kazan 53 F 29.74
ADS_62 ERS1454714 ERR1749024 ADS Kazan 44 M 20.05
ADS_63 ERS1454715 ERR1749025 ADS Kazan 52 M 23.94
ADS_64 ERS1454716 ERR1749026 ADS Kazan 43 M 25.98
ADS_65 ERS1454717 ERR1749027 ADS Kazan 47 M 24.54
ADS_66 ERS1454718 ERR1749028 ADS Kazan 57 M 22.72
ADS_67 ERS1454719 ERR1749029 ADS Kazan 57 M 26.78
ADS_68 ERS1454720 ERR1749030 ADS Kazan 51 M 29.75
ADS_69 ERS1454721 ERR1749031 ADS Kazan 33 M 25.47
ADS_7 ERS1454722 ERR1749032 ADS Saint-Petersburg 37 M 21.46
ADS_70 ERS1454723 ERR1749033 ADS Kazan 32 M 19.25
ADS_71 ERS1454724 ERR1749034 ADS Kazan 60 F 35.49
ADS_72 ERS1454725 ERR1749035 ADS Kazan 41 M 25.66
ADS_8 ERS1454726 ERR1749036 ADS Saint-Petersburg 56 M 20.17
ADS_9 ERS1454727 ERR1749037 ADS Saint-Petersburg 56 M 21.19
ALC_1 ERS1454728 ERR1749038 ALC Moscow 46 M 33.33
ALC_10 ERS1454729 ERR1749039 ALC Moscow 58 F 25.08
ALC_11 ERS1454730 ERR1749040 ALC Moscow 55 M 24.49
ALC_12 ERS1454731 ERR1749041 ALC Moscow 37 M 28.53
ALC_13 ERS1454732 ERR1749042 ALC Moscow 32 M 37.65
ALC_14 ERS1454733 ERR1749043 ALC Moscow 39 F 23.44
ALC_15 ERS1454734 ERR1749044 ALC Moscow 50 F 27.34
ALC_16 ERS1454735 ERR1749045 ALC Moscow 53 M 26.78
ALC_17 ERS1454736 ERR1749046 ALC Moscow 54 M 30.45
ALC_18 ERS1454737 ERR1749047 ALC Moscow 40 M 23.89
ALC_19 ERS1454738 ERR1749048 ALC Moscow 50 M 30.02
ALC_2 ERS1454739 ERR1749049 ALC Moscow 41 M 23.93
ALC_20 ERS1454740 ERR1749050 ALC Moscow 52 M 20.05
ALC_21 ERS1454741 ERR1749051 ALC Moscow 52 M 22.83
ALC_22 ERS1454742 ERR1749052 ALC Moscow 52 M 28.39
ALC_23 ERS1454743 ERR1749053 ALC Moscow 52 M 24.9
ALC_24 ERS1454744 ERR1749054 ALC Moscow 54 M 26.59
ALC_25 ERS1454745 ERR1749055 ALC Moscow 44 M 30.25
ALC_26 ERS1454746 ERR1749056 ALC Moscow 55 M 33.91
ALC_27 ERS1454747 ERR1749057 ALC Moscow 47 M 25.99
ALC_3 ERS1454748 ERR1749058 ALC Moscow 57 M 25
ALC_4 ERS1454749 ERR1749059 ALC Moscow 52 F 22.77
ALC_5 ERS1454750 ERR1749060 ALC Moscow 58 M 30.93
ALC_6 ERS1454751 ERR1749061 ALC Moscow 49 F 27.06
ALC_7 ERS1454752 ERR1749062 ALC Moscow 42 M 31.83
ALC_8 ERS1454753 ERR1749063 ALC Moscow 57 M 24.07
ALC_9 ERS1454754 ERR1749064 ALC Moscow 44 M 30.72
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2. Experimental design, materials and methods

2.1. 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”.

2.2. 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).

2.3. 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.

Acknowledgments

This work was financially supported by Ministry of Education and Science of the Russian Federation (unique project identifier RFMEFI60414X0119).

Footnotes

Transparency document

Transparency data associated with this article can be found in the online version at http://dx.doi. org/10.1016/j.dib.2017.01.008.

Transparency document. Supplementary material

Supplementary material

mmc1.pdf (1.2MB, pdf)

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Reference

  • 1.Tyakht A.V., Kostryukova E.S., Popenko A.S., Belenikin M.S., Pavlenko A.V., Larin A.K., Karpova I.Y., Selezneva O.V., Semashko T.A., Ospanova E.A., Babenko V.V., Maev I.V., Cheremushkin S.V., Kucheryavyy Y.A., Shcherbakov P.L., Grinevich V.B., Efimov O.I., Sas E.I., Abdulkhakov R.A., Abdulkhakov S.R., Lyalyukova E.A., Livzan M.A., Vlassov V.V., Sagdeev R.Z., Tsukanov V.V., Osipenko M.F., Kozlova I.V., Tkachev A.V., Sergienko V.I., Alexeev D.G., Govorun V.M. Human gut microbiota community structures in urban and rural populations in Russia. Nat. Commun. 2013;4:2469. doi: 10.1038/ncomms3469. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

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Supplementary Materials

Supplementary material

mmc1.pdf (1.2MB, pdf)

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