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Kolzhetsov N, Markelova N, Frolova M, Alikina O, Glazunova O, Safonova L, Kalashnikova I, Yudin V, Makarov V, Keskinov A, Yudin S, Troshina D, Rechkina V, Shcherbakova V, Shavkunov K, Ozoline O. Enterotype-Dependent Probiotic-Mediated Changes in the Male Rat Intestinal Microbiome In Vivo and In Vitro. Int J Mol Sci 2024; 25:4558. [PMID: 38674145 PMCID: PMC11049970 DOI: 10.3390/ijms25084558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Beneficial properties of lactic acid bacteria have been known long ago, but particular interest in probiotics has arisen in the last two decades due to the understanding of the important role of intestinal microflora in human life. Thus, the ability of probiotics to support healthy homeostasis of gut microbiomes has received particular attention. Here, we evaluated the effect of a probiotic consisting of Bifidobacterium longum and Lacticaseibacillus paracasei on the gut microbiome of male rats, assessed their persistence in the fecal biota, and compared probiotic-mediated changes in vitro and in vivo. As expected, microbiomes of two enterotypes were identified in the feces of 21 animals, and it turned out that even a single dose of the probiotic altered the microbial composition. Upon repeated administration, the E1 biota temporarily acquired properties of the E2 type. Being highly sensitive to the intervention of probiotic bacteria at the phylum and genus levels, the fecal microbiomes retained the identity of their enterotypes when transferred to a medium optimized for gut bacteria. For the E2 biota, even similarities between probiotic-mediated reactions in vitro and in vivo were detected. Therefore, fecal-derived microbial communities are proposed as model consortia to optimize the response of resident bacteria to various agents.
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Affiliation(s)
- Nikolay Kolzhetsov
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Natalia Markelova
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Maria Frolova
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Olga Alikina
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Olga Glazunova
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Lubov Safonova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Irina Kalashnikova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Vladimir Yudin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Valentin Makarov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Anton Keskinov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Sergey Yudin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Daria Troshina
- Faculty of Biotechnology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Viktoria Rechkina
- Laboratory of Anaerobic Microorganisms, Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (V.R.); (V.S.)
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (V.R.); (V.S.)
| | - Konstantin Shavkunov
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Olga Ozoline
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
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Shevchenko A, Shalaginova I, Katserov D, Matskova L, Shiryaeva N, Dyuzhikova N. Post-stress changes in the gut microbiome composition in rats with different levels of nervous system excitability. PLoS One 2023; 18:e0295709. [PMID: 38079399 PMCID: PMC10712864 DOI: 10.1371/journal.pone.0295709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
The gut-brain axis is a critical communication system influencing the interactions between the gastrointestinal tract (GI) and the central nervous system (CNS). The gut microbiota plays a significant role in this axis, affecting the development and function of the nervous system. Stress-induced psychopathologies, such as depression and anxiety, have been linked to the gut microbiota, but underlying mechanisms and genetic susceptibility remain unclear. In this study, we examined stress-induced changes in the gut microbiome composition in two rat strains with different levels of nervous system excitability: high threshold (HT strain) and low threshold (LT strain). Rats were exposed to long-term emotional and painful stress using the Hecht protocol, and fecal samples were collected at multiple time points before and after stress exposure. Using 16S rRNA amplicon sequencing, we assessed the qualitative and quantitative changes in the gut microbiota. Our results revealed distinct microbial diversity between the two rat strains, with the HT strain displaying higher diversity compared to the LT strain. Notably, under prolonged stress, the HT strain showed an increase in relative abundance of microorganisms from the genera Faecalibacterium and Prevotella in fecal samples. Additionally, both strains exhibited a decrease in Lactobacillus abundance following stress exposure. Our findings provide valuable insights into the impact of hereditary nervous system excitability on the gut microbiome composition under stress conditions. Understanding the gut-brain interactions in response to stress may open new avenues for comprehending stress-related psychopathologies and developing potential therapeutic interventions targeted at the gut microbiota. However, further research is needed to elucidate the exact mechanisms underlying these changes and their implications for stress-induced disorders. Overall, this study contributes to the growing body of knowledge on the gut-brain axis and its significance in stress-related neurobiology.
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Affiliation(s)
- Alla Shevchenko
- Educational and Scientific Cluster “Institute of Medicine and Life Sciences (MEDBIO)”, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Irina Shalaginova
- Educational and Scientific Cluster “Institute of Medicine and Life Sciences (MEDBIO)”, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Dmitriy Katserov
- Educational and Scientific Cluster “Institute of Medicine and Life Sciences (MEDBIO)”, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Ludmila Matskova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalia Shiryaeva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Natalia Dyuzhikova
- Pavlov Institute of Physiology of the Russian Academy of Sciences, Saint-Petersburg, Russia
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Gao Y, Ding P, Wang J, Zhang C, Ji G, Wu T. Application of metabolomics in irritable bowel syndrome in recent 5 years. Int Immunopharmacol 2023; 124:110776. [PMID: 37603947 DOI: 10.1016/j.intimp.2023.110776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/23/2023]
Abstract
Irritable bowel syndrome (IBS) is one of the most common functional gastrointestinal disorders worldwide, characterized by chronic abdominal pain or discomfort and altered bowel habits. To date, the exact pathogenesis of IBS remains elusive, but is clearly multifactorial, including environmental and host factors. However, the management of patients with IBS is challenging and the current diagnostic and therapeutic modalities have unsatisfactory outcomes. Therefore, it is important to develop more effective methods to diagnose IBS early. Metabolomics studies the metabolites most closely related to patient characteristics, which can provide useful clinical biomarkers that can be applied to IBS and may open up new diagnostic approaches. Traditional Chinese medicine (TCM) can play a role in improving symptoms and protecting target organs, but its mechanism needs to be studied in depth. In this review, based on PubMed/MEDLINE and other databases, we searched metabolomics studies related to IBS in the past 5 years, including those related to clinical studies and animal studies, as well as literatures on TCM interventions in IBS, to provide an updated overview of the application of metabolomics to the diagnosis and treatment of IBS and the improvement of IBS by TCM.
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Affiliation(s)
- Ying Gao
- Institute of Digestive Disease, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Peilun Ding
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Junmin Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Caiyun Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guang Ji
- Institute of Digestive Disease, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China.
| | - Tao Wu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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Widjaja F, Rietjens IMCM. From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes. Biomedicines 2023; 11:2658. [PMID: 37893032 PMCID: PMC10603957 DOI: 10.3390/biomedicines11102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine-feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either -20 °C for up to a few months or -80 °C for a longer period-up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality.
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Affiliation(s)
- Frances Widjaja
- Division of Toxicology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
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