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Yan Y, Xu J, Huang W, Fan Y, Li Z, Tian M, Ma J, Lu X, Liang J. Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China. Microorganisms 2024; 12:911. [PMID: 38792738 PMCID: PMC11124135 DOI: 10.3390/microorganisms12050911] [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: 04/14/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Microbial communities inhabiting sedimentary environments in river source regions serve as pivotal indicators of pristine river ecosystems. While the correlation between antibiotic resistome and pathogenicity with core gut bacteria in humans is well established, there exists a significant knowledge gap concerning the interaction of antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) with specific microbes in river source basins, often referred to as "terrestrial gut". Understanding the microbial composition, including bacteria and resident genetic elements such as ARGs, HPB, Mobile Genetic Elements (MGEs), and Virulence Factors (VFs), within natural habitats against the backdrop of global change, is imperative. To address this gap, an enrichment-based culturomics complementary along with metagenomics was conducted in this study to characterize the microbial biobank and provide preliminary ecological insights into profiling the dissemination of ARGs in the Lancang River Source Basin. Based on our findings, in the main stream of the Lancang River Source Basin, 674 strains of bacteria, comprising 540 strains under anaerobic conditions and 124 under aerobic conditions, were successfully isolated. Among these, 98 species were identified as known species, while 4 were potential novel species. Of these 98 species, 30 were HPB relevant to human health. Additionally, bacA and bacitracin emerged as the most abundant ARGs and antibiotics in this river, respectively. Furthermore, the risk assessment of ARGs predominantly indicated the lowest risk rank (Rank Ⅳ) in terms of endangering human health. In summary, enrichment-based culturomics proved effective in isolating rare and unknown bacteria, particularly under anaerobic conditions. The emergence of ARGs showed limited correlation with MGEs, indicating minimal threats to human health within the main stream of the Lancang River Source Basin.
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Affiliation(s)
- Yi Yan
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Jialiang Xu
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Wenmin Huang
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Yufeng Fan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Zhenpeng Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Mingkai Tian
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Jinsheng Ma
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Xin Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
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Yun JU, Jung HS, Jung MJ, Song HS, Kim YB, Kim Y, Kim JG, Roh SW, Lee SH, Lee JS, Whon TW. Cutibacterium equinum sp. nov., isolated from horse faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 37910171 DOI: 10.1099/ijsem.0.006099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Strain CBA3108T is a Gram-positive, non-spore-forming, obligately anaerobic bacterium isolated from horse faecal samples obtained in Jeju Island, Republic of Korea. The cells of CBA3108T are non-motile short rods that have been assessed as catalase-positive and oxidase-negative. Growth of the strain occurs under the following conditions: 25-45 °C (optimum, 35 °C); pH 6-9 (optimum, pH 6); and in the presence of 0-6 % (w/v) NaCl (optimum, 2%). Major fatty acids in the strain include C15 : 0 iso and C15 : 0 iso DMA, while major polar lipids include phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. Based on phylogenetic analysis using 16S rRNA gene sequences, strain CBA3108T forms a phyletic lineage distinct from other closely related species within the genus Cutibacterium. It was found to be most closely related to Cutibacterium avidum ATCC 25577T (98.27 % 16S rRNA gene sequence similarity) and other strains within the genus (≤98.0 %). The genomic DNA G+C content of strain CBA3108T was 63.2 mol%. The in silico DNA-DNA hybridization values of strain CBA3108T with C. avidum ATCC 25577T, C. porci WCA-380-WT-3AT and C. acnes subsp. acnes DSM 1897T were 33.6, 21.7 and 22.7 %, respectively. Its phenotypic, chemotaxonomic and molecular properties support the hypothesis that strain CBA3108T represents a novel species in the genus Cutibacterium, for which we propose the name Cutibacterium equinum sp. nov. The type strain is CBA3108T (=KACC 22889T=JCM 35966T).
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Affiliation(s)
- Jeong Ui Yun
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
- Department of Life Science, Chosun University, Gwangju 61452, Republic of Korea
| | - Hye Su Jung
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
- Biobank, Institut Pasteur Korea, Seongnam, 13488, Republic of Korea
| | - Mi-Ja Jung
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hye Seon Song
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Yeon Bee Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Yujin Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Joon-Gyu Kim
- Department of Equine Science, Cheju Halla University, Jeju, 63092, Republic of Korea
| | - Seong Woon Roh
- Microbiome Research Team, LISCure Biosciences Inc., Seongnam 13486, Republic of Korea
| | - Se Hee Lee
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jun Sik Lee
- Department of Life Science, Chosun University, Gwangju 61452, Republic of Korea
| | - Tae Woong Whon
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
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Jung HS, Yun JU, Jung MJ, Song HS, Kim YB, Kim Y, Kim JG, Jeon CO, Roh SW, Whon TW, Lee SH. Peptoniphilus equinus sp. nov., a novel Gram-stain-positive anaerobic coccus isolated from the faeces of a thoroughbred racehorse. Int J Syst Evol Microbiol 2023; 73. [PMID: 37750780 DOI: 10.1099/ijsem.0.006053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
A novel, anaerobic, Gram-stain-positive coccoid strain, CBA3646T, was isolated from the faeces of a thoroughbred racehorse. Phylogenetic analysis based on 16S rRNA gene sequencing yielded results indicative of CBA3646T representing a member of the genus Peptoniphilus, with the species most closely related to it being Peptoniphilus asaccharolyticus DSM 20463T, with a similarity of 94.79 %. DNA-DNA relatedness and average nucleotide identity values between CBA3646T and P. asaccharolyticus DSM 20463T were 21.4 and 67.6 %, respectively. CBA3646T has a circular chromosomal genome of 1 709 189 bp (45.5 mol% DNA G+C content), containing 1652 genes in total, 1584 predicted protein-coding genes, 3 complete rRNA loci and 47 tRNA genes. The cells were non-motile diplococci, catalase-positive and oxidase-negative. Growth of CBA3646T was observed at 20-40 °C (optimal temperature, 35 °C) and in the presence of 0-4 % (w/v) NaCl (optimum concentration, 1 %). The major fatty acids (>10 %) of CBA3646T were C16 : 0, C18 : 1ω9c and C18 : 1ω9c dimethyl acetal, with its major polar lipids being diphosphatidylglycerol and phosphatidylglycerol. The elucidated phylogenetic, physiological, chemotaxonomic and molecular properties are indicative of strain CBA3646T representing a novel species of the genus Peptoniphilus, or which the name Peptoniphilus equinus sp. nov. is proposed. The type strain is CBA3646T (= KACC 22890T = JCM 35845T).
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Affiliation(s)
- Hye Su Jung
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
- Biobank, Institut Pasteur Korea, Seongnam, 13488, Republic of Korea
| | - Jeong Ui Yun
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Mi-Ja Jung
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hye Seon Song
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Yeon Bee Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Yujin Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Joon-Gyu Kim
- Department of Equine Science, Cheju Halla University, Jeju, 63092, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong Woon Roh
- Microbiome Research Team, LISCure Biosciences Inc., Seongnam 13486, Republic of Korea
| | - Tae Woong Whon
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Se Hee Lee
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
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Mann AE, O'Connell LM, Osagie E, Akhigbe P, Obuekwe O, Omoigberale A, Kelly C, Coker MO, Richards VP. Impact of HIV on the Oral Microbiome of Children Living in Sub-Saharan Africa, Determined by Using an rpoC Gene Fragment Metataxonomic Approach. Microbiol Spectr 2023; 11:e0087123. [PMID: 37428077 PMCID: PMC10434123 DOI: 10.1128/spectrum.00871-23] [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: 02/27/2023] [Accepted: 06/11/2023] [Indexed: 07/11/2023] Open
Abstract
Children living with HIV have a higher prevalence of oral diseases, including caries, but the mechanisms underlying this higher prevalence are not well understood. Here, we test the hypothesis that HIV infection is associated with a more cariogenic oral microbiome, characterized by an increase in bacteria involved in the pathogenesis of caries. We present data generated from supragingival plaques collected from 484 children representing three exposure groups: (i) children living with HIV (HI), (ii) children who were perinatally exposed but uninfected (HEU), and (iii) unexposed and therefore uninfected children (HUU). We found that the microbiome of HI children is distinct from those of HEU and HUU children and that this distinction is more pronounced in diseased teeth than healthy teeth, suggesting that the impact of HIV is more severe as caries progresses. Moreover, we report both an increase in bacterial diversity and a decrease in community similarity in our older HI cohort compared to our younger HI cohort, which may in part be a prolonged effect of HIV and/or its treatment. Finally, while Streptococcus mutans is often a dominant species in late-stage caries, it tended to be found at lower frequency in our HI cohort than in other groups. Our results highlight the taxonomic diversity of the supragingival plaque microbiome and suggest that broad and increasingly individualistic ecological shifts are responsible for the pathogenesis of caries in children living with HIV, coupled with a diverse and possibly severe impact on known cariogenic taxa that potentially exacerbates caries. IMPORTANCE Since its recognition as a global epidemic in the early 1980s, approximately 84.2 million people have been diagnosed with HIV and 40.1 million people have died from AIDS-related illnesses. The development and increased global availability of antiretroviral treatment (ART) regimens have dramatically reduced the mortality rate of HIV and AIDS, yet approximately 1.5 million new infections were reported in 2021, 51% of which are in sub-Saharan Africa. People living with HIV have a higher prevalence of caries and other chronic oral diseases, the mechanisms of which are not well understood. Here, we used a novel genetic approach to characterize the supragingival plaque microbiome of children living with HIV and compared it to the microbiomes of uninfected and perinatally exposed children to better understand the role of oral bacteria in the etiology of tooth decay in the context of HIV exposure and infection.
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Affiliation(s)
- Allison E. Mann
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Lauren M. O'Connell
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Esosa Osagie
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Paul Akhigbe
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Ozoemene Obuekwe
- University of Benin Teaching Hospital, Benin, Edo State, Nigeria
| | | | - Colton Kelly
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- School of Dentistry, University of the Pacific, San Francisco, California, USA
| | - the DOMHaIN Study Team
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- Institute of Human Virology Nigeria, Abuja, Nigeria
- University of Benin Teaching Hospital, Benin, Edo State, Nigeria
- Department of Oral Biology, Rutgers School of Dental Medicine, Rutgers University, Newark, New Jersey, USA
- School of Dentistry, University of the Pacific, San Francisco, California, USA
| | - Modupe O. Coker
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Department of Oral Biology, Rutgers School of Dental Medicine, Rutgers University, Newark, New Jersey, USA
| | - Vincent P. Richards
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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Oren A, Garrity G. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2022; 72. [PMID: 35647792 DOI: 10.1099/ijsem.0.005331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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