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Stockdale SR, Harrington RS, Shkoporov AN, Khokhlova EV, Daly KM, McDonnell SA, O'Reagan O, Nolan JA, Sheehan D, Lavelle A, Draper LA, Shanahan F, Ross RP, Hill C. Metagenomic assembled plasmids of the human microbiome vary across disease cohorts. Sci Rep 2022; 12:9212. [PMID: 35654877 PMCID: PMC9163076 DOI: 10.1038/s41598-022-13313-y] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 05/17/2022] [Indexed: 12/15/2022] Open
Abstract
We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample β-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses.
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Affiliation(s)
- S R Stockdale
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland.
| | - R S Harrington
- School of Microbiology, University College Cork, Co. Cork, Ireland
| | - A N Shkoporov
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - E V Khokhlova
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - K M Daly
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - S A McDonnell
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - O O'Reagan
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - J A Nolan
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - D Sheehan
- Department of Medicine, University College Cork, Co. Cork, Ireland
| | - A Lavelle
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland.,Department of Medicine, University College Cork, Co. Cork, Ireland
| | - L A Draper
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - F Shanahan
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland.,Department of Medicine, University College Cork, Co. Cork, Ireland
| | - R P Ross
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - C Hill
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland. .,School of Microbiology, University College Cork, Co. Cork, Ireland.
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Efimov BA, Chaplin AV, Shcherbakova VA, Suzina NE, Podoprigora IV, Shkoporov AN. Prevotella rara sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:3818-3825. [PMID: 30339117 DOI: 10.1099/ijsem.0.003066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 12/22/2022] Open
Abstract
A strain of obligately anaerobic, Gram-stain-negative rods was isolated from human faeces and characterized both phenotypically and genotypically. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed the strain to represent a member of the genus Prevotella, distant from the species with validly published names, with the closest relationship to Prevotella oryzae. The strain was moderately saccharolytic and proteolytic. The predominant menaquinones were MK-13 and MK-12. The major cellular long-chain fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 45.7 mol%. On the basis of chemotaxonomic and genotypic properties, it was concluded that the strain represent a novel species within the genus Prevotella, for which the name Prevotellarara sp. nov. is proposed. The type strain of Prevotellarara is 109T (=VKM B-2992T=DSM 105141T).
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Affiliation(s)
- Boris A Efimov
- 1Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Andrei V Chaplin
- 1Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Victoria A Shcherbakova
- 2Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Natalia E Suzina
- 2Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Irina V Podoprigora
- 3Department of Microbiology, Peoples' Friendship University of Russia, Moscow 11719, Russia
| | - Andrei N Shkoporov
- 1Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia.,4APC Microbiome Institute, University College Cork, Cork, Ireland
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Pikina AP, Shkoporov AN, Kulagina EV, Khokhlova EV, Chaplin AV, Volodin NN, Kafarskaya LI, Korotkly NG, Efimov BA. [Comparative Genotyping of Staphylococcus aureus Strains Isolated from Skin Lesions, Nasal Cavities, and Feces of Children with Atopic Dermatitis]. ACTA ACUST UNITED AC 2018; 71:367-74. [PMID: 29297666 DOI: 10.15690/vramn695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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 The lesion of skin of the majority atopic dermatitis patients is chronically colonized by bacteria belonging to the species Staphylococcus aureus. Topical antibacterial and anti-inflammatory therapy treatment are often ineffective due to fast recolonization by S. aureus and exacerbation of allergic process. Aims Our aim was to determine a frequency of S. aureus colonization in skin lesions, mucous membranes of the nasal cavity and intestine of children with atopic dermatitis, to compare the genotypes of Staphylococcus aureus strains isolated from different biotopes of atopic dermatitis patients, and to clarify whether the intestinal and nasal cavities microbiota may act as a source of S. aureus recolonization of skin lesions. Materials and Methods Bacteriological examination of fecal samples, skin, and nasal swabs was conducted in 38 atopic dermatitis patients. The pure bacterial cultures of S. aureus were identified using API Staph (Biomerieux, France) and Vitek 2 MS (Biomerieux, France). Isolates of S. aureus were subjected to genotyping by analysis of rRNA internal 16S-23S rRNA spacer regions and high resolution melting analysis (HMR) of polymorphic spa X-regions. Results 99% S. aureus strains were successfully identified using MALDI-TOF mass-spectrometry. S. aureus cultures were isolated from all biotopes in 31,6% of children, from skin and nasal cavities — in 42% of cases, from skin and feces — in 2,6% of cases, only from skin — in 10,5%, from nasal cavities and feces — in 2,6%, and only from nasal cavities — in 2,6% of cases. In 8% of children, S. aureus was not detected in any of the biotopes. Genotyping of the isolates enabled the detection of 17 different genotypes. A match between the genotypes of skin and nasal strains, and skin and fecal strains was observed in 88% and 61% of the cases respectively. Conclusions The observed a high-frequency matching genotypes suggests the possibility of migration of S. aureus strains inside biotopes in humans and the absence of specialization to colonization of any of the niches.
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Shkoporov AN, Efimov BA, Kondova I, Ouwerling B, Chaplin AV, Shcherbakova VA, Langermans JAM. Peptococcus simiae sp. nov., isolated from rhesus macaque faeces and emended description of the genus Peptococcus. Int J Syst Evol Microbiol 2016; 66:5187-5191. [PMID: 27613234 DOI: 10.1099/ijsem.0.001494] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A study of the faecal microbiome in three healthy female rhesus macaques revealed the presence of a novel obligately anaerobic, chemoorganoheterotrophic, non-sporing, coccoid, non-motile, Gram-stain-positive bacterial species. Three strains of this species, designated as M108T, M916-1/1, and M919-2/1, were non-haemolytic, H2S-positive, catalase-positive, bile- and NaCl-sensitive and required peptone for growth. Strains also were asaccharolytic, able to utilize sulfite, thiosulfate and elemental sulfur as electron acceptors, and produced acetic and butyric acids as metabolic end-products. Strain M108T is characterized by the prevalence of C14 : 0, C16 : 0 and C18 : 1ω9cis dimethyl acetal among the cellular fatty acids, and the presence of MK-10 menaquinone. The DNA G+C content was found to be 51 mol%. Phylogenetic analysis of partial 16S rRNA gene sequences of strains M108T, M916-1/1 and M919-2/1 placed these strains into the genus Peptococcus (family Peptococcaceae). On the basis of phenotypic and genotypic properties we conclude that these strains represent a novel bacterial species for which the name Peptococcus simiae sp. nov. is proposed. The type strain is M108T (=DSM 100347T=VKM B-2932T).
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Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Boris A Efimov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Ivanela Kondova
- Animal Science Department, Biomedical Primate Research Center, P.O. Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Boudewijn Ouwerling
- Animal Science Department, Biomedical Primate Research Center, P.O. Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Andrei V Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Victoria A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Jan A M Langermans
- Animal Science Department, Biomedical Primate Research Center, P.O. Box 3306, 2280 GH Rijswijk, The Netherlands
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Shkoporov AN, Chaplin AV, Khokhlova EV, Shcherbakova VA, Motuzova OV, Bozhenko VK, Kafarskaia LI, Efimov BA. Alistipes inops sp. nov. and Coprobacter secundus sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2016; 65:4580-4588. [PMID: 26377180 DOI: 10.1099/ijsem.0.000617] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Culture-based study of the faecal microbiome in two adult female subjects revealed the presence of two obligately anaerobic, non-spore-forming, rod-shaped, non-motile, Gram-negative bacterial strains that represent novel species. The first strain, designated 627T, was a fastidious, slow-growing, indole-positive bacterium with a non-fermentative type of metabolism.The strain was characterized by the production of acetic and succinic acids as metabolic end products, the prevalence of iso-C15 : 0 fatty acid and the presence of menaquinones MK-10 and MK-11. The DNA G+C content was found to be 56.6 mol%. The second strain, designated 177T, was capable of fermenting a rich collection of carbohydrate substrates, producing acetic acid as a terminal product. The strain was indole-negative and resistant to bile. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0 (in a 1 : 1 ratio) and the predominant menaquinone was MK-11.The DNA G+C content was 37.8 mol%. A phylogenomic analysis of the draft genomes of strains 627T and 177T placed these bacteria in the genera Alistipes(family Rikenellaceae) and Coprobacter (family Porphyromonadaceae), respectively.On the basis of the phenotypic and genotypic properties of strains 627T and 177T, we conclude that these strains from human faeces represent two novel bacterial species, for which the names Alistipes inops sp. nov. (type strain 627T5DSM 28863T5VKM B-2859T) and Coprobacter secundus sp. nov. (type strain 177T=DSM 28864T=VKM B-2857T) are proposed.
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Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Department of Molecular Biology and Experimental Tumor Therapies, Russian Scientific Center of Roentgenoradiology, Moscow 117997, Russia
| | - Andrei V Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Ekaterina V Khokhlova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Victoria A Shcherbakova
- Laboratory of Anaerobic Microorganisms, Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Oksana V Motuzova
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Moscow 117997, Russia
| | - Vladimir K Bozhenko
- Department of Molecular Biology and Experimental Tumor Therapies, Russian Scientific Center of Roentgenoradiology, Moscow 117997, Russia
| | - Lyudmila I Kafarskaia
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Boris A Efimov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
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Shkoporov AN, Chaplin AV, Shcherbakova VA, Suzina NE, Kafarskaia LI, Bozhenko VK, Efimov BA. Ruthenibacterium lactatiformans gen. nov., sp. nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces. Int J Syst Evol Microbiol 2016; 66:3041-3049. [PMID: 27154556 DOI: 10.1099/ijsem.0.001143] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Two novel strains of Gram-stain-negative, rod-shaped, obligately anaerobic, non-spore-forming, non-motile bacteria were isolated from the faeces of healthy human subjects. The strains, designated as 585-1T and 668, were characterized by mesophilic fermentative metabolism, production of d-lactic acid, succinic acid and acetic acid as end products of d-glucose fermentation, prevalence of C18 : 1ω9, C18 : 1ω9 aldehyde, C16 : 0 and C16 : 1ω7c fatty acids, presence of glycine, glutamic acid, lysine, alanine and aspartic acid in the petidoglycan peptide moiety and lack of respiratory quinones. Whole genome sequencing revealed the DNA G+C content was 56.4-56.6 mol%. The complete 16S rRNA gene sequences of the two strains shared 91.7/91.6 % similarity with Anaerofilum pentosovorans FaeT, 91.3/91.2 % with Gemmiger formicilis ATCC 27749T and 88.9/88.8 % with Faecalibacterium prausnitzii ATCC 27768T. On the basis of chemotaxonomic and genomic properties it was concluded that the strains represent a novel species in a new genus within the family Ruminococcaceae, for which the name Ruthenibacterium lactatiformans gen. nov., sp. nov. is proposed. The type strain of Ruthenibacterium lactatiformans is 585-1T (=DSM 100348T=VKM B-2901T).
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Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Andrei V Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Victoria A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Natalia E Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Lyudmila I Kafarskaia
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Vladimir K Bozhenko
- Department of Molecular Biology and Experimental Tumor Therapies, Russian Scientific Center of Roentgenoradiology, Moscow 117997, Russia
| | - Boris A Efimov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
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Chaplin AV, Efimov BA, Smeianov VV, Kafarskaia LI, Pikina AP, Shkoporov AN. Intraspecies Genomic Diversity and Long-Term Persistence of Bifidobacterium longum. PLoS One 2015; 10:e0135658. [PMID: 26275230 PMCID: PMC4537262 DOI: 10.1371/journal.pone.0135658] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/23/2015] [Indexed: 12/28/2022] Open
Abstract
Members of genus Bifidobacterium are Gram-positive bacteria, representing a large part of the human infant microbiota and moderately common in adults. However, our knowledge about their diversity, intraspecific phylogeny and long-term persistence in humans is still limited. Bifidobacterium longum is generally considered to be the most common and prevalent species in the intestinal microbiota. In this work we studied whole genome sequences of 28 strains of B. longum, including 8 sequences described in this paper. Part of these strains were isolated from healthy children during a long observation period (up to 10 years between isolation from the same patient). The three known subspecies (longum, infantis and suis) could be clearly divided using sequence-based phylogenetic methods, gene content and the average nucleotide identity. The profiles of glycoside hydrolase genes reflected the different ecological specializations of these three subspecies. The high impact of horizontal gene transfer on genomic diversity was observed, which is possibly due to a large number of prophages and rapidly spreading plasmids. The pan-genome characteristics of the subspecies longum corresponded to the open pan-genome model. While the major part of the strain-specific genetic loci represented transposons and phage-derived regions, a large number of cell envelope synthesis genes were also observed within this category, representing high variability of cell surface molecules. We observed the cases of isolation of high genetically similar strains of B. longum from the same patients after long periods of time, however, we didn’t succeed in the isolation of genetically identical bacteria: a fact, reflecting the high plasticity of microbiota in children.
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Affiliation(s)
- Andrei V Chaplin
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Boris A Efimov
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vladimir V Smeianov
- Department of Natural Sciences, Medical Institute, North Caucasus State Academy for Humanities and Technologies, Cherkessk, Russia
| | - Lyudmila I Kafarskaia
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alla P Pikina
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Andrei N Shkoporov
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
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Shkoporov AN, Khokhlova EV, Savochkin KA, Kafarskaia LI, Efimov BA. Production of biologically active scFv and VHH antibody fragments in Bifidobacterium longum. FEMS Microbiol Lett 2015; 362:fnv083. [PMID: 25994292 DOI: 10.1093/femsle/fnv083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2015] [Indexed: 01/01/2023] Open
Abstract
Bifidobacteria constitute a significant part of healthy intestinal microbiota in adults and infants and present a promising platform for construction of genetically modified probiotic agents for treatment of gastrointestinal disorders. In this study, three strains of Bifidobacterium longum were constructed that express and secrete biologically active single-chain antibodies against human TNF-α and Clostridium difficile exotoxin A. Anti-TNF-α scFv antibody D2E7 was produced at the level of 25 μg L(-1) in broth culture and was mostly retained in the cytoplasm, while VHH-type antibodies A20.1 and A26.8 against C. difficile exotoxin A were produced at the levels of 0.3-1 mg L(-1) and secreted very efficiently. The biological activity of both antibody types was demonstrated in the mammalian cell-based assays. Expression of A20.1 and A26.8 was also observed in vivo after intragastric administration of transformed B. longum strains to (C57/BL6 × DBA/2)F1 mice. The obtained B. longum strains may serve as prototypes for construction of novel probiotic medications against inflammatory bowel disease and C. difficile-associated disease.
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Affiliation(s)
- A N Shkoporov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Ostrovitjanova str. 1, Moscow 117997, Russia Pharmbacter LLC, Skladochnaya ul., 1 - 1, Moscow 127018, Russia
| | - E V Khokhlova
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Ostrovitjanova str. 1, Moscow 117997, Russia
| | - K A Savochkin
- Pharmbacter LLC, Skladochnaya ul., 1 - 1, Moscow 127018, Russia
| | - L I Kafarskaia
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Ostrovitjanova str. 1, Moscow 117997, Russia
| | - B A Efimov
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Ostrovitjanova str. 1, Moscow 117997, Russia
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Chaplin AV, Brzhozovskii AG, Parfenova TV, Kafarskaia LI, Volodin NN, Shkoporov AN, Ilina EN, Efimov BA. [Species Diversity of Bifidobacteria in the Intestinal Microbiota Studied Using MALDI-TOF Mass-Spectrometry]. Vestn Ross Akad Med Nauk 2015:435-440. [PMID: 26710526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND The members of genus Bifidobacterium represent a significant part of intestinal microbiota in adults and predominate in infants. Species repertoire of the intestinal bifidobacteria is known to be subjected to major changes with age; however, many details of this process are still to be elucidated. OBJECTIVE Our aim was to study the diversity of intestinal bifidobacteria and changes of their qualitative and quantitative composition characteristics during the process of growing up using MALDI-TOF mass-spectrometric analysis ofpure bacterial cultures. METHODS A cross-sectional study of bifidobacteria in the intestinal microbiota was performed in 93 healthy people of the ages from 1 month to 57 years. Strains were identified using Microflex LT MALDI-TOF MS, the confirmation was performed by 16S rRNA gene fragment sequencing. RESULTS 93% of isolated bifidobacterial strains were successfully identified using MALDI-TOF mass-spectrometry. At least two of the strains from each species were additionally identified by 16S rRNA gene fragment sequencing, in all of the cases the results were the same. It was shown that the total concentration of bifidobacteria decreases with age (p<0.001) as well as the frequency of isolation of Bifidobacterium bifidum (p=0.020) and Bifidobacterium breve (p<0.001), and the frequency of isolation of Bifidobacterium adolescentis, increases (p<0.001), representing the continuous process of transformation of microbiota. CONCLUSION The method of MALDI-TOF mass spectrometry demonstrated the ability to perform rapid and reliable identification of bifidobacteria that allowed the study of changes in the quantitative and qualitative characteristics of human microbiota in the process of growing up.
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Bozhenko VK, Shramova EI, Shishkin AM, Ivanov AV, Khokhlova EV, Lebedin YS, Shkoporov AN. Characteristics of new monomolecular chimeric T-cell receptors to carcinoembryonic antigen. Bull Exp Biol Med 2013; 156:165-71. [PMID: 24319717 DOI: 10.1007/s10517-013-2302-2] [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] [Indexed: 11/24/2022]
Abstract
We described two original genetic constructs encoding chimeric monomolecular T-cell receptors, where the effector T-cell receptor fragment was linked with the antigen-recognizing part consisting of two variable fragments of two different antibodies to carcinoembryonic antigen. Following transfection, these receptors were expressed on the cell surface and bound carcinoembryonic antigen. Human peripheral blood lymphocytes transfected with the above constructs demonstrated high cytotoxic activity against HCT116 cells expressing carcinoembryonic antigen.
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Affiliation(s)
- V K Bozhenko
- Russian Scientific Center of Roentgenoradiology, Ministry of Health of the Russian Federation; N. I. Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation; XEMA Company, Moscow, Russia.
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Pyrkov TV, Sevostyanova IA, Schmalhausen EV, Shkoporov AN, Vinnik AA, Muronetz VI, Severin FF, Fedichev PO. Structure-Based Design of Small-Molecule Ligands of Phosphofructokinase-2 Activating or Inhibiting Glycolysis. ChemMedChem 2013; 8:1322-9. [DOI: 10.1002/cmdc.201300154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Indexed: 12/25/2022]
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Shkoporov AN, Khokhlova EV, Chaplin AV, Kafarskaia LI, Nikolin AA, Polyakov VY, Shcherbakova VA, Chernaia ZA, Efimov BA. Coprobacter fastidiosus gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from infant faeces. Int J Syst Evol Microbiol 2013; 63:4181-4188. [PMID: 23771624 DOI: 10.1099/ijs.0.052126-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A novel obligately anaerobic, non-spore-forming, rod-shaped, non-motile Gram-reaction-negative bacterium was isolated from infant faeces. The strain, designated NSB1(T), was able to grow on rich media at 30-37 °C, in the presence of up to 2 % (w/v) Oxgall and 2 % (w/v) NaCl. Cells of strain NSB1(T) produced catalase, but not urease and indole. Aesculin was not hydrolysed. The strain was able to utilize d-glucose, lactose, maltose, mannose and raffinose as electron donors. When grown on d-glucose, the main metabolic end products were propionic and acetic acids, with a minor product being succinic acid. The major cellular fatty acids, iso-C15 : 0 and anteiso-C15 : 0, were present at a 1 : 1 molar ratio. The major menaquinone was MK-11. The DNA G+C content was found to be 38.5 mol%. According to 16S rRNA gene sequence analysis strain NSB1(T) is a member of the family Porphyromonadaceae, phylum Bacteroidetes. The closest relatives of the strain were Barnesiella viscericola (88.2 % identity) and Barnesiella intestinihominis (87.4 % identity). On the basis of phenotypic and genotypic properties of strain NSB1(T) we conclude that this strain represent a novel species in a new genus within the family of Porphyromonadaceae for which the name Coprobacter fastidiosus gen. nov., sp. nov. is proposed. The type strain of the species is NSB1(T) ( = DSM 26242(T), = VKM B-2743(T)).
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Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology and Virology, Russian National Research Medical University, Moscow 117997, Russia
| | - Ekaterina V Khokhlova
- Department of Microbiology and Virology, Russian National Research Medical University, Moscow 117997, Russia
| | - Andrei V Chaplin
- Department of Microbiology and Virology, Russian National Research Medical University, Moscow 117997, Russia
| | - Lyudmila I Kafarskaia
- Department of Microbiology and Virology, Russian National Research Medical University, Moscow 117997, Russia
| | - Alexei A Nikolin
- Department of Chemistry, Russian National Research Medical University, Moscow 117997, Russia
| | - Vladimir Yu Polyakov
- Department of Electron Microscopy, Belozersky Institute of Physicochemical Biology, Moscow State University, Moscow 119992, Russia
| | - Victoria A Shcherbakova
- Laboratory of Anaerobic Microorganisms, Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Zoya A Chernaia
- Department of Microbiology and Virology, Russian National Research Medical University, Moscow 117997, Russia
| | - Boris A Efimov
- Department of Microbiology and Virology, Russian National Research Medical University, Moscow 117997, Russia
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Shkoporov AN, Khokhlova EV, Kulagina EV, Smeianov VV, Kuchmiy AA, Kafarskaya LI, Efimov BA. Analysis of a novel 8.9kb cryptic plasmid from Bacteroides uniformis, its long-term stability and spread within human microbiota. Plasmid 2012. [PMID: 23201047 DOI: 10.1016/j.plasmid.2012.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The analysis of plasmid content in dominant Bacteroidales order intestinal strains isolated from the same child at a 5 year interval identified a 8.9 kb plasmid in Bacteroides uniformis BUN24 strain isolated at age 6 and indistinguishably sized plasmids in the isolates of B. uniformis, B. vulgatus, B. intesinalis, and Parabacteroides distasonis at age 11. We sequenced a B. uniformis BUN24 plasmid, designated pBUN24, and using molecular surveys of diverse species we established that this 8944bp molecule (G+C content 43.5%) represents a novel family of small cryptic Bacteroidales plasmids. The replication region of pBUN24 was experimentally localized to a 1707-bp fragment that includes a putative repA gene, coding for a protein of Rep_3 superfamily of replication proteins of theta-type plasmids preceded by a putative iteron-containing origin of replication. The other open reading frames (ORFs) identified in pBUN24 sequence include a putative tad-ata-type toxin-antitoxin and mobA-mobB mobilization modules, as well as seven additional cryptic ORFs. The interaction of Tad and Ada components demonstrated by a pull-down assay and the toxicity of Tad in Escherichia coli host suggests the functionality of the plasmid addiction module. Re-sequencing of plasmids in two Bacteroides strains isolated at the age of 11 showed 100% nucleotide identity to pBUN24. This data supports the notion that this plasmid is transmissible to other Bacteroidales strains in the natural ecosystem. The possible roles of toxin-antitoxin system and other proteins encoded by pBUN24 in providing an apparent ecological advantage to the plasmid-harbouring strains of a bacterial symbiont in the human gut deserve further investigation.
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Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology and Virology, The Russian National Research Medical University, 1, Ostrovitjanova St., Moscow 117997, Russia.
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14
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Khokhlova EV, Smeianov VV, Efimov BA, Kafarskaia LI, Pavlova SI, Shkoporov AN. Anti-inflammatory properties of intestinal Bifidobacterium strains isolated from healthy infants. Microbiol Immunol 2012; 56:27-39. [PMID: 22040047 DOI: 10.1111/j.1348-0421.2011.00398.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Certain Bifidobacterium strains have been shown to inhibit inflammatory responses in intestinal epithelial cells. However, the precise mechanisms of these effects, including the chemical nature of the active compounds, remain to be elucidated. Here partial characterization of the anti-inflammatory properties of Bifidobacterium strains isolated from feces of healthy infants is reported. It was found that conditioned media (CM) of all strains studied are capable of attenuating tumor necrosis factor-α (TNF-α) and lipopolysaccharide- (LPS) induced inflammatory responses in the HT-29 cell line. In contrast, neither killed bifidobacterial cells, nor cell-free extracts showed such activities. Further investigations resulted in attribution of this activity to heat-stable, non-lipophilic compound(s) resistant to protease and nuclease treatments and of molecular weight less than 3 kDa. The anti-inflammatory effects were dose- and time-dependent and associated with inhibition of IκB phosphorylation and nuclear factor-κ light chain enhancer of activated B cells (NF-κB)-dependent promoter activation. The combined treatments of cells with CMs and either LPS or TNF-α, but not with CMs alone, resulted in upregulation of transforming growth factor-β1, IκBζ, and p21(CIP) mRNAs. Our data suggest certain species-specificities of the anti-inflammatory properties of bifidobacteria. This observation should prompt additional validation studies using larger set of strains and employing the tools of comparative genomics.
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Affiliation(s)
- Ekaterina V Khokhlova
- Department of Microbiology and Virology, Russian State Medical University, Moscow, Russia
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15
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Khokhlova EV, Efimov BA, Kafarskaia LI, Shkoporov AN. Heterologous expression of secreted biologically active human interleukin-10 in Bifidobacterium breve. Arch Microbiol 2010; 192:769-74. [PMID: 20631991 DOI: 10.1007/s00203-010-0606-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 07/03/2010] [Accepted: 07/05/2010] [Indexed: 10/19/2022]
Abstract
Construction of Bifidobacterium breve capable of production of secreted biologically active human interleukin-10 (hIL-10) is described. ORF coding for full-length mature human interleukin-10 was cloned into a series of expression vectors. This resulted in generation of translational fusions between hIL-10 and signal peptides sequences derived from Bifidobacterium breve genes sec2, apuB and B. adolescentis gene amyB under the control of constitutively active bifidobacterial promoter. We have shown that fusion to amyB signal peptide resulted in highest expression level of hIL-10 at the mRNA and protein level. Secreted hIL-10 was highly unstable in bifidobacterial culture supernatants in standard growth conditions. However, incubation of stationary cultures in buffered tissue culture medium resulted in production of stable biologically active hIL-10, albeit in low amounts (1.9 ng/ml).
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Affiliation(s)
- E V Khokhlova
- Department of Microbiology and Virology, Russian State Medical University, Moscow, Russian Federation
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16
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Khokhlova EV, Shkoporov AN, Volodin NN, Efimov BA, Pavlov KA, Kafarskaia LI. Relationship between suppression of E6 and E7 virus oncogenes and expression of apoptosis and cell cycle genes in cervical cancer culture. Bull Exp Biol Med 2010; 149:73-7. [PMID: 21113463 DOI: 10.1007/s10517-010-0879-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The effects of short interfering RNA suppressing the expression of E6 and E7 human papilloma virus (type 18) on the expression of apoptosis and cell cycle genes were studied in HeLa cells. Changes in the transcription profiles were evaluated using DNA microarray and real-time reverse-transcription PCR. Cell transfection with anti-E6 and anti-E7 short interfering RNA moderately reduced the expression of mRNA for CDC25C, GRB2, GTSE1, and PLK1 genes and induced expression of CDKN1A (p21(CIP)) gene mRNA. In addition, culture proliferation was inhibited and morphological changes characteristic of differentiation and cell aging developed.
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Shkoporov AN, Efimov BA, Khokhlova EV, Steele JL, Kafarskaia LI, Smeianov VV. Characterization of plasmids from human infant Bifidobacterium strains: sequence analysis and construction of E. coli-Bifidobacterium shuttle vectors. Plasmid 2008; 60:136-48. [PMID: 18652842 DOI: 10.1016/j.plasmid.2008.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 06/26/2008] [Accepted: 06/27/2008] [Indexed: 11/29/2022]
Abstract
A survey of infant fecal Bifidobacterium isolates for plasmid DNA revealed that a significant portion of the strains, 17.6%, carry small plasmids. The majority of plasmid-harboring strains belonged to the Bifidobacterium longum/infantis group. Most of the plasmids could be assigned into two groups based on their sizes and the restriction profiles. Three plasmids, pB44 (3.6 kb) from B. longum, pB80 (4.9 kb) from Bifidobacterium bifidum, and pB21a (5.2kb) from Bifidobacterium breve were sequenced. While the former two plasmids were found to be highly similar to previously characterized rolling-circle replicating pKJ36 and pKJ56, respectively, the third plasmid, pB21a, does not share significant nucleotide homology with known plasmids. However, it might be placed into the pCIBb1-like group of bifidobacterial rolling-plasmids based on the homology of its Rep protein and the overall molecular organization. Two sets of Escherichia coli-Bifidobacterium shuttle vectors constructed based on pB44 and pB80 replicons were capable of transforming B. bifidum and B. breve strains with efficiency up to 3x10(4)cfu/microg DNA. Additionally, an attempt was made to employ a broad host range conjugation element, RP4, in developing of E. coli-Bifidobacterium gene transfer system.
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Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology, Russia State Medical University, Moscow, Russia
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Shkoporov AN, Khokhlova EV, Efimov BA, Kafarskaia LI. [Expression of green fluorescent protein (GFP) gene of Aequorea victoria [correction of Aequoria victoria] in Lactobacillus plantarum bacterium ]. Zh Mikrobiol Epidemiol Immunobiol 2008:33-37. [PMID: 18819405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Results of development of shuttle expressing plasmid vector Escherichia coli-Lactobacillus which allowed high level expression of heterologous genes in lactobacilli are represented. Vector pTRKH2 which is able to replicate in E. coli and in wide range of Gram-positive bacteria was used as the base. In order to provide high level of cloned gene expression constitutive-active synthetic promoter, site of initiation of translation, and terminator of transcription were introduced in the vector. Functional activity of this vector was confirmed using green fluorescent protein (GFP) gene from Aequoria victoria. Transformation of model strain by gfp gene-carrying plasmid resulted in appearance of typical fluorescent phenotype.
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Shkoporov AN, Efimov BA, Khokhlova EV, Kafarskaia LI, Smeianov VV. Production of human basic fibroblast growth factor (FGF-2) in Bifidobacterium breve using a series of novel expression/secretion vectors. Biotechnol Lett 2008; 30:1983-8. [PMID: 18575808 DOI: 10.1007/s10529-008-9772-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 06/04/2008] [Accepted: 06/06/2008] [Indexed: 11/27/2022]
Abstract
Four E. coli-Bifidobacterium shuttle vectors were constructed using Bifidobacterium plasmids, pB44 and pB80. The vectors carry two bifidobacterial promoters, a signal peptide-encoding sequence, sec2, of Bifidobacterium breve, and a transcriptional terminator from hup gene of Bifidobacterium longum. Functionality of the constructs were tested using human FGF-2 gene. The expression of FGF-2 was detected by Western blotting in B. breve transformed with three of the vectors. The highest amount of FGF-2 was produced upon transformation with pESH86, which is a pB80-based plasmid carrying FGF-2 under control of a hup promoter (Phup). Similarly, the level of FGF-2 mRNA transcribed from pESH86 was approximately threefold higher, 882 +/- 70 AU (arbitrary units), when compared to those transcribed from pB44-based pESH46 (Phup) (289 +/- 65 AU) and pESH47 (Pgap) (282 +/- 37 AU). These results suggest the vectors have the potential for production of exported fusion proteins in bifidobacteria and the expression levels can be regulated through the employment of different bifidobacterial promoters and/or replicons.
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Affiliation(s)
- A N Shkoporov
- Department of Microbiology and Virology, Russian State Medical University, Moscow, Russian Federation
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Efimov BA, Shkoporov AN, Khokhlova EV, Afanas'ev SS, Kulagina EV, Kafarskaia LI. [Bifidobacterial plasmids and their application to genetic engineering]. Vestn Ross Akad Med Nauk 2008:16-21. [PMID: 18368765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Representatives of Bifidobacterium genus are considered to play many important roles in intestinal homeostasis. On the other hand, their molecular biology and genetics have been poorly studied. In order to broaden our understanding of their health-promoting mechanisms, it is extremely important to possess tools to manipulate them genetically. Another challenging task is to take advantage of genetic engineering technology for designing new probiotic bifidobacteria with unique therapeutic properties. An important step in such work is to isolate and characterize small bifidobacterial plasmids, which can be applied to the construction of cloning vectors. This article presents a review of several pioneering studied devoted to bifidobacterial plasmids and genetic engineering with bifidobacteria. Trends in and prospects of molecular genetics of bifidobacteria are discussed as well.
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Shkoporov AN, Kafarskaia LI, Afanas'ev SS, Smeianov VV, Kirillov MI, Postnikova EA, Maksimov FE, Khokhlova EV, Efimov BA. [A molecular-and-genetic analysis of species and strain diversity of bifidobacteria in early childhood]. Vestn Ross Akad Med Nauk 2006:45-50. [PMID: 16496956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The species and strain composition of bifidobacteria in 29 children both sexes, aged 8 to 16 months, was studied. Species-specific primers and PCR were used to determine to which species the predominant strains of bifidobacteria, isolated from feces by cultural methods, belonged. Bifidobacteria were found in 28 (96.5%) children; their number was 10.2 +/- 0.7 ECU per a gram of the material. B. longum and B. bifidum were frequent (71.4 and 53.5%, respectively). The level of quantitative detection used in the study also allowed revealing of B. catenulatum (17.9%) and B. breve (14.4%). A high titer of B. dentium was found in one case (3.6%). B. adolescentis and B. angulatum were not found in any patient. The average number of species found in one child was 1.7 +/- 0.7. RAPD-PCR and investigation of plasmid profile were used to determine possible belonging of the isolates to different strains. The average number of strains per one sample was 2.3 +/- 1.2. Nine unique plasmid bifidobacterial strains were isolated from 7 children. In 3 children the intestinal tract was found to be colonized by both plasmid and non-plasmid-carrying strains of one bifidobacterial species.
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Kafarskaia LI, Volodin NN, Efimov BA, Afanas'ev SS, Shkoporov AN. [Peculiarities of microbial colonization of the intestinal tract in newborns and pre-term infants in intensive care units]. Vestn Ross Akad Med Nauk 2006:10-5. [PMID: 16496949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The aim of the study was to compare the development of intestinal microflora in clinically healthy newborns, born by mothers with physiological pregnancy, and in small premature infants, who were treated in intensive care units (ICU) using various regimens of antibacterial therapy. The study revealed that the most frequent bacteria found in the intestinal tract of healthy infants at the and of neonatal period were bifidobacteria, enterobacteria, and coagulase-negative staphylococci and enterococci. Together with large quantity of autochtonous bacteria, the study revealed conditionally pathogenic microorganisms, such as klebsiella and coagulase-positive staphylococci at the end of neonatal period. The intestinal microflora of premature infants in ICU, treated with a combination of third generation cephalosporins and aminoglycosides from the first hours of life, was characterized by total absence of indigenous microflora, and prevalence of enterococci and staphylococci. The results show that the first stage of antibacterial therapy of preterm infants in ICU should be based upon the principles of selective decontamination.
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