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Sonets IV, Solovyev MA, Ivanova VA, Vasiluev PA, Kachalkin AV, Ochkalova SD, Korobeynikov AI, Razin SV, Ulianov SV, Tyakht AV. Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider. Food Microbiol 2024; 121:104520. [PMID: 38637082 DOI: 10.1016/j.fm.2024.104520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 04/20/2024]
Abstract
Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.
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Affiliation(s)
- Ignat V Sonets
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.
| | - Mikhail A Solovyev
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | | | - Petr A Vasiluev
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Research Center for Medical Genetics, Moscow, Russia
| | - Aleksey V Kachalkin
- Department of Soil Biology, Faculty of Soil Science, Lomonosov Moscow State University, Moscow, Russia; G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, Russia
| | - Sofia D Ochkalova
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, Saint Petersburg, 197101, Russia; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, 199004, Russia
| | - Anton I Korobeynikov
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, 199004, Russia; Department of Statistical Modelling, Saint Petersburg State University, Saint Petersburg, 199004, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - Alexander V Tyakht
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
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2
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Sonets IV, Dovidchenko NV, Ulianov SV, Yarina MS, Koshechkin SI, Razin SV, Krasnopolskaya LM, Tyakht AV. Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing. J Fungi (Basel) 2023; 9:1020. [PMID: 37888276 PMCID: PMC10608111 DOI: 10.3390/jof9101020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/28/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023] Open
Abstract
Ganoderma lucidum exhibits the ability to synthesize a diverse range of biologically active molecules with significant pharmaceutical potential, including xylomannan and fucogalactan, which have demonstrated antitumor activity. However, there exists considerable intra-species variability in the capacity to produce these metabolites at high concentrations, likely reflecting the high genomic diversity observed from a limited number of strains sequenced to date. We employed high-throughput shotgun sequencing to obtain the complete genome sequence of G. lucidum strain 5.1, which is distinguished by its remarkable xylomannan synthesis capabilities. Through the utilization of semi-automatic reordering based on conformation capture (Hi-C) data, we substantially enhanced the assembly process, resulting in the generation of 12 chromosome-level scaffolds with a cumulative length of 39 Mbp. By employing both de novo and homology-based approaches, we performed comprehensive annotation of the genome, thereby identifying a diverse repertoire of genes likely involved in polysaccharide biosynthesis. The genome sequence generated in this study serves as a valuable resource for elucidating the molecular mechanisms underlying the medicinal potential of Ganoderma species, discovering novel pharmaceutically valuable compounds, and elucidating the ecological mechanisms of the species. Furthermore, the chromosome contact map obtained for the first time for this species extends our understanding of 3D fungal genomics and provides insights into the functional and structural organization within the fungal kingdom.
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Affiliation(s)
- Ignat V. Sonets
- Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia; (I.V.S.); (S.V.U.); (S.V.R.); (A.V.T.)
| | - Nikita V. Dovidchenko
- Knomics LLC, 34 Bld. 1 Narodnogo Opolcheniya Street, 123423 Moscow, Russia; (N.V.D.); (S.I.K.)
- Institute of Protein Research, 4 Institutskaya Street, 142290 Pushchino, Russia
| | - Sergey V. Ulianov
- Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia; (I.V.S.); (S.V.U.); (S.V.R.); (A.V.T.)
- Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | - Maria S. Yarina
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, 119021 Moscow, Russia;
| | - Stanislav I. Koshechkin
- Knomics LLC, 34 Bld. 1 Narodnogo Opolcheniya Street, 123423 Moscow, Russia; (N.V.D.); (S.I.K.)
| | - Sergey V. Razin
- Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia; (I.V.S.); (S.V.U.); (S.V.R.); (A.V.T.)
- Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | | | - Alexander V. Tyakht
- Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia; (I.V.S.); (S.V.U.); (S.V.R.); (A.V.T.)
- Knomics LLC, 34 Bld. 1 Narodnogo Opolcheniya Street, 123423 Moscow, Russia; (N.V.D.); (S.I.K.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia
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3
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Gavrilov AA, Evko GS, Galitsyna AA, Ulianov SV, Kochetkova TV, Merkel AY, Tyakht AV, Razin SV. RNA-DNA interactomes of three prokaryotes uncovered by proximity ligation. Commun Biol 2023; 6:473. [PMID: 37120653 PMCID: PMC10148824 DOI: 10.1038/s42003-023-04853-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
Proximity ligation approaches, which are widely used to study the spatial organization of the genome, also make it possible to reveal patterns of RNA-DNA interactions. Here, we use RedC, an RNA-DNA proximity ligation approach, to assess the distribution of major RNA types along the genomes of E. coli, B. subtilis, and thermophilic archaeon T. adornatum. We find that (i) messenger RNAs preferentially interact with their cognate genes and the genes located downstream in the same operon, which is consistent with polycistronic transcription; (ii) ribosomal RNAs preferentially interact with active protein-coding genes in both bacteria and archaea, indicating co-transcriptional translation; and (iii) 6S noncoding RNA, a negative regulator of bacterial transcription, is depleted from active genes in E. coli and B. subtilis. We conclude that the RedC data provide a rich resource for studying both transcription dynamics and the function of noncoding RNAs in microbial organisms.
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Affiliation(s)
- Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Grigory S Evko
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 117312, Moscow, Russia
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 117312, Moscow, Russia
| | - Alexander V Tyakht
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
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Tkacheva ON, Klimenko NS, Kashtanova DA, Tyakht AV, Maytesyan LV, Akopyan AA, Koshechkin SI, Strazhesko ID. Gut Microbiome in Post-COVID-19 Patients Is Linked to Immune and Cardiovascular Health Status but Not COVID-19 Severity. Microorganisms 2023; 11:microorganisms11041036. [PMID: 37110459 PMCID: PMC10144658 DOI: 10.3390/microorganisms11041036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The composition of the gut microbiome stores the imprints of prior infections and other impacts. COVID-19 can cause changes in inflammatory status that persist for a considerable time after infection ends. As the gut microbiome is closely associated with immunity and inflammation, the infection severity might be linked to its community structure dynamics. Using 16S rRNA sequencing of stool samples, we investigated the microbiome three months after the end of the disease/infection or SARS-CoV-2 contact in 178 post-COVID-19 patients and those who contacted SARS-CoV-2 but were not infected. The cohort included 3 groups: asymptomatic subjects (n = 48), subjects who contacted COVID-19 patients with no further infection (n = 46), and severe patients (n = 86). Using a novel compositional statistical algorithm (nearest balance) and the concept of bacterial co-occurrence clusters (coops), we compared microbiome compositions between the groups as well as with multiple categories of clinical parameters including: immunity, cardiovascular parameters and markers of endothelial dysfunction, and blood metabolites. Although a number of clinical indicators varied drastically across the three groups, no differences in microbiome features were identified between them at this follow-up point. However, there were multiple associations between the microbiome features and clinical data. Among the immunity parameters, the relative lymphocyte number was linked to a balance including 14 genera. Cardiovascular parameters were associated with up to four bacterial cooperatives. Intercellular adhesion molecule 1 was linked to a balance including ten genera and one cooperative. Among the blood biochemistry parameters, calcium was the only parameter associated with the microbiome via a balance of 16 genera. Our results suggest comparable recovery of the gut community structure in the post-COVID-19 period, independently of severity or infection status. The multiple identified associations of clinical analysis data with the microbiome provide hypotheses about the participation of specific taxa in regulating immunity and homeostasis of cardiovascular and other body systems in health, as well as their disruption in SARS-CoV-2 infections and other diseases.
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Affiliation(s)
- Olga N Tkacheva
- The "Russian Clinical Research Center for Gerontology" of the Ministry of Healthcare of the Russian Federation, Pirogov Russian National Research Medical University, 16 1st Leonova Str., 129226 Moscow, Russia
| | - Natalia S Klimenko
- Atlas Biomed Group-Knomx LLC, Tintagel House, 92 Albert Embankment, Lambeth, London SE1 7TY, UK
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilova Str., 119334 Moscow, Russia
| | - Daria A Kashtanova
- The "Russian Clinical Research Center for Gerontology" of the Ministry of Healthcare of the Russian Federation, Pirogov Russian National Research Medical University, 16 1st Leonova Str., 129226 Moscow, Russia
| | - Alexander V Tyakht
- Atlas Biomed Group-Knomx LLC, Tintagel House, 92 Albert Embankment, Lambeth, London SE1 7TY, UK
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilova Str., 119334 Moscow, Russia
| | - Lilit V Maytesyan
- The "Russian Clinical Research Center for Gerontology" of the Ministry of Healthcare of the Russian Federation, Pirogov Russian National Research Medical University, 16 1st Leonova Str., 129226 Moscow, Russia
| | - Anna A Akopyan
- The "Russian Clinical Research Center for Gerontology" of the Ministry of Healthcare of the Russian Federation, Pirogov Russian National Research Medical University, 16 1st Leonova Str., 129226 Moscow, Russia
| | - Stanislav I Koshechkin
- Atlas Biomed Group-Knomx LLC, Tintagel House, 92 Albert Embankment, Lambeth, London SE1 7TY, UK
| | - Irina D Strazhesko
- The "Russian Clinical Research Center for Gerontology" of the Ministry of Healthcare of the Russian Federation, Pirogov Russian National Research Medical University, 16 1st Leonova Str., 129226 Moscow, Russia
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5
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Romanov VA, Karasev IA, Klimenko NS, Koshechkin SI, Tyakht AV, Malikhova OA. Luminal and Tumor-Associated Gut Microbiome Features Linked to Precancerous Lesions Malignancy Risk: A Compositional Approach. Cancers (Basel) 2022; 14:5207. [PMID: 36358626 PMCID: PMC9653741 DOI: 10.3390/cancers14215207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 08/30/2023] Open
Abstract
Colorectal cancer is the third most commonly diagnosed cancer worldwide. Human gut microbiome plays important roles in protecting against it, as well as contributing to its onset and progression. Identification of specific bacterial taxa associated with early stages of colorectal cancer may help develop effective microbiome-based diagnostics. For precancerous lesions, links of their characteristics to luminal and tumor-associated microbiome composition are to be elucidated. Paired stool and tumor brush biopsy samples were collected from 50 patients with precancerous lesions and early forms of colon cancer; their microbial communities were profiled using high-throughput 16S rRNA sequencing. We showed that the microbiome differences between stool and biopsy samples can be to a high extent computationally corrected. Compositionality-aware statistical analysis of microbiome composition revealed its associations with the number of lesions, lesion type, location and malignization pathway. A major determinant of precancerous lesions malignancy risk-the number of lesions-was positively associated with the abundance of H2S-producing taxa. Our results contribute to the basis for developing early non-invasive colorectal cancer diagnostics via identifying microorganisms likely participating in early stages of cancer pathogenesis.
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Affiliation(s)
- Vladimir A. Romanov
- Atlas Biomed Group—Knomx LLC, Tintagel House, 92 Albert Embankment, Lambeth, London SE1 7TY, UK
| | - Ivan A. Karasev
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia, 24 Kashirskoe Shosse, 115478 Moscow, Russia
| | - Natalia S. Klimenko
- Atlas Biomed Group—Knomx LLC, Tintagel House, 92 Albert Embankment, Lambeth, London SE1 7TY, UK
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilova Str., 119334 Moscow, Russia
| | - Stanislav I. Koshechkin
- Atlas Biomed Group—Knomx LLC, Tintagel House, 92 Albert Embankment, Lambeth, London SE1 7TY, UK
| | - Alexander V. Tyakht
- Atlas Biomed Group—Knomx LLC, Tintagel House, 92 Albert Embankment, Lambeth, London SE1 7TY, UK
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilova Str., 119334 Moscow, Russia
| | - Olga A. Malikhova
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia, 24 Kashirskoe Shosse, 115478 Moscow, Russia
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6
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Klimenko NS, Odintsova VE, Revel-Muroz A, Tyakht AV. The hallmarks of dietary intervention-resilient gut microbiome. NPJ Biofilms Microbiomes 2022; 8:77. [PMID: 36209276 PMCID: PMC9547895 DOI: 10.1038/s41522-022-00342-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/28/2022] [Indexed: 11/18/2022] Open
Abstract
Maintaining equilibrium of the gut microbiome is crucial for human health. Diet represents an important and generally accessible natural channel of controlling the nutrients supply to the intestinal microorganisms. Although many studies showed that dietary interventions can specifically modulate gut microbiome composition, further progress of the approach is complicated by interindividual variability of the microbial community response. The reported causes of this variability include the baseline microbiome composition features, but it is unclear whether any of them are intervention-specific. Here, we applied a unified computational framework to investigate the variability of microbiome response measured as beta diversity in eight various dietary interventions using previously published 16S rRNA sequencing datasets. We revealed a number of baseline microbiome features which determine the microbiome response in an intervention-independent manner. One of the most stable associations, reproducible for different interventions and enterotypes, was a negative dependence of the response on the average number of genes per microorganism in the community—an indicator of the community functional redundancy. Meanwhile, many revealed microbiome response determinants were enterotype-specific. In Bact1 and Rum enterotypes, the response was negatively correlated with the baseline abundance of their main drivers. Additionally, we proposed a method for preliminary assessment of the microbiome response. Our study delineats the universal features determining microbiome response to diverse interventions. The proposed approach is promising for understanding the mechanisms of gut microbiome stability and improving the efficacy of personalised microbiome-tailored interventions.
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Affiliation(s)
- Natalia S Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Vera E Odintsova
- Atlas Biomed Group - Knomx LLC, Tintagel House, 92 Albert Embankment, Lambeth, London, SE1 7TY, UK
| | - Anastasia Revel-Muroz
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander V Tyakht
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Atlas Biomed Group - Knomx LLC, Tintagel House, 92 Albert Embankment, Lambeth, London, SE1 7TY, UK
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7
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Magnitov MD, Garaev AK, Tyakht AV, Ulianov SV, Razin SV. Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments. BMC Bioinformatics 2022; 23:116. [PMID: 35366792 PMCID: PMC8976968 DOI: 10.1186/s12859-022-04654-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/25/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Understanding the role of various factors in 3D genome organization is essential to determine their impact on shaping large-scale chromatin units such as euchromatin (A) and heterochromatin (B) compartments. At this level, chromatin compaction is extensively modulated when transcription and epigenetic profiles change upon cell differentiation and response to various external impacts. However, detailed analysis of chromatin contact patterns within and between compartments is complicated because of a lack of suitable computational methods.
Results
We developed a tool, Pentad, to perform calculation, visualisation and quantitative analysis of the average chromatin compartment from the Hi-C matrices in cis, trans, and specified genomic distances. As we demonstrated by applying Pentad to publicly available Hi-C datasets, it helps to reliably detect redistribution of contact frequency in the chromatin compartments and assess alterations in the compartment strength.
Conclusions
Pentad is a simple tool for the analysis of changes in chromatin compartmentalization in various biological conditions. Pentad is freely available at https://github.com/magnitov/pentad.
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Ulianov SV, Velichko A, Magnitov MD, Luzhin A, Golov AK, Ovsyannikova N, Kireev II, Gavrikov A, Mishin A, Garaev AK, Tyakht AV, Gavrilov A, Kantidze OL, Razin SV. Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells. Nucleic Acids Res 2021; 49:10524-10541. [PMID: 33836078 PMCID: PMC8501969 DOI: 10.1093/nar/gkab249] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes within the cell nucleus. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM) and Hi-C techniques, we studied the effects of 1,6-hexanediol (1,6-HD)-mediated LLPS disruption/modulation on higher-order chromatin organization in living cells. We found that 1,6-HD treatment caused the enlargement of nucleosome clutches and their more uniform distribution in the nuclear space. At a megabase-scale, chromatin underwent moderate but irreversible perturbations that resulted in the partial mixing of A and B compartments. The removal of 1,6-HD from the culture medium did not allow chromatin to acquire initial configurations, and resulted in more compact repressed chromatin than in untreated cells. 1,6-HD treatment also weakened enhancer-promoter interactions and TAD insulation but did not considerably affect CTCF-dependent loops. Our results suggest that 1,6-HD-sensitive LLPS plays a limited role in chromatin spatial organization by constraining its folding patterns and facilitating compartmentalization at different levels.
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Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Artem K Velichko
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Mikhail D Magnitov
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
| | - Artem V Luzhin
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Arkadiy K Golov
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
| | - Natalia Ovsyannikova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Igor I Kireev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology, and Perinatology, 117997 Moscow, Russia
| | - Alexey S Gavrikov
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexander S Mishin
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Azat K Garaev
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
| | - Alexander V Tyakht
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Alexey A Gavrilov
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Omar L Kantidze
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Science, 119334 Moscow, Russia
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9
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Iablokov SN, Klimenko NS, Efimova DA, Shashkova T, Novichkov PS, Rodionov DA, Tyakht AV. Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases. Front Mol Biosci 2021; 7:603740. [PMID: 33537340 PMCID: PMC7848230 DOI: 10.3389/fmolb.2020.603740] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome is of utmost importance to human health. While a healthy microbiome can be represented by a variety of structures, its functional capacity appears to be more important. Gene content of the community can be assessed by “shotgun” metagenomics, but this approach is still too expensive. High-throughput amplicon-based surveys are a method of choice for large-scale surveys of links between microbiome, diseases, and diet, but the algorithms for predicting functional composition need to be improved to achieve good precision. Here we show how feature engineering based on microbial phenotypes, an advanced method for functional prediction from 16S rRNA sequencing data, improves identification of alterations of the gut microbiome linked to the disease. We processed a large collection of published gut microbial datasets of inflammatory bowel disease (IBD) patients to derive their community phenotype indices (CPI)—high-precision semiquantitative profiles aggregating metabolic potential of the community members based on genome-wide metabolic reconstructions. The list of selected metabolic functions included metabolism of short-chain fatty acids, vitamins, and carbohydrates. The machine-learning approach based on microbial phenotypes allows us to distinguish the microbiome profiles of healthy controls from patients with Crohn's disease and from ones with ulcerative colitis. The classifiers were comparable in quality to conventional taxonomy-based classifiers but provided new findings giving insights into possible mechanisms of pathogenesis. Feature-wise partial dependence plot (PDP) analysis of contribution to the classification result revealed a diversity of patterns. These observations suggest a constructive basis for defining functional homeostasis of the healthy human gut microbiome. The developed features are promising interpretable candidate biomarkers for assessing microbiome contribution to disease risk for the purposes of personalized medicine and clinical trials.
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Affiliation(s)
- Stanislav N Iablokov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Natalia S Klimenko
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Tatiana Shashkova
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Pavel S Novichkov
- PhenoBiome Inc., San Francisco, CA, United States.,Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Alexander V Tyakht
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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10
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Magnitov MD, Kuznetsova VS, Ulianov SV, Razin SV, Tyakht AV. Benchmark of software tools for prokaryotic chromosomal interaction domain identification. Bioinformatics 2020; 36:4560-4567. [PMID: 32492116 PMCID: PMC7653553 DOI: 10.1093/bioinformatics/btaa555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 01/01/2023] Open
Abstract
Motivation The application of genome-wide chromosome conformation capture (3C) methods to prokaryotes provided insights into the spatial organization of their genomes and identified patterns conserved across the tree of life, such as chromatin compartments and contact domains. Prokaryotic genomes vary in GC content and the density of restriction sites along the chromosome, suggesting that these properties should be considered when planning experiments and choosing appropriate software for data processing. Diverse algorithms are available for the analysis of eukaryotic chromatin contact maps, but their potential application to prokaryotic data has not yet been evaluated. Results Here, we present a comparative analysis of domain calling algorithms using available single-microbe experimental data. We evaluated the algorithms’ intra-dataset reproducibility, concordance with other tools and sensitivity to coverage and resolution of contact maps. Using RNA-seq as an example, we showed how orthogonal biological data can be utilized to validate the reliability and significance of annotated domains. We also suggest that in silico simulations of contact maps can be used to choose optimal restriction enzymes and estimate theoretical map resolutions before the experiment. Our results provide guidelines for researchers investigating microbes and microbial communities using high-throughput 3C assays such as Hi-C and 3C-seq. Availability and implementation The code of the analysis is available at https://github.com/magnitov/prokaryotic_cids. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mikhail D Magnitov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine.,Group of Genome Spatial Organization, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141700, Russia
| | - Veronika S Kuznetsova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141700, Russia.,Group of Bioinformatics
| | - Sergey V Ulianov
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.,Department of Biology, Moscow State University, Moscow 119234, Russia
| | - Sergey V Razin
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.,Department of Biology, Moscow State University, Moscow 119234, Russia
| | - Alexander V Tyakht
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine.,Group of Bioinformatics
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11
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Glushchenko OE, Prianichnikov NA, Olekhnovich EI, Manolov AI, Tyakht AV, Starikova EV, Odintsova VE, Kostryukova ES, Ilina EI. VERA: agent-based modeling transmission of antibiotic resistance between human pathogens and gut microbiota. Bioinformatics 2020; 35:3803-3811. [PMID: 30825306 DOI: 10.1093/bioinformatics/btz154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION The resistance of bacterial pathogens to antibiotics is one of the most important issues of modern health care. The human microbiota can accumulate resistance determinants and transfer them to pathogenic microbiota by means of horizontal gene transfer. Thus, it is important to develop methods of prediction and monitoring of antibiotics resistance in human populations. RESULTS We present the agent-based VERA model, which allows simulation of the spread of pathogens, including the possible horizontal transfer of resistance determinants from a commensal microbiota community. The model considers the opportunity of residents to stay in the town or in a medical institution, have incorrect self-treatment, treatment with several antibiotics types and transfer and accumulation of resistance determinants from commensal microorganism to a pathogen. In this model, we have also created an assessment of optimum observation frequency of infection spread among the population. Investigating model behavior, we show a number of non-linear dependencies, including the exponential nature of the dependence of the total number of those infected on the average resistance of a pathogen. As the model infection, we chose infection with Shigella spp., though it could be applied to a wide range of other pathogens. AVAILABILITY AND IMPLEMENTATION Source code and binaries VERA and VERA.viewer are freely available for download at github.com/lpenguin/microbiota-resistome. The code is written in Java, JavaScript and R for Linux platform. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Oksana E Glushchenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia.,Moscow State University, Moscow, Russia
| | - Nikita A Prianichnikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Evgenii I Olekhnovich
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Alexander I Manolov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Alexander V Tyakht
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia.,ITMO University, Saint Petersburg, Russia
| | - Elizaveta V Starikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Vera E Odintsova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Elena S Kostryukova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Elena I Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
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12
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Andrianova NV, Popkov VA, Klimenko NS, Tyakht AV, Baydakova GV, Frolova OY, Zorova LD, Pevzner IB, Zorov DB, Plotnikov EY. Microbiome-Metabolome Signature of Acute Kidney Injury. Metabolites 2020; 10:metabo10040142. [PMID: 32260384 PMCID: PMC7241241 DOI: 10.3390/metabo10040142] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/15/2022] Open
Abstract
Intestinal microbiota play a considerable role in the host’s organism, broadly affecting its organs and tissues. The kidney can also be the target of the microbiome and its metabolites (especially short-chain fatty acids), which can influence renal tissue, both by direct action and through modulation of the immune response. This impact is crucial, especially during kidney injury, because the modulation of inflammation or reparative processes could affect the severity of the resulting damage or recovery of kidney function. In this study, we compared the composition of rat gut microbiota with its outcome, in experimental acute ischemic kidney injury and named the bacterial taxa that play putatively negative or positive roles in the progression of ischemic kidney injury. We investigated the link between serum creatinine, urea, and a number of metabolites (acylcarnitines and amino acids), and the relative abundance of various bacterial taxa in rat feces. Our analysis revealed an increase in levels of 32 acylcarnitines in serum, after renal ischemia/reperfusion and correlation with creatinine and urea, while levels of three amino acids (tyrosine, tryptophan, and proline) had decreased. We detected associations between bacterial abundance and metabolite levels, using a compositionality-aware approach—Rothia and Staphylococcus levels were positively associated with creatinine and urea levels, respectively. Our findings indicate that the gut microbial community contains specific members whose presence might ameliorate or, on the contrary, aggravate ischemic kidney injury. These bacterial taxa could present perspective targets for therapeutical interventions in kidney pathologies, including acute kidney injury.
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Affiliation(s)
- Nadezda V. Andrianova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Vasily A. Popkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia
| | - Natalia S. Klimenko
- Atlas Biomed Group - Knomics LLC, Skolkovo Innovation center, Moscow 143026, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Alexander V. Tyakht
- Atlas Biomed Group - Knomics LLC, Skolkovo Innovation center, Moscow 143026, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | | | - Olga Y. Frolova
- Institute of Mitoengineering MSU» LLC, Leninskiye Gory 1, 119192 Moscow, Russia
| | - Ljubava D. Zorova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia
| | - Irina B. Pevzner
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia
| | - Dmitry B. Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia
- Correspondence: (D.B.Z.); (E.Y.P.); Tel.: +7-495-939-5944 (E.Y.P.)
| | - Egor Y. Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow 119991, Russia
- Correspondence: (D.B.Z.); (E.Y.P.); Tel.: +7-495-939-5944 (E.Y.P.)
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13
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Klimenko NS, Tyakht AV, Toshchakov SV, Shevchenko MA, Korzhenkov AA, Afshinnekoo E, Mason CE, Alexeev DG. Co-occurrence patterns of bacteria within microbiome of Moscow subway. Comput Struct Biotechnol J 2020; 18:314-322. [PMID: 32071708 PMCID: PMC7016200 DOI: 10.1016/j.csbj.2020.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 12/19/2022] Open
Abstract
Microbial ecosystems of the built environments have become key mediators of health as people worldwide tend to spend large amount of time indoors. Underexposure to microbes at an early age is linked to increased risks of allergic and autoimmune diseases. Transportation systems are of particular interest, as they are globally the largest space for interactions between city-dwellers. Here we performed the first pilot study of the Moscow subway microbiome by analyzing swabs collected from 5 types of surfaces at 4 stations using high-throughput 16S rRNA gene sequencing. The study was conducted as a part of The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) project. The most abundant microbial taxa comprising the subway microbiome originated from soil and human skin. Microbiome diversity was positively correlated with passenger traffic. No substantial evidence of major human pathogens presence was found. Co-occurrence analysis revealed clusters of microbial genera including combinations of microbes likely originating from different niches. The clusters as well as the most abundant microbes were similar to ones obtained for the published data on New-York City subway microbiome. Our results suggest that people are the main source and driving force of diversity in subway-associated microbiome. The data form a basis for a wider survey of Moscow subway microbiome to explore its longitudinal dynamics by analyzing an extended set of sample types and stations. Complementation of methods with viability testing, "shotgun" metagenomics, sequencing of bacterial isolates and culturomics will provide insights for public health, biosafety, microbial ecology and urban design.
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Affiliation(s)
- Natalia S. Klimenko
- Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar Str., Building 42, Premise 1, Room 1639, Moscow 143026, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Vavilova Str., 34/5, Moscow 119334, Russia
| | - Alexander V. Tyakht
- Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar Str., Building 42, Premise 1, Room 1639, Moscow 143026, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Vavilova Str., 34/5, Moscow 119334, Russia
| | - Stepan V. Toshchakov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova Sq., 1, Moscow 123182, Russia
| | - Margarita A. Shevchenko
- Immanuel Kant Baltic Federal University, Universitetskaya Str., 2, Room 106, Kaliningrad 236040, Russia
| | - Aleksei A. Korzhenkov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova Sq., 1, Moscow 123182, Russia
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Dmitry G. Alexeev
- Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar Str., Building 42, Premise 1, Room 1639, Moscow 143026, Russia
- ITMO University, Kronverkskiy Pr., 49, St. Petersburg 197101, Russia
- Novosibirsk State University, Pirogova Str., 1, Novosibirsk 630073, Russia
- Atlas Biomed Group, 92 Albert Embankment, Lambeth, London SE1 7TT, UK
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14
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019. [PMID: 31285584 DOI: 10.1038/s41564-019-04904-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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15
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019; 4:1727-1736. [PMID: 31285584 DOI: 10.1101/527796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/22/2019] [Indexed: 05/26/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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16
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Olekhnovich EI, Manolov AI, Samoilov AE, Prianichnikov NA, Malakhova MV, Tyakht AV, Pavlenko AV, Babenko VV, Larin AK, Kovarsky BA, Starikova EV, Glushchenko OE, Safina DD, Markelova MI, Boulygina EA, Khusnutdinova DR, Malanin SY, Abdulkhakov SR, Abdulkhakov RA, Grigoryeva TV, Kostryukova ES, Govorun VM, Ilina EN. Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy. Front Microbiol 2019; 10:1902. [PMID: 31507546 PMCID: PMC6718723 DOI: 10.3389/fmicb.2019.01902] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/02/2019] [Indexed: 01/07/2023] Open
Abstract
The human gut microbiome plays an important role both in health and disease. Use of antibiotics can alter gut microbiota composition, which can lead to various deleterious events. Here we report a whole genome sequencing metagenomic/genomic study of the intestinal microbiota changes caused by Helicobacter pylori (HP) eradication therapy. Using approaches for metagenomic data analysis we revealed a statistically significant decrease in alpha-diversity and relative abundance of Bifidobacterium adolescentis due to HP eradication therapy, while the relative abundance of Enterococcus faecium increased. We have detected changes in general metagenome resistome profiles as well: after HP eradication therapy, the ermB, CFX group, and tetQ genes were overrepresented, while tetO and tetW genes were underrepresented. We have confirmed these results with genome-resolved metagenomic approaches. MAG (metagenome-assembled genomes) abundance profiles have changed dramatically after HP eradication therapy. Focusing on ermB gene conferring resistance to macrolides, which were included in the HP eradication therapy scheme, we have shown a connection between antibiotic resistance genes (ARGs) and some overrepresented MAGs. Moreover, some E. faecium strains isolated from stool samples obtained after HP eradication have manifested greater antibiotic resistance in vitro in comparison to other isolates, as well as the higher number of ARGs conferring resistance to macrolides and tetracyclines.
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Affiliation(s)
- Evgenii I. Olekhnovich
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Alexander I. Manolov
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrey E. Samoilov
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Nikita A. Prianichnikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Maja V. Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Alexander V. Tyakht
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Alexander V. Pavlenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vlad V. Babenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrey K. Larin
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Boris A. Kovarsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Elizaveta V. Starikova
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Oksana E. Glushchenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | | | | | - Dilyara R. Khusnutdinova
- Kazan Federal University, Kazan, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | | | - Sayar R. Abdulkhakov
- Kazan Federal University, Kazan, Russia
- Kazan State Medical University, Kazan, Russia
| | | | | | - Elena S. Kostryukova
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vadim M. Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Elena N. Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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17
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Danilova NA, Abdulkhakov SR, Grigoryeva TV, Markelova MI, Vasilyev IY, Boulygina EA, Ardatskaya MD, Pavlenko AV, Tyakht AV, Odintsova AK, Abdulkhakov RA. Markers of dysbiosis in patients with ulcerative colitis and Crohn's disease. TERAPEVT ARKH 2019; 91:17-24. [PMID: 31094471 DOI: 10.26442/00403660.2019.04.000211] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIM The aim of the study was to study the taxonomic and functional composition of the gut microbiota in ulcerative colitis (UC) and Crohn's disease (CD) patients to identify key markers of dysbiosis in IBD. MATERIALS AND METHODS Fecal samples obtained from 95 IBD patients (78 UC and 17 CD) as well as 96 healthy volunteers were used for whole-genome sequencing carried out on the SOLiD 5500 W platform. Taxonomic profiling was performed by aligning the reeds, not maped on hg19, on MetaPhlAn2 reference database. Reeds were mapped using the HUNAnN2 algorithm to the ChocoPhlAn database to assess the representation of microbial metabolic pathways. Short-chain fatty acids (SCFA) level were measured in fecal samples by gas-liquid chromatographic analysis. RESULTS Changes in IBD patients gut microbiota were characterized by an increase in the representation of Proteobacteria and Bacteroidetes phyla bacteria and decrease in the number of Firmicutes phylum bacteria and Euryarchaeota phylum archaea; a decrease in the alpha-diversity index, relative representation of butyrate-producing, hydrogen-utilizing bacteria, and Methanobrevibacter smithii; increase in the relative representation of Ruminococcus gnavus in UC and CD patients and Akkermansia muciniphila in CD patients. Reduction of Butyryl-CoA: acetate CoA transferase gene relative representation in CD patients, decrease of absolute content of SCFA total number as well as particular SCFAs and main SCFAs ratio in IBD patients may indicate inhibition of functional activity and number of anaerobic microflora and/or an change in SCFA utilization by colonocytes. CONCLUSION the revealed changes can be considered as typical signs of dysbiosis in IBD patients and can be used as potential targets for IBD patients personalized treatment development.
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Affiliation(s)
| | - S R Abdulkhakov
- Kazan Federal University, Kazan, Russia.,Kazan State Medical University of the Ministry of Health of the Russian Federation, Kazan, Russia
| | | | | | | | | | - M D Ardatskaya
- Central State Medical Academy of Administrative Department of the President of the Russian Federation, Moscow, Russia
| | - A V Pavlenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, Russia
| | - A V Tyakht
- Institute of Gene Biology of RAS, Moscow, Russi
| | - A Kh Odintsova
- Republican Clinical Hospital of the Ministry of Health of the Republic of Tatarstan, Kazan, Russia
| | - R A Abdulkhakov
- Kazan State Medical University of the Ministry of Health of the Russian Federation, Kazan, Russia
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18
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Tyakht AV, Manolov AI, Kanygina AV, Ischenko DS, Kovarsky BA, Popenko AS, Pavlenko AV, Elizarova AV, Rakitina DV, Baikova JP, Ladygina VG, Kostryukova ES, Karpova IY, Semashko TA, Larin AK, Grigoryeva TV, Sinyagina MN, Malanin SY, Shcherbakov PL, Kharitonova AY, Khalif IL, Shapina MV, Maev IV, Andreev DN, Belousova EA, Buzunova YM, Alexeev DG, Govorun VM. Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses. BMC Genomics 2018; 19:968. [PMID: 30587114 PMCID: PMC6307143 DOI: 10.1186/s12864-018-5306-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/23/2018] [Indexed: 12/12/2022] Open
Abstract
Background Crohn’s disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated. Methods We performed a metagenomic study investigating the gut microbiota of patients with Crohn’s disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability. Results The abnormal shifts in the microbial community structures in Crohn’s disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes. Conclusions The genomic diversity of Crohn’s disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn’s disease and the development of new strategies for the prevention and treatment of this disease. Electronic supplementary material The online version of this article (10.1186/s12864-018-5306-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander V Tyakht
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700. .,ITMO University, 49 Kronverkskiy pr, Saint-Petersburg, Russian Federation, 197101.
| | - Alexander I Manolov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Alexandra V Kanygina
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Dmitry S Ischenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Boris A Kovarsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Anna S Popenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Alexander V Pavlenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Anna V Elizarova
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Daria V Rakitina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Julia P Baikova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Valentina G Ladygina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Elena S Kostryukova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Irina Y Karpova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Tatyana A Semashko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Andrei K Larin
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Tatyana V Grigoryeva
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008
| | - Mariya N Sinyagina
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008
| | - Sergei Y Malanin
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008
| | - Petr L Shcherbakov
- Moscow Clinical Scientific Center, 86 Shosse Entuziastov St., Moscow, Russian Federation, 111123
| | - Anastasiya Y Kharitonova
- Clinical and Research Institute of Emergency Children's Surgery and Trauma, 22 Bolshaya Polyanka St., Moscow, Russian Federation, 119180
| | - Igor L Khalif
- State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation, 123423
| | - Marina V Shapina
- State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation, 123423
| | - Igor V Maev
- Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation, 127473
| | - Dmitriy N Andreev
- Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation, 127473
| | - Elena A Belousova
- Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation, 129110
| | - Yulia M Buzunova
- Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation, 129110
| | - Dmitry G Alexeev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Vadim M Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700.,M.M. Shemyakin - Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, Russian Federation, 117997
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19
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Olekhnovich EI, Vasilyev AT, Ulyantsev VI, Kostryukova ES, Tyakht AV. MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota. Bioinformatics 2018; 34:434-444. [PMID: 29092015 DOI: 10.1093/bioinformatics/btx681] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 10/27/2017] [Indexed: 11/14/2022] Open
Abstract
Motivation Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens. Results We developed MetaCherchant-an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph. The algorithm was validated on a number of simulated and published datasets, as well as applied to new 'shotgun' metagenomes of gut microbiota from patients with Helicobacter pylori who underwent antibiotic therapy. Genomic context was reconstructed for several major resistance genes. Taxonomic annotation of the context suggests that within a single metagenome, the resistance genes can be contained in genomes of multiple species. MetaCherchant allows reconstruction of mobile elements with resistance genes within the genomes of bacteria using metagenomic data. Application of MetaCherchant in differential mode produced specific graph structures suggesting the evidence of possible resistance gene transmission within a mobile element that occurred as a result of the antibiotic therapy. MetaCherchant is a promising tool giving researchers an opportunity to get an insight into dynamics of resistance transmission in vivo basing on metagenomic data. Availability and implementation Source code and binaries are freely available for download at https://github.com/ctlab/metacherchant. The code is written in Java and is platform-independent. Cotanct ulyantsev@rain.ifmo.ru. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Evgenii I Olekhnovich
- Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation
| | - Artem T Vasilyev
- ITMO University, Saint Petersburg, Russian Federation.,JetBrains Research, Russian Federation
| | | | - Elena S Kostryukova
- Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation
| | - Alexander V Tyakht
- Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation.,ITMO University, Saint Petersburg, Russian Federation
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20
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Kashtanova DA, Tkacheva ON, Doudinskaya EN, Strazhesko ID, Kotovskaya YV, Popenko AS, Tyakht AV, Alexeev DG. Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study. Microorganisms 2018; 6:microorganisms6040098. [PMID: 30257444 PMCID: PMC6313665 DOI: 10.3390/microorganisms6040098] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 12/11/2022] Open
Abstract
The aim of this paper was to study gut microbiota composition in patients with different metabolic statuses. Methods: 92 participants aged 25–76 years (26 of whom were men), with confirmed absence of cardiovascular and other chronic diseases (but with the possible presence of cardiovascular risk factors) were included. Carotid ultrasound examinations, 16S rRNA sequencing of stool samples and diet assessments were performed. Statistical analysis was performed using R programming language, 3.1.0. Results: Enterotyping yielded two clusters differentiated by alpha-diversity. Intima-media thickness was higher in the cluster with lower diversity (adj. p < 0.001). Obesity was associated with higher Serratia (adj. p = 0.003) and Prevotella (adj. p < 0.0003) in relative abundance. Abdominal obesity was associated with higher abundance of Serratia (adj. p = 0.004) and Prevotella (adj. p = 0.0008) and lower levels of Oscillospira (adj. p = 0.0005). Glucose metabolism disturbances were associated with higher Blautia (adj. p = 0.0007) and Serratia (adj. p = 0.003) prevalence. Arterial hypertension was associated with high Blautia levels (adj. p = 0.002). The Blautia genus strongly correlated with low resistant starch consumption (adj. p = 0.007). A combination of high-fat diet and elevated Blautia levels was very common for diabetes mellitus type 2 patients (adj. p = 0.0001). Conclusion: The results show that there is a relationship between metabolic changes and higher representation of opportunistic pathogens and low diversity of gut microbiota even in apparently healthy participants.
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Affiliation(s)
- Daria A Kashtanova
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, bld. 16, 1st Leonova Street, Moscow 129226, Russia.
| | - Olga N Tkacheva
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, bld. 16, 1st Leonova Street, Moscow 129226, Russia.
| | - Ekaterina N Doudinskaya
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, bld. 16, 1st Leonova Street, Moscow 129226, Russia.
| | - Irina D Strazhesko
- Medical Research and Education Center, Lomonosov Moscow State University, 1 Leninskie Gory, Moscow 119991, Russia.
| | - Yulia V Kotovskaya
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, bld. 16, 1st Leonova Street, Moscow 129226, Russia.
| | - Anna S Popenko
- Atlas Biomed Group, Tintagel House, 92 Albert Embankment, Lambeth, London SE1 7TP, UK.
| | - Alexander V Tyakht
- Atlas Biomed Group, Tintagel House, 92 Albert Embankment, Lambeth, London SE1 7TP, UK.
| | - Dmitry G Alexeev
- Atlas Biomed Group, Tintagel House, 92 Albert Embankment, Lambeth, London SE1 7TP, UK.
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21
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Yarygin KS, Kovarsky BA, Bibikova TS, Melnikov DS, Tyakht AV, Alexeev DG. ResistoMap-online visualization of human gut microbiota antibiotic resistome. Bioinformatics 2018; 33:2205-2206. [PMID: 28334267 PMCID: PMC5870722 DOI: 10.1093/bioinformatics/btx134] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/13/2017] [Indexed: 12/12/2022] Open
Abstract
Abstract We created ResistoMap—a Web-based interactive visualization of the presence of genetic determinants conferring resistance to antibiotics, biocides and heavy metals in human gut microbiota. ResistoMap displays the data on more than 1500 published gut metagenomes of world populations including both healthy subjects and patients. Multiparameter display filters allow visual assessment of the associations between the meta-data and proportions of resistome. The geographic map navigation layer allows to state hypotheses regarding the global trends of antibiotic resistance and correlates the gut resistome variations with the national clinical guidelines on antibiotics application. Availability and Implementation ResistoMap was implemented using AngularJS, CoffeeScript, D3.js and TopoJSON. The tool is publicly available at http://resistomap.rcpcm.org. Contact yarygin@phystech.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Konstantin S Yarygin
- Moscow Institute of Physics and Technology (MIPT), 9 Institutskiy per, Dolgoprudny, Moscow Region, Russian Federation.,Federal Research and Clinical Centre of Physical-Chemical Medicine (FRCC PCM), Malaya Pirogovskaya 1a, Moscow, Russian Federation
| | - Boris A Kovarsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine (FRCC PCM), Malaya Pirogovskaya 1a, Moscow, Russian Federation
| | | | | | - Alexander V Tyakht
- Moscow Institute of Physics and Technology (MIPT), 9 Institutskiy per, Dolgoprudny, Moscow Region, Russian Federation.,Federal Research and Clinical Centre of Physical-Chemical Medicine (FRCC PCM), Malaya Pirogovskaya 1a, Moscow, Russian Federation
| | - Dmitry G Alexeev
- Moscow Institute of Physics and Technology (MIPT), 9 Institutskiy per, Dolgoprudny, Moscow Region, Russian Federation.,Federal Research and Clinical Centre of Physical-Chemical Medicine (FRCC PCM), Malaya Pirogovskaya 1a, Moscow, Russian Federation
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22
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Alifirova VM, Zhukova NG, Zhukova IA, Mironova YS, Petrov VA, Izhboldina OP, Titova MA, Latypova AV, Nikitina MA, Dorofeeva YB, Saltykova IV, Tyakht AV, Kostryukova ES, Sazonov AE. [Correlation Between Emotional-Affective Disorders and Gut Microbiota Composition in Patients with Parkinson’s Disease]. ACTA ACUST UNITED AC 2018; 71:427-35. [PMID: 29298003 DOI: 10.15690/vramn734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Background Despite the efforts of scientific community the data available on the correlation between emotional-affective symptoms of Parkinson’s disease and changes in microbiome is still scarce. Deeper studies of nonmotor symptoms evident in premotor stages of the disease and the reciprocal influence of microbiota may help to understand the etiology and pathogenesis of PD neurodegeneration better. Aim of the Study Discover the relations between emotional-affective disorders prevalent in PD population and changes in gut microbiota composition. Methods 51 patient diagnosed with PD participated in the study. Every participant’s emotional-affective state was examined using Beck’s Depression Inventory (BDI) and Hospital Anxiety and Depression Scale (HADS). Taxonomic richness of microbiome was studied using 16S ribosomal RNA gene sequencing, bioinformatics, and statistical analysis. Results Anxiety and depression are prevalent affective disorders in patients with PD. In our study, most of the subjects demonstrated certain anxiety and depression. Taxonomic diversity of gut microbiota in BP was increasing with the increase in anxiety levels, reaching the maximum in the group with subclinical anxiety, and decreasing in the group with clinically significant anxiety disorder. At the species level, patients with clinically significant anxiety had higher abundance of Clostridium clariflavum compared to the anxiety-free patients. Patients with moderate depression were characterized by the higher prevalence of Christensenella minuta, Clostridium disporicum, and Oscillibacter valericigenes compared to subjects without depression or with mild depression. Conclusion The data we received in our study allow better understanding of PD pathogenesis.
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23
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Dubinkina VB, Tyakht AV, Odintsova VY, Yarygin KS, Kovarsky BA, Pavlenko AV, Ischenko DS, Popenko AS, Alexeev DG, Taraskina AY, Nasyrova RF, Krupitsky EM, Shalikiani NV, Bakulin IG, Shcherbakov PL, Skorodumova LO, Larin AK, Kostryukova ES, Abdulkhakov RA, Abdulkhakov SR, Malanin SY, Ismagilova RK, Grigoryeva TV, Ilina EN, Govorun VM. Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease. Microbiome 2017; 5:141. [PMID: 29041989 PMCID: PMC5645934 DOI: 10.1186/s40168-017-0359-2] [Citation(s) in RCA: 253] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 10/02/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction. In order to differentiate the effects of these two factors, we conducted a comparative "shotgun" metagenomic survey of 99 patients with the alcohol dependence syndrome represented by two cohorts-with and without liver cirrhosis. The taxonomic and functional composition of the gut microbiota was subjected to a multifactor analysis including comparison with the external control group. RESULTS Alcoholic dependence and liver cirrhosis were associated with profound shifts in gut community structures and metabolic potential across the patients. The specific effects on species-level community composition were remarkably different between cohorts with and without liver cirrhosis. In both cases, the commensal microbiota was found to be depleted. Alcoholic dependence was inversely associated with the levels of butyrate-producing species from the Clostridiales order, while the cirrhosis-with multiple members of the Bacteroidales order. The opportunist pathogens linked to alcoholic dependence included pro-inflammatory Enterobacteriaceae, while the hallmarks of cirrhosis included an increase of oral microbes in the gut and more frequent occurrence of abnormal community structures. Interestingly, each of the two factors was associated with the expressed enrichment in many Bifidobacterium and Lactobacillus-but the exact set of the species was different between alcoholic dependence and liver cirrhosis. At the level of functional potential, the patients showed different patterns of increase in functions related to alcohol metabolism and virulence factors, as well as pathways related to inflammation. CONCLUSIONS Multiple shifts in the community structure and metabolic potential suggest strong negative influence of alcohol dependence and associated liver dysfunction on gut microbiota. The identified differences in patterns of impact between these two factors are important for planning of personalized treatment and prevention of these pathologies via microbiota modulation. Particularly, the expansion of Bifidobacterium and Lactobacillus suggests that probiotic interventions for patients with alcohol-related disorders using representatives of the same taxa should be considered with caution. Taxonomic and functional analysis shows an increased propensity of the gut microbiota to synthesis of the toxic acetaldehyde, suggesting higher risk of colorectal cancer and other pathologies in alcoholics.
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Affiliation(s)
- Veronika B. Dubinkina
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region, 141700 Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1304 W. Springfield Avenue Urbana, Champaign, IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, Urbana, IL 61801 USA
| | - Alexander V. Tyakht
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
- ITMO University, Kronverkskiy pr. 49, Saint-Petersburg, 197101 Russia
| | - Vera Y. Odintsova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Konstantin S. Yarygin
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region, 141700 Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Boris A. Kovarsky
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Alexander V. Pavlenko
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region, 141700 Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Dmitry S. Ischenko
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region, 141700 Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Anna S. Popenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Dmitry G. Alexeev
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region, 141700 Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Anastasiya Y. Taraskina
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Bekhtereva 3, Saint-Petersburg, 192019 Russia
| | - Regina F. Nasyrova
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Bekhtereva 3, Saint-Petersburg, 192019 Russia
| | - Evgeny M. Krupitsky
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Bekhtereva 3, Saint-Petersburg, 192019 Russia
| | - Nino V. Shalikiani
- Moscow Clinical Scientific Center, Shosse Entuziastov 86, Moscow, 111123 Russia
| | - Igor G. Bakulin
- Moscow Clinical Scientific Center, Shosse Entuziastov 86, Moscow, 111123 Russia
| | - Petr L. Shcherbakov
- Moscow Clinical Scientific Center, Shosse Entuziastov 86, Moscow, 111123 Russia
| | - Lyubov O. Skorodumova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Andrei K. Larin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Elena S. Kostryukova
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region, 141700 Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | | | - Sayar R. Abdulkhakov
- Kazan State Medical University, Butlerova 49, Kazan, 420012 Russia
- Kazan Federal University, Kremlyovskaya 18, Kazan, 420008 Russia
| | | | | | | | - Elena N. Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
| | - Vadim M. Govorun
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region, 141700 Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435 Russia
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24
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Glushchenko OE, Samoilov AE, Olekhnovich EI, Kovarsky BA, Tyakht AV, Pavlenko AV, Babenko VV, Larin AK, Kostryukova ES, Malakhova MV, Ilina EN, Abdulkhakov RA, Safina DI, Grigoryeva TV, Abdulkhakov SR, Govorun VM. Data on gut metagenomes of the patients with Helicobacter pylori infection before and after the antibiotic therapy. Data Brief 2017; 11:68-71. [PMID: 28138506 PMCID: PMC5256668 DOI: 10.1016/j.dib.2017.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 12/29/2016] [Accepted: 01/11/2017] [Indexed: 11/25/2022] Open
Abstract
Antibiotic therapy can lead to the disruption of gut microbiota community with possible negative outcomes for human health. One of the diseases for which the treatment scheme commonly included antibiotic intake is Helicobacter pylori infection. The changes in taxonomic and functional composition of microbiota in patients can be assessed using “shotgun” metagenomic sequencing. Ten stool samples were collected from 4 patients with Helicobacter pylori infection before and directly after the H. pylori eradication course. Additionally, for two of the subjects, the samples were collected 1 month after the end of the treatment. The samples were subject to “shotgun” (whole-genome) metagenomic sequencing using Illumina HiSeq platform. The reads are deposited in the ENA (project ID: PRJEB18265).
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Affiliation(s)
- Oksana E Glushchenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Andrei E Samoilov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia; Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Evgenii I Olekhnovich
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Boris A Kovarsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Alexander V Tyakht
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia; Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Alexander V Pavlenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia; Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Vlad V Babenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Andrei K Larin
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Elena S Kostryukova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia; Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Maja V Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Elena N Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | | | - Dilyara I Safina
- Kazan Federal University, Kremlyovskaya 18, Kazan 420008, Russia
| | | | - Sayar R Abdulkhakov
- Kazan State Medical University, Butlerova 49, Kazan 420012, Russia; Kazan Federal University, Kremlyovskaya 18, Kazan 420008, Russia
| | - Vadim M Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia; Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia
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Tyakht AV, Dubinkina VB, Odintsova VY, Yarygin KS, Kovarsky BA, Pavlenko AV, Ischenko DS, Popenko AS, Alexeev DG, Taraskina AY, Nasyrova RF, Krupitski EM, Shalikiani NV, Bakulin IG, Shcherbakov PL, Skorodumova LO, Larin AK, Kostryukova ES, Abdulkhakov RA, Abdulkhakov SR, Malanin SY, Ismagilova RK, Grigoryeva TV, Ilina EN, Govorun VM. Data on gut metagenomes of the patients with alcoholic dependence syndrome and alcoholic liver cirrhosis. Data Brief 2017; 11:98-102. [PMID: 28138508 PMCID: PMC5257029 DOI: 10.1016/j.dib.2017.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 12/28/2016] [Accepted: 01/11/2017] [Indexed: 12/03/2022] Open
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).
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Affiliation(s)
- Alexander V Tyakht
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Veronika B Dubinkina
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Vera Y Odintsova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Konstantin S Yarygin
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Boris A Kovarsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Alexander V Pavlenko
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Dmitry S Ischenko
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Anna S Popenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Dmitry G Alexeev
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Anastasiya Y Taraskina
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Bekhtereva 3, Saint-Petersburg 192019, Russia
| | - Regina F Nasyrova
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Bekhtereva 3, Saint-Petersburg 192019, Russia
| | - Evgeny M Krupitski
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Bekhtereva 3, Saint-Petersburg 192019, Russia
| | - Nino V Shalikiani
- Moscow Clinical Scientific Center, Shosse Entuziastov 86, Moscow 111123, Russia
| | - Igor G Bakulin
- Moscow Clinical Scientific Center, Shosse Entuziastov 86, Moscow 111123, Russia
| | - Petr L Shcherbakov
- Moscow Clinical Scientific Center, Shosse Entuziastov 86, Moscow 111123, Russia
| | - Lyubov O Skorodumova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Andrei K Larin
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Elena S Kostryukova
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | | | - Sayar R Abdulkhakov
- Kazan State Medical University, Butlerova 49, Kazan 420012, Russia; Kazan Federal University, Kremlyovskaya 18, Kazan 420008, Russia
| | - Sergey Y Malanin
- Kazan Federal University, Kremlyovskaya 18, Kazan 420008, Russia
| | | | | | - Elena N Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Vadim M Govorun
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia
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Poverennaya EV, Kopylov AT, Ponomarenko EA, Ilgisonis EV, Zgoda VG, Tikhonova OV, Novikova SE, Farafonova TE, Kiseleva YY, Radko SP, Vakhrushev IV, Yarygin KN, Moshkovskii SA, Kiseleva OI, Lisitsa AV, Sokolov AS, Mazur AM, Prokhortchouk EB, Skryabin KG, Kostrjukova ES, Tyakht AV, Gorbachev AY, Ilina EN, Govorun VM, Archakov AI. State of the Art of Chromosome 18-Centric HPP in 2016: Transcriptome and Proteome Profiling of Liver Tissue and HepG2 Cells. J Proteome Res 2016; 15:4030-4038. [PMID: 27527821 DOI: 10.1021/acs.jproteome.6b00380] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A gene-centric approach was applied for a large-scale study of expression products of a single chromosome. Transcriptome profiling of liver tissue and HepG2 cell line was independently performed using two RNA-Seq platforms (SOLiD and Illumina) and also by Droplet Digital PCR (ddPCR) and quantitative RT-PCR. Proteome profiling was performed using shotgun LC-MS/MS as well as selected reaction monitoring with stable isotope-labeled standards (SRM/SIS) for liver tissue and HepG2 cells. On the basis of SRM/SIS measurements, protein copy numbers were estimated for the Chromosome 18 (Chr 18) encoded proteins in the selected types of biological material. These values were compared with expression levels of corresponding mRNA. As a result, we obtained information about 158 and 142 transcripts for HepG2 cell line and liver tissue, respectively. SRM/SIS measurements and shotgun LC-MS/MS allowed us to detect 91 Chr 18-encoded proteins in total, while an intersection between the HepG2 cell line and liver tissue proteomes was ∼66%. In total, there were 16 proteins specifically observed in HepG2 cell line, while 15 proteins were found solely in the liver tissue. Comparison between proteome and transcriptome revealed a poor correlation (R2 ≈ 0.1) between corresponding mRNA and protein expression levels. The SRM and shotgun data sets (obtained during 2015-2016) are available in PASSEL (PASS00697) and ProteomeExchange/PRIDE (PXD004407). All measurements were also uploaded into the in-house Chr 18 Knowledgebase at http://kb18.ru/protein/matrix/416126 .
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Affiliation(s)
| | - Arthur T Kopylov
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Elena A Ponomarenko
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | | | - Victor G Zgoda
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Olga V Tikhonova
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Svetlana E Novikova
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Tatyana E Farafonova
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Yana Yu Kiseleva
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Igor V Vakhrushev
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Konstantin N Yarygin
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.,Pirogov Russian National Research Medical University , Ostrovitianov Str. 1, Moscow 117997, Russia
| | - Olga I Kiseleva
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Andrey V Lisitsa
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Alexey S Sokolov
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Alexander M Mazur
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Egor B Prokhortchouk
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Konstantin G Skryabin
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Elena S Kostrjukova
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Alexander V Tyakht
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Alexey Yu Gorbachev
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Elena N Ilina
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Vadim M Govorun
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Alexander I Archakov
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
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Ulyantsev VI, Kazakov SV, Dubinkina VB, Tyakht AV, Alexeev DG. MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data. Bioinformatics 2016; 32:2760-7. [PMID: 27259541 DOI: 10.1093/bioinformatics/btw312] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 05/16/2016] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION High-throughput metagenomic sequencing has revolutionized our view on the structure and metabolic potential of microbial communities. However, analysis of metagenomic composition is often complicated by the high complexity of the community and the lack of related reference genomic sequences. As a start point for comparative metagenomic analysis, the researchers require efficient means for assessing pairwise similarity of the metagenomes (beta-diversity). A number of approaches were used to address this task, however, most of them have inherent disadvantages that limit their scope of applicability. For instance, the reference-based methods poorly perform on metagenomes from previously unstudied niches, while composition-based methods appear to be too abstract for straightforward interpretation and do not allow to identify the differentially abundant features. RESULTS We developed MetaFast, an approach that allows to represent a shotgun metagenome from an arbitrary environment as a modified de Bruijn graph consisting of simplified components. For multiple metagenomes, the resulting representation is used to obtain a pairwise similarity matrix. The dimensional structure of the metagenomic components preserved in our algorithm reflects the inherent subspecies-level diversity of microbiota. The method is computationally efficient and especially promising for an analysis of metagenomes from novel environmental niches. AVAILABILITY AND IMPLEMENTATION Source code and binaries are freely available for download at https://github.com/ctlab/metafast The code is written in Java and is platform independent (tested on Linux and Windows x86_64). CONTACT ulyantsev@rain.ifmo.ru SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Veronika B Dubinkina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russian Federation
| | - Alexander V Tyakht
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russian Federation
| | - Dmitry G Alexeev
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russian Federation
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Ogorodova LM, Fedosenko SV, Popenko AS, Petrov VA, Tyakht AV, Saltykova IV, Deev IA, Kulikov ES, Kirillova NA, Govorun VM, Kostryukova ES. [Comparison Study of Oropharyngeal Microbiota in Case of Bronchial Asthma and Chronic Obstructive Pulmonary Disease in Different Severity Levels]. ACTA ACUST UNITED AC 2016:669-78. [PMID: 27093794 DOI: 10.15690/vramn532] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGRAUND The result of comparative study of oropharyngeal microbiota taxonomic composition in patients with different severity level of bronchial asthma (BA) and chronic obstructive pulmonary disease (COPD) is presented in this paper. AIMS To compare oropharyngeal microbiota composition in case of bronchial asthma and chronic obstructive pulmonary disease in different severity levels. METODS 138 patients, 50 with BA and 88 with COPD were studied. For each patient was collected anamnesis vitae, swab from the back of the throat and performed physical examination. High-throughput 16S ribosomal RNA gene sequencing and bioinformatic analysis was employed to characterize the microbial communities. RESULTS As a result of the study wasfound a number of differences on various taxonomic levels in microbiota's composition within group of patients with different severity level of BA and group of patients with different severity level of COPD and between those groups. COPD patients with GOLD 1-2 in comparison with GOLD 3-4 patiens are marked by prevalence of species Brevibacterium aureum, genus Scardovia, Coprococcus, Haemophilus, Moryella, Dialister, Paludibacter and decrease of Prevotella melaninogenica species. BA patients with severe uncontrolled asthma in comparison with patients which have mild persistent asthma are marked by decrease of Prevotella and increase of species Bifidobacterium longum, Prevotella nanceiensis, Neisseria cinerea, Aggregatibacter segnis and genus Odoribacter, Alloiococcus, Lactobacillus, Megasphaera, Parvimonas, Sneathia. Patient's microbiota in BA group in comparison with COPD group is characterized by the prevalence of Prevotella melaninogenica and genus Selenomonas, Granulicatella u Gemella, and decrease of Prevotella nigrescens, Haemophilus influenza and genus Aggregatibacter, Alloiococcus, Catonella, Mycoplasma, Peptoniphilus u Sediminibacterium. There are no differences between microbiota composition in case of severe uncontrolled BA and very severe COPD. CONCLUSION Lack of differences in oropharyngeal microbiota taxonomic composition between patients with severe uncontrolled BA and very severe COPD allow us to suggest a similarity of bronchopulmonary system condition in case of diseases' severe stages.
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Shalikiani NV, Bakulin IG, Dubinkina VB, Ishchenko DS, Alexeev DG, Tyakht AV, Pavlenko AV, Ilyina EN, Kostryukova ES, Taraskina AE, Skorodumova LO, Maev IV, Govorun VM. [Specific features of the enteric microbiota composition in patients with alcoholic liver cirrhosis]. TERAPEVT ARKH 2016; 87:59-65. [PMID: 26978420 DOI: 10.17116/terarkh2015871259-65] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AIM To establish the specific features of the taxonomic and functional composition of the enteric microbiota in patients with alcoholic liver cirrhosis (LC). SUBJECTS AND METHODS Metagenomic analysis was used to study the taxonomic composition and functional potential of the enteric microbiota in 20 patients with alcoholic LC. Total DNA was isolated from the patients' fecal samples; thereafter full genome sequencing was carried out. The metagenomic analysis yielded the results of the relative taxonomic and functional abundance of microbial species in the test samples. These were comparatively analyzed with the previously published metagenomic datasets of healthy population cohorts in the Russian Federation, as well as in Denmark, China, and the USA. RESULTS In the majority of patients, the dominant part of the intestinal community represented bacterial species constituting the normal human intestinal flora. At the same time, abnormal gut microbiota composition, which was suggestive of marked dysbacteriosis, was identified in a number of patients. In addition, pooled analysis of the data could identify a number of species with a statistically significantly increase and decrease in the relative abundance as compared to the control groups. Thus, the enteric microbiota of the patients with alcoholic LC showed a high proportion of bacteria characteristic of the oral cavity. Analysis of the pooled metabolic potential of the microbiota in these patients demonstrated the higher abundance of enzyme genes involved in alcohol metabolism. CONCLUSION In the patients with alcoholic LC, the microbiota composition changes identified in individual bacterial species may be associated with gastrointestinal comorbidities, such as chronic erosive gastritis, chronic pancreatitis, and gastric ulcer. The alterations occurring in alcoholic cirrhosis promote the penetration and generation of oral cavity-specific microorganisms in the human intestine. This may a potential biomarker for the diagnosis of liver diseases. The bacterial enzyme genes involved in alcohol metabolism have an increased abundance in patients with alcoholic LC and healthy volunteers from the Russian Federation.
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Affiliation(s)
- N V Shalikiani
- Moscow Clinical Research and Practical Center, Moscow Healthcare Department, Moscow, Russia
| | - I G Bakulin
- Moscow Clinical Research and Practical Center, Moscow Healthcare Department, Moscow, Russia
| | - V B Dubinkina
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - D S Ishchenko
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia; Research Institute of Physicochemical Medicine, Federal Biomedical Agency of Russia, Moscow, Russia
| | - D G Alexeev
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia; Research Institute of Physicochemical Medicine, Federal Biomedical Agency of Russia, Moscow, Russia
| | - A V Tyakht
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia; Research Institute of Physicochemical Medicine, Federal Biomedical Agency of Russia, Moscow, Russia
| | - A V Pavlenko
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia; Research Institute of Physicochemical Medicine, Federal Biomedical Agency of Russia, Moscow, Russia
| | - E N Ilyina
- Research Institute of Physicochemical Medicine, Federal Biomedical Agency of Russia, Moscow, Russia
| | - E S Kostryukova
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia; Research Institute of Physicochemical Medicine, Federal Biomedical Agency of Russia, Moscow, Russia; Kazan Federal University, Kazan, Russia
| | - A E Taraskina
- Research Institute of Physicochemical Medicine, Federal Biomedical Agency of Russia, Moscow, Russia
| | - L O Skorodumova
- Research Institute of Physicochemical Medicine, Federal Biomedical Agency of Russia, Moscow, Russia
| | - I V Maev
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of Russia, Moscow, Russia
| | - V M Govorun
- Research Institute of Physicochemical Medicine, Federal Biomedical Agency of Russia, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
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Dubinkina VB, Tyakht AV, Ilina EN, Ischenko DS, Kovarsky BA, Yarygin KS, Pavlenko AV, Popenko AS, Alexeev DG, Taraskina AE, Nasyrova RF, Krupitski EM, Skorodumova LO, Larin AK, Kostryukova ES, Govorun VM. [Metagenomic analysis of taxonomic and functional changes in gut microbiota of patients with alcoholic dependence syndrome]. Biomed Khim 2016; 61:742-9. [PMID: 26716747 DOI: 10.18097/pbmc20156106742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Here we present the first metagenomic study of gut microbiota in patients with alcohol dependence syndrome (ADS) performed in the whole-genome ("shotgun") format. Taxonomic analysis highlighted changes in community "drivers" abundance previously associated with inflammatory processes (including increase in Ruminococcus gnavus and torques, as well as decrease in Faecalibacterium and Akkermansia). Microbiota of alcoholics manifested presence of specific opportunistic pathogens rarely detected in healthy control subjects of the world. Differential analysis of metabolic potential basing on changes in KEGG Orthology groups abundance revealed increase in pathways associated with response to oxidative stress. Analysis of two specific gene groups--alcohol metabolism and virulence factors--also showed increase in comparison with the control groups. We suggest that gut microbiota distinct in alcoholics by both taxonomic and functional composition plays role in modulating the effect of alcohol on host organism.
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Affiliation(s)
- V B Dubinkina
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - A V Tyakht
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - E N Ilina
- Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - D S Ischenko
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - B A Kovarsky
- Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - K S Yarygin
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - A V Pavlenko
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - A S Popenko
- Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - D G Alexeev
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - A E Taraskina
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Saint-Petersburg, Russia
| | - R F Nasyrova
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Saint-Petersburg, Russia
| | - E M Krupitski
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Saint-Petersburg, Russia
| | - L O Skorodumova
- Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - A K Larin
- Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - E S Kostryukova
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - V M Govorun
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
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Dubinkina VB, Ischenko DS, Ulyantsev VI, Tyakht AV, Alexeev DG. Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis. BMC Bioinformatics 2016; 17:38. [PMID: 26774270 PMCID: PMC4715287 DOI: 10.1186/s12859-015-0875-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/14/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging type of genomic data - containing sequences of all genes from the totality of a complex microbial community. Recently, researchers started to analyze metagenomes using reference-free methods based on the analysis of oligonucleotides (k-mers) frequency spectrum previously applied to isolated genomes. However, little is known about their correlation with the existing approaches for metagenomic feature extraction, as well as the limits of applicability. Here we evaluated a metagenomic pairwise dissimilarity measure based on short k-mer spectrum using the example of human gut microbiota, a biomedically significant object of study. RESULTS We developed a method for calculating pairwise dissimilarity (beta-diversity) of "shotgun" metagenomes based on short k-mer spectra (5 ≤ k ≤ 11). The method was validated on simulated metagenomes and further applied to a large collection of human gut metagenomes from the populations of the world (n=281). The k-mer spectrum-based measure was found to behave similarly to one based on mapping to a reference gene catalog, but different from one using a genome catalog. This difference turned out to be associated with a significant presence of viral reads in a number of metagenomes. Simulations showed limited impact of bacterial genetic variability as well as sequencing errors on k-mer spectra. Specific differences between the datasets from individual populations were identified. CONCLUSIONS Our approach allows rapid estimation of pairwise dissimilarity between metagenomes. Though we applied this technique to gut microbiota, it should be useful for arbitrary metagenomes, even metagenomes with novel microbiota. Dissimilarity measure based on k-mer spectrum provides a wider perspective in comparison with the ones based on the alignment against reference sequence sets. It helps not to miss possible outstanding features of metagenomic composition, particularly related to the presence of an unknown bacteria, virus or eukaryote, as well as to technical artifacts (sample contamination, reads of non-biological origin, etc.) at the early stages of bioinformatic analysis. Our method is complementary to reference-based approaches and can be easily integrated into metagenomic analysis pipelines.
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Affiliation(s)
- Veronika B Dubinkina
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
| | - Dmitry S Ischenko
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
| | | | - Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
| | - Dmitry G Alexeev
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
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Tyakht AV, Ilina EN, Alexeev DG, Ischenko DS, Gorbachev AY, Semashko TA, Larin AK, Selezneva OV, Kostryukova ES, Karalkin PA, Vakhrushev IV, Kurbatov LK, Archakov AI, Govorun VM. RNA-Seq gene expression profiling of HepG2 cells: the influence of experimental factors and comparison with liver tissue. BMC Genomics 2014; 15:1108. [PMID: 25511409 PMCID: PMC4378340 DOI: 10.1186/1471-2164-15-1108] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/11/2014] [Indexed: 12/12/2022] Open
Abstract
Background Human hepatoma HepG2 cells are used as an in vitro model of the human liver. High-throughput transcriptomic sequencing is an advanced approach for assessing the functional state of a tissue or cell type. However, the influence of experimental factors, such as the sample preparation method and inter-laboratory variation, on the transcriptomic profile has not been evaluated. Results The whole-transcriptome sequencing of HepG2 cells was performed using the SOLiD platform and validated using droplet digital PCR. The gene expression profile was compared to the results obtained with the same sequencing method in another laboratory and using another sample preparation method. We also compared the transcriptomic profile HepG2 cells with that of liver tissue. Comparison of the gene expression profiles between the HepG2 cell line and liver tissue revealed the highest variation, followed by HepG2 cells submitted to two different sample preparation protocols. The lowest variation was observed between HepG2 cells prepared by two different laboratories using the same protocol. The enrichment analysis of the genes that were differentially expressed between HepG2 cells and liver tissue mainly revealed the cancer-associated gene signature of HepG2 cells and the activation of the response to chemical stimuli in the liver tissue. The HepG2 transcriptome obtained with the SOLiD platform was highly correlated with the published transcriptome obtained with the Illumina and Helicos platforms, with moderate correspondence to microarrays. Conclusions In the present study, we assessed the influence of experimental factors on the HepG2 transcriptome and identified differences in gene expression between the HepG2 cell line and liver cells. These findings will facilitate robust experimental design in the fields of pharmacology and toxicology. Our results were supported by a comparative analysis with previous HepG2 gene expression studies. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1108) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia.
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Abstract
A multitude of metagenomic studies has brought to light an enormous richness of human gut microbiota compositions. In this space of possible configurations, clinical specialists are trying to mine the markers of healthy microbiota via case-control and longitudinal studies. We have discovered potentially beneficial communities while examining the microbial diversity in rural Russians in comparison with the urban dwellers. In this addendum, we further examine the data by elaborating on some of the less common types and suggesting the possible co-metabolism of their drivers. In the light of the first validated clinically effective bacterial transplantation, we discuss the concept of a reference healthy microbiota, outline the problems encountered on the way to its restoration in the developed world, and speculate if rural communities can serve as a source for its prototype.
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Affiliation(s)
- Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine; Moscow, Russia,Correspondence to: Alexander V Tyakht,
| | - Dmitry G Alexeev
- Research Institute of Physico-Chemical Medicine; Moscow, Russia,Moscow Institute of Physics and Technology; Dolgoprudny, Russia
| | - Anna S Popenko
- Research Institute of Physico-Chemical Medicine; Moscow, Russia
| | - Elena S Kostryukova
- Research Institute of Physico-Chemical Medicine; Moscow, Russia,Kazan' (Volga Region) Federal University; Kazan', Russia
| | - Vadim M Govorun
- Research Institute of Physico-Chemical Medicine; Moscow, Russia,Moscow Institute of Physics and Technology; Dolgoprudny, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences; Moscow, Russia
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Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AV, Larin AK, Karpova IY, Selezneva OV, Semashko TA, Ospanova EA, Babenko VV, Maev IV, Cheremushkin SV, Kucheryavyy YA, Shcherbakov PL, Grinevich VB, Efimov OI, Sas EI, Abdulkhakov RA, Abdulkhakov SR, Lyalyukova EA, Livzan MA, Vlassov VV, Sagdeev RZ, Tsukanov VV, Osipenko MF, Kozlova IV, Tkachev AV, Sergienko VI, Alexeev DG, Govorun VM. Human gut microbiota community structures in urban and rural populations in Russia. Nat Commun 2014; 4:2469. [PMID: 24036685 PMCID: PMC3778515 DOI: 10.1038/ncomms3469] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 08/20/2013] [Indexed: 02/06/2023] Open
Abstract
The microbial community of the human gut has a crucial role in sustaining host homeostasis. High-throughput DNA sequencing has delineated the structural and functional configurations of gut metagenomes in world populations. The microbiota of the Russian population is of particular interest to researchers, because Russia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Here we conduct a shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects, which reveals novel microbial community structures. The communities from several rural regions display similarities within each region and are dominated by the bacterial taxa associated with the healthy gut. Functional analysis shows that the metabolic pathways exhibiting differential abundance in the novel types are primarily associated with the trade-off between the Bacteroidetes and Firmicutes phyla. The specific signatures of the Russian gut microbiota are likely linked to the host diet, cultural habits and socioeconomic status.
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Affiliation(s)
- Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119435, Russia
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Ponomarenko EA, Kopylov AT, Lisitsa AV, Radko SP, Kiseleva YY, Kurbatov LK, Ptitsyn KG, Tikhonova OV, Moisa AA, Novikova SE, Poverennaya EV, Ilgisonis EV, Filimonov AD, Bogolubova NA, Averchuk VV, Karalkin PA, Vakhrushev IV, Yarygin KN, Moshkovskii SA, Zgoda VG, Sokolov AS, Mazur AM, Prokhortchouck EB, Skryabin KG, Ilina EN, Kostrjukova ES, Alexeev DG, Tyakht AV, Gorbachev AY, Govorun VM, Archakov AI. Chromosome 18 transcriptoproteome of liver tissue and HepG2 cells and targeted proteome mapping in depleted plasma: update 2013. J Proteome Res 2013; 13:183-90. [PMID: 24328317 DOI: 10.1021/pr400883x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the results obtained in 2012-2013 by the Russian Consortium for the Chromosome-centric Human Proteome Project (C-HPP). The main scope of this work was the transcriptome profiling of genes on human chromosome 18 (Chr 18), as well as their encoded proteome, from three types of biomaterials: liver tissue, the hepatocellular carcinoma-derived cell line HepG2, and blood plasma. The transcriptome profiling for liver tissue was independently performed using two RNaseq platforms (SOLiD and Illumina) and also by droplet digital PCR (ddPCR) and quantitative RT-PCR. The proteome profiling of Chr 18 was accomplished by quantitatively measuring protein copy numbers in the three types of biomaterial (the lowest protein concentration measured was 10(-13) M) using selected reaction monitoring (SRM). In total, protein copy numbers were estimated for 228 master proteins, including quantitative data on 164 proteins in plasma, 171 in the HepG2 cell line, and 186 in liver tissue. Most proteins were present in plasma at 10(8) copies/μL, while the median abundance was 10(4) and 10(5) protein copies per cell in HepG2 cells and liver tissue, respectively. In summary, for liver tissue and HepG2 cells a "transcriptoproteome" was produced that reflects the relationship between transcript and protein copy numbers of the genes on Chr 18. The quantitative data acquired by RNaseq, PCR, and SRM were uploaded into the "Update_2013" data set of our knowledgebase (www.kb18.ru) and investigated for linear correlations.
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Affiliation(s)
- Elena A Ponomarenko
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences , 10 Pogodinskaya Street, Moscow 119121, Russia
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Zgoda VG, Kopylov AT, Tikhonova OV, Moisa AA, Pyndyk NV, Farafonova TE, Novikova SE, Lisitsa AV, Ponomarenko EA, Poverennaya EV, Radko SP, Khmeleva SA, Kurbatov LK, Filimonov AD, Bogolyubova NA, Ilgisonis EV, Chernobrovkin AL, Ivanov AS, Medvedev AE, Mezentsev YV, Moshkovskii SA, Naryzhny SN, Ilina EN, Kostrjukova ES, Alexeev DG, Tyakht AV, Govorun VM, Archakov AI. Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells. J Proteome Res 2012; 12:123-34. [PMID: 23256950 DOI: 10.1021/pr300821n] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The final goal of the Russian part of the Chromosome-centric Human Proteome Project (C-HPP) was established as the analysis of the chromosome 18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells with the sensitivity of 10(-18) M. Using SRM, we have recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2 cells. On the basis of the results of the survey, the SRM assays were drafted for 250 proteins: 41 proteins were found only in the liver tissue, 82 proteins were specifically detected in depleted plasma, and 127 proteins were mapped in both samples. The targeted analysis of HepG2 cells was carried out for 49 proteins; 41 of them were successfully registered using ordinary SRM and 5 additional proteins were registered using a combination of irreversible binding of proteins on CN-Br Sepharose 4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq and RT-PCR has shown a significant correlation (r = 0.78) for 42 gene transcripts. A pilot affinity-based interactome analysis was performed for cytochrome b5 using analytical and preparative optical biosensor fishing followed by MS analysis of the fished proteins. All of the data on the proteome complement of the Chr 18 have been integrated into our gene-centric knowledgebase ( www.kb18.ru ).
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Affiliation(s)
- Victor G Zgoda
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Russia
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Tyakht AV, Popenko AS, Belenikin MS, Altukhov IA, Pavlenko AV, Kostryukova ES, Selezneva OV, Larin AK, Karpova IY, Alexeev DG. MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads. Source Code Biol Med 2012; 7:13. [PMID: 23216677 PMCID: PMC3599743 DOI: 10.1186/1751-0473-7-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 11/27/2012] [Indexed: 11/10/2022]
Abstract
MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors’ knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from
http://hmpdacc.org). MALINA is made freely available on the web at
http://malina.metagenome.ru. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.
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Affiliation(s)
- Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine of Russian Federal Medico-Biological Agency (RIPCM), Malaya Pirogovskaya 1a, Moscow, 119435, Russia.
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