1
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Holmberg SM, Feeney RH, Prasoodanan P K V, Puértolas-Balint F, Singh DK, Wongkuna S, Zandbergen L, Hauner H, Brandl B, Nieminen AI, Skurk T, Schroeder BO. The gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids. Nat Commun 2024; 15:3502. [PMID: 38664378 PMCID: PMC11045866 DOI: 10.1038/s41467-024-47594-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Beneficial gut bacteria are indispensable for developing colonic mucus and fully establishing its protective function against intestinal microorganisms. Low-fiber diet consumption alters the gut bacterial configuration and disturbs this microbe-mucus interaction, but the specific bacteria and microbial metabolites responsible for maintaining mucus function remain poorly understood. By using human-to-mouse microbiota transplantation and ex vivo analysis of colonic mucus function, we here show as a proof-of-concept that individuals who increase their daily dietary fiber intake can improve the capacity of their gut microbiota to prevent diet-mediated mucus defects. Mucus growth, a critical feature of intact colonic mucus, correlated with the abundance of the gut commensal Blautia, and supplementation of Blautia coccoides to mice confirmed its mucus-stimulating capacity. Mechanistically, B. coccoides stimulated mucus growth through the production of the short-chain fatty acids propionate and acetate via activation of the short-chain fatty acid receptor Ffar2, which could serve as a new target to restore mucus growth during mucus-associated lifestyle diseases.
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Affiliation(s)
- Sandra M Holmberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Rachel H Feeney
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Vishnu Prasoodanan P K
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Fabiola Puértolas-Balint
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Dhirendra K Singh
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Supapit Wongkuna
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Lotte Zandbergen
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Hans Hauner
- Institute in Nutritional Medicine, TU Munich, Munich, Germany
- TU Munich, School of Medicine, Munich, Germany
| | - Beate Brandl
- ZIEL Institute for Food and Health, TU Munich, Munich, Germany
| | - Anni I Nieminen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Thomas Skurk
- ZIEL Institute for Food and Health, TU Munich, Munich, Germany
| | - Bjoern O Schroeder
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
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2
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Wongkuna S, Ambat A, Ghimire S, Mattiello SP, Maji A, Kumar R, Antony L, Chankhamhaengdecha S, Janvilisri T, Nelson E, Doerner KC, More S, Behr M, Scaria J. Identification of a microbial sub-community from the feral chicken gut that reduces Salmonella colonization and improves gut health in a gnotobiotic chicken model. Microbiol Spectr 2024; 12:e0162123. [PMID: 38315031 PMCID: PMC10913435 DOI: 10.1128/spectrum.01621-23] [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: 04/18/2023] [Accepted: 12/16/2023] [Indexed: 02/07/2024] Open
Abstract
A complex microbial community in the gut may prevent the colonization of enteric pathogens such as Salmonella. Some individual or a combination of species in the gut may confer colonization resistance against Salmonella. To gain a better understanding of the colonization resistance against Salmonella enterica, we isolated a library of 1,300 bacterial strains from feral chicken gut microbiota which represented a total of 51 species. Using a co-culture assay, we screened the representative species from this library and identified 30 species that inhibited Salmonella enterica subspecies enterica serovar Typhimurium in vitro. To improve the Salmonella inhibition capacity, from a pool of fast-growing species, we formulated 66 bacterial blends, each of which composed of 10 species. Bacterial blends were more efficient in inhibiting Salmonella as compared to individual species. The blend that showed maximum inhibition (Mix10) also inhibited other serotypes of Salmonella frequently found in poultry. The in vivo effect of Mix10 was examined in a gnotobiotic and conventional chicken model. The Mix10 consortium significantly reduced Salmonella load at day 2 post-infection in gnotobiotic chicken model and decreased intestinal tissue damage and inflammation in both models. Cell-free supernatant of Mix10 did not show Salmonella inhibition, indicating that Mix10 inhibits Salmonella through either nutritional competition, competitive exclusion, or through reinforcement of host immunity. Out of 10 species, 3 species in Mix10 did not colonize, while 3 species constituted more than 70% of the community. Two of these species were previously uncultured bacteria. Our approach could be used as a high-throughput screening system to identify additional bacterial sub-communities that confer colonization resistance against enteric pathogens and its effect on the host.IMPORTANCESalmonella colonization in chicken and human infections originating from Salmonella-contaminated poultry is a significant problem. Poultry has been identified as the most common food linked to enteric pathogen outbreaks in the United States. Since multi-drug-resistant Salmonella often colonize chicken and cause human infections, methods to control Salmonella colonization in poultry are needed. The method we describe here could form the basis of developing gut microbiota-derived bacterial blends as a microbial ecosystem therapeutic against Salmonella.
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Affiliation(s)
- Supapit Wongkuna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Achuthan Ambat
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Sudeep Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Samara Paula Mattiello
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Abhijit Maji
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Roshan Kumar
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Linto Antony
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Eric Nelson
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Kinchel C. Doerner
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Sunil More
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Melissa Behr
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma, USA
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3
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Naama M, Telpaz S, Awad A, Ben-Simon S, Harshuk-Shabso S, Modilevsky S, Rubin E, Sawaed J, Zelik L, Zigdon M, Asulin N, Turjeman S, Werbner M, Wongkuna S, Feeney R, Schroeder BO, Nyska A, Nuriel-Ohayon M, Bel S. Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress. Cell Host Microbe 2023; 31:433-446.e4. [PMID: 36738733 PMCID: PMC10016318 DOI: 10.1016/j.chom.2023.01.006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023]
Abstract
Colonic goblet cells are specialized epithelial cells that secrete mucus to physically separate the host and its microbiota, thus preventing bacterial invasion and inflammation. How goblet cells control the amount of mucus they secrete is unclear. We found that constitutive activation of autophagy in mice via Beclin 1 enables the production of a thicker and less penetrable mucus layer by reducing endoplasmic reticulum (ER) stress. Accordingly, genetically inhibiting Beclin 1-induced autophagy impairs mucus secretion, while pharmacologically alleviating ER stress results in excessive mucus production. This ER-stress-mediated regulation of mucus secretion is microbiota dependent and requires the Crohn's-disease-risk gene Nod2. Overproduction of mucus alters the gut microbiome, specifically expanding mucus-utilizing bacteria, such as Akkermansia muciniphila, and protects against chemical and microbial-driven intestinal inflammation. Thus, ER stress is a cell-intrinsic switch that limits mucus secretion, whereas autophagy maintains intestinal homeostasis by relieving ER stress.
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Affiliation(s)
- Maria Naama
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Shahar Telpaz
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Aya Awad
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Shira Ben-Simon
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | | | | | - Elad Rubin
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Jasmin Sawaed
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Lilach Zelik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Mor Zigdon
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Nofar Asulin
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michal Werbner
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Supapit Wongkuna
- Department of Molecular Biology, Umeå University, Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Rachel Feeney
- Department of Molecular Biology, Umeå University, Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Bjoern O Schroeder
- Department of Molecular Biology, Umeå University, Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Abraham Nyska
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Shai Bel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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4
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Phanchana M, Harnvoravongchai P, Wongkuna S, Phetruen T, Phothichaisri W, Panturat S, Pipatthana M, Charoensutthivarakul S, Chankhamhaengdecha S, Janvilisri T. Frontiers in antibiotic alternatives for Clostridioides difficile infection. World J Gastroenterol 2021; 27:7210-7232. [PMID: 34876784 PMCID: PMC8611198 DOI: 10.3748/wjg.v27.i42.7210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/12/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile (C. difficile) is a gram-positive, anaerobic spore-forming bacterium and a major cause of antibiotic-associated diarrhea. Humans are naturally resistant to C. difficile infection (CDI) owing to the protection provided by healthy gut microbiota. When the gut microbiota is disturbed, C. difficile can colonize, produce toxins, and manifest clinical symptoms, ranging from asymptomatic diarrhea and colitis to death. Despite the steady-if not rising-prevalence of CDI, it will certainly become more problematic in a world of antibiotic overuse and the post-antibiotic era. C. difficile is naturally resistant to most of the currently used antibiotics as it uses multiple resistance mechanisms. Therefore, current CDI treatment regimens are extremely limited to only a few antibiotics, which include vancomycin, fidaxomicin, and metronidazole. Therefore, one of the main challenges experienced by the scientific community is the development of alternative approaches to control and treat CDI. In this Frontier article, we collectively summarize recent advances in alternative treatment approaches for CDI. Over the past few years, several studies have reported on natural product-derived compounds, drug repurposing, high-throughput library screening, phage therapy, and fecal microbiota transplantation. We also include an update on vaccine development, pre- and pro-biotics for CDI, and toxin antidote approaches. These measures tackle CDI at every stage of disease pathology via multiple mechanisms. We also discuss the gaps and concerns in these developments. The next epidemic of CDI is not a matter of if but a matter of when. Therefore, being well-equipped with a collection of alternative therapeutics is necessary and should be prioritized.
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Affiliation(s)
- Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | | | - Supapit Wongkuna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Wichuda Phothichaisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Supakan Panturat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Methinee Pipatthana
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sitthivut Charoensutthivarakul
- School of Bioinnovation and Bio-based Product Intelligence, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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5
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Ghimire S, Wongkuna S, Sankaranarayanan R, Ryan EP, Bhat GJ, Scaria J. Positive Synergistic Effects of Quercetin and Rice Bran on Human Gut Microbiota Reduces Enterobacteriaceae Family Abundance and Elevates Propionate in a Bioreactor Model. Front Microbiol 2021; 12:751225. [PMID: 34659185 PMCID: PMC8516403 DOI: 10.3389/fmicb.2021.751225] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/01/2021] [Indexed: 12/31/2022] Open
Abstract
Dietary fiber and flavonoids have substantial influence on the human gut microbiota composition that significantly impact health. Recent studies with dietary supplements such as quercetin and rice bran have shown beneficial impacts on the host alongside a positive influence of the gut microbiota. The specific bacterial species impacted by quercetin or rice bran in the diet is not well understood. In this study, we used a minibioreactor array system as a model to determine the effect of quercetin and rice bran individually, as well as in combination, on gut microbiota without the confounding host factors. We found that rice bran exerts higher shift in gut microbiome composition when compared to quercetin. At the species level, Acidaminococcus intestini was the only significantly enriched taxa when quercetin was supplemented, while 15 species were enriched in rice bran supplementation and 13 were enriched when quercetin and rice bran were supplemented in combination. When comparing the short chain fatty acid production, quercetin supplementation increased isobutyrate production while propionate dominated the quercetin and rice bran combined group. Higher levels of propionate were highly correlated to the lower abundance of the potentially pathogenic Enterobacteriaceae family. These findings suggest that the combination of quercetin and rice bran serve to enrich beneficial bacteria and reduce potential opportunistic pathogens. In vivo studies are necessary to determine how this synergy of quercetin and rice bran on microbiota impact host health.
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Affiliation(s)
- Sudeep Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD, United States
| | - Supapit Wongkuna
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD, United States
| | - Ranjini Sankaranarayanan
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, United States
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - G Jayarama Bhat
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, United States
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD, United States
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6
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Wongkuna S, Janvilisri T, Phanchana M, Harnvoravongchai P, Aroonnual A, Aimjongjun S, Malaisri N, Chankhamhaengdecha S. Temporal Variations in Patterns of Clostridioides difficile Strain Diversity and Antibiotic Resistance in Thailand. Antibiotics (Basel) 2021; 10:antibiotics10060714. [PMID: 34199301 PMCID: PMC8231780 DOI: 10.3390/antibiotics10060714] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 01/04/2023] Open
Abstract
Clostridioides difficile has been recognized as a life-threatening pathogen that causes enteric diseases, including antibiotic-associated diarrhea and pseudomembranous colitis. The severity of C. difficile infection (CDI) correlates with toxin production and antibiotic resistance of C. difficile. In Thailand, the data addressing ribotypes, toxigenic, and antimicrobial susceptibility profiles of this pathogen are scarce and some of these data sets are limited. In this study, two groups of C. difficile isolates in Thailand, including 50 isolates collected from 2006 to 2009 (THA group) and 26 isolates collected from 2010 to 2012 (THB group), were compared for toxin genes and ribotyping profiles. The production of toxins A and B were determined on the basis of toxin gene profiles. In addition, minimum inhibitory concentration of eight antibiotics were examined for all 76 C. difficile isolates. The isolates of the THA group were categorized into 27 A−B+CDT− (54%) and 23 A-B-CDT- (46%), while the THB isolates were classified into five toxigenic profiles, including six A+B+CDT+ (23%), two A+B+CDT− (8%), five A−B+CDT+ (19%), seven A−B+CDT− (27%), and six A−B−CDT− (23%). By visually comparing them to the references, only five ribotypes were identified among THA isolates, while 15 ribotypes were identified within THB isolates. Ribotype 017 was the most common in both groups. Interestingly, 18 unknown ribotyping patterns were identified. Among eight tcdA-positive isolates, three isolates showed significantly greater levels of toxin A than the reference strain. The levels of toxin B in 3 of 47 tcdB-positive isolates were significantly higher than that of the reference strain. Based on the antimicrobial susceptibility test, metronidazole showed potent efficiency against most isolates in both groups. However, high MIC values of cefoxitin (MICs 256 μg/mL) and chloramphenicol (MICs ≥ 64 μg/mL) were observed with most of the isolates. The other five antibiotics exhibited diverse MIC values among two groups of isolates. This work provides evidence of temporal changes in both C. difficile strains and patterns of antimicrobial resistance in Thailand.
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Affiliation(s)
- Supapit Wongkuna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.W.); (T.J.)
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.W.); (T.J.)
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Phurt Harnvoravongchai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
| | - Amornrat Aroonnual
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Sathid Aimjongjun
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Natamon Malaisri
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
| | - Surang Chankhamhaengdecha
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
- Correspondence:
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7
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Wongkuna S, Ghimire S, Chankhamhaengdecha S, Janvilisri T, Scaria J. Description of Collinsella avium sp. nov., a new member of the Collinsella genus isolated from the ceacum of feral chicken. New Microbes New Infect 2021; 42:100902. [PMID: 34168883 PMCID: PMC8207210 DOI: 10.1016/j.nmni.2021.100902] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 04/19/2021] [Accepted: 05/09/2021] [Indexed: 11/17/2022] Open
Abstract
An obligately anaerobic, non-motile and Gram-positive rod bacterium, strain SW219 was isolated from ceacum of feral chickens. Based on 16S rRNA sequence analysis, the strain SW219 exhibited 97.88% similarity to Collinsella massiliensis strain GD3 strain, the closest valid species. The genome size of SW219 was 2.58 Mbp with 64.5 mol% of G+C content. The phenotypic and genotypic analysis suggested that the strain SW219 is a new species belonging to the family Coriobacteriaceae within the Actinobacteria phylum, which the name Collinsella avium sp. nov. is proposed. The type strain of Collinsella avium is SW219 (= DSM 109235T and = CCOS 1884T).
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Affiliation(s)
- S. Wongkuna
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
- South Dakota Center for Biologics Research and Commercialization, SD, USA
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - S. Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
- South Dakota Center for Biologics Research and Commercialization, SD, USA
| | | | - T. Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - J. Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
- South Dakota Center for Biologics Research and Commercialization, SD, USA
- Corresponding author: J. Scaria, Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
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8
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Wongkuna S, Ghimire S, Chankhamhaengdecha S, Janvilisri T, Scaria J. Mediterraneibacter catenae SW178 sp. nov., an intestinal bacterium of feral chicken. PeerJ 2021; 9:e11050. [PMID: 33986975 PMCID: PMC8086573 DOI: 10.7717/peerj.11050] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
A Gram-positive, coccobacillus, white raised and circular with an entire edge colony, and obligately anaerobic bacterium, strain SW178 was isolated from the cecum content of feral chickens in Brookings, South Dakota, USA. The most closely related strain based on 16S rRNA gene sequence analysis of strain SW178 was Mediterraneibacter torques ATCC 27756T (Ruminococcus torques ATCC 27756T) with 96.94% similarity. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. The optimal temperature and pH for growth in modified brain heart infusion (BHI-M) medium were 45 °C and pH 7.5, respectively. The sole carbon sources of the strain were dextrin, L-fucose, D-galacturonic, α-D-glucose, L-rhamnose and D-sorbitol. The primary cellular fatty acids were C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal (DMA). Based on the genotypic and phenotypic comparison, we proposed that strain SW178 belong to the genus Mediterraneibacter in the family Lachnospiraceae as a novel species, in which the name Mediterraneibacter catenae is proposed. The type strain is SW178 (= DSM 109242T = CCOS 1886T).
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Affiliation(s)
- Supapit Wongkuna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States
| | - Sudeep Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, United States
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, United States
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9
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Ghimire S, Wongkuna S, Scaria J. Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces. PeerJ 2020; 8:e10071. [PMID: 33083133 PMCID: PMC7543727 DOI: 10.7717/peerj.10071] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 09/09/2020] [Indexed: 01/08/2023] Open
Abstract
A Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502T was isolated from healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the family Erysipelotrichaceae. Within this family, Clostridium innocuum ATCC 14501T, Longicatena caecimuris strain PG-426-CC-2, Eubacterium dolichum DSM 3991T and E. tortuosum DSM 3987T(=ATCC 25548T) were its closest taxa with 95.28%, 94.17%, 93.25%, and 92.75% 16S rRNA sequence identities respectively. The strain SG502T placed itself close to C. innocuum in the 16S rRNA phylogeny. The members of genus Clostridium within family Erysipelotrichaceae was proposed to be reassigned to genus Erysipelatoclostridium to resolve the misclassification of genus Clostridium. Therefore, C. innocuum was also classified into this genus temporarily with the need to reclassify it in the future because of its difference in genomic properties. Similarly, genome sequencing of the strain and comparison with its 16S phylogenetic members and proposed members of the genus Erysipelatoclostridium, SG502T warranted a separate genus even though its 16S rRNA similarity was >95% when comapred to C. innocuum. The strain was 71.8% similar at ANI, 19.8% [17.4–22.2%] at dDDH and 69.65% similar at AAI to its closest neighbor C. innocuum. The genome size was nearly 2,683,792 bp with 32.88 mol% G+C content, which is about half the size of C. innocuum genome and the G+C content revealed 10 mol% difference. Phenotypically, the optimal growth temperature and pH for the strain SG502T were 37 °C and 7.0 respectively. Acetate was the major short-chain fatty acid product of the strain when grown in BHI-M medium. The major cellular fatty acids produced were C18:1ω9c, C18:0and C16:0. Thus, based on the polyphasic analysis, for the type strain SG502T (=DSM 107282T= CCOS 1889T), the name Dakotella fusiforme gen. nov., sp. nov., is proposed.
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Affiliation(s)
- Sudeep Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States of America
| | - Supapit Wongkuna
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States of America
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States of America
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10
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Wongkuna S, Ghimire S, Janvilisri T, Doerner K, Chankhamhaengdecha S, Scaria J. Taxono-genomics description of Olsenella lakotia SW165 T sp. nov., a new anaerobic bacterium isolated from cecum of feral chicken. F1000Res 2020; 9:1103. [PMID: 33024551 PMCID: PMC7520715 DOI: 10.12688/f1000research.25823.1] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
Background: The microbial community residing in the animal gastrointestinal tract play a crucial role in host health. Because of the high complexity of gut microbes, many microbes remain unclassified. Deciphering the role of each bacteria in health and diseases is only possible after its culture, identification, and characterization. During the culturomics study of feral chicken cecal sample, we cultured a possible novel strain SW165
T. Methods: For the possible novel strain SW165
T, phenotypic characterization was performed using colony morphology, Gram staining, growth in different temperature and pH and motility. Biochemical assays included carbon source utilization, enzymatic activity, cellular fatty acids and short chain fatty acid production. 16S rRNA sequencing and whole genome sequencing and comparison was performed for genetic analysis. Results: This strain was isolated from cecal content of feral chickens in Brookings, South Dakota, USA. Phylogenetic analyses based on 16S rRNA gene sequence revealed that the closest valid neighbor was
Olsenella profusa DSM 13989
T (96.33% similarity) within the family
Atopobiaceae. Cells were Gram-strain-positive and obligately anaerobic bacilli in chains. The optimum temperature and pH for the growth of the microorganism were 37-45
oC and pH 6.0-7.5 respectively. This strain produced acetic acid as the primary fermentation product. Major fatty acids were C
12:0, C
14:0, C
14:0 DMA and summed feature 1 (C
13:1 at 12-13 and C
14:0 aldehyde). Strain SW165
T exhibited a genome size of 2.43 Mbp with a G+C content of 67.59 mol%, which is the second highest G+C content among members of the genus
Olsenella. The digital DNA-DNA hybridization and OrthoANI values between SW165
T and DSM 13989
T were only 17.6 ± 5.3 and 74.35%, respectively. Conclusion: Based on the phenotypic, biochemical, and genomic analyses, we propose the new species of the genus
Olsenella, and name it
Olsenella lakotia SW165
T sp. nov., (=DSM 107283 =CCOS 1887) as the type strain.
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Affiliation(s)
- Supapit Wongkuna
- Doctor of Philosophy Program in Biochemistry (International Program), Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, 57007, USA
| | - Sudeep Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, 57007, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, 57007, USA
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Kinchel Doerner
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, 57007, USA
| | | | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, 57007, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, 57007, USA
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Ghimire S, Wongkuna S, Kumar R, Nelson E, Christopher-Hennings J, Scaria J. Genome sequence and description of Blautia brookingsii SG772 sp. nov., a novel bacterial species isolated from human faeces. New Microbes New Infect 2020; 34:100648. [PMID: 32055403 PMCID: PMC7005547 DOI: 10.1016/j.nmni.2019.100648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 06/26/2019] [Revised: 12/02/2019] [Accepted: 12/27/2019] [Indexed: 02/08/2023] Open
Abstract
An anaerobic isolate SG772 belonging to the genus Blautia was isolated from a healthy human faecal sample. When compared using 16s rRNA sequence identity, SG772 showed only 94.46% similarity with its neighbour species Blautia stercoris. As strain SG772 showed both phenotypic and genomic differences from other members of the type species within the genus Blautia, we propose the designation of SG772 as novel species 'Blautia brookingsii SG772T'.
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Affiliation(s)
- S Ghimire
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - S Wongkuna
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - R Kumar
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - E Nelson
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - J Christopher-Hennings
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - J Scaria
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, SD, USA
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Wongkuna S, Ghimire S, Antony L, Chankhamhaengdecha S, Janvilisri T, Scaria J. Sellimonas caecigallum sp. nov., description and genome sequence of a new member of the Sellimonas genus isolated from the cecum of feral chicken. New Microbes New Infect 2019; 33:100626. [PMID: 31993203 PMCID: PMC6974783 DOI: 10.1016/j.nmni.2019.100626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 07/24/2019] [Revised: 10/23/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022] Open
Abstract
An obligately anaerobic, non-motile, Gram-positive coccobacillus strain SW451 was isolated from pooled caecum contents of feral chickens. Based on taxono-genomic, and biochemical analyses, the strain SW451 represents a new species of the genus Sellimonas, for which the name Sellimonas caecigallum sp. nov. is proposed. The type strain of Sellimonas caecigallum is SW451 (=DSM 109473T = CCOS 1879T).
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Affiliation(s)
- S Wongkuna
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD, USA.,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - S Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD, USA
| | - L Antony
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD, USA
| | - S Chankhamhaengdecha
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - T Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - J Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD, USA
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