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Basta DW, Campbell IW, Sullivan EJ, Hotinger JA, Hullahalli K, Waldor MK. Inducible transposon mutagenesis for genome-scale forward genetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595064. [PMID: 38826325 PMCID: PMC11142078 DOI: 10.1101/2024.05.21.595064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Transposon insertion sequencing (Tn-seq) is a powerful method for genome-scale functional genetics in bacteria. However, its effectiveness is often limited by a lack of mutant diversity, caused by either inefficient transposon delivery or stochastic loss of mutants due to population bottlenecks. Here, we introduce "InducTn-seq", which leverages inducible mutagenesis for temporal control of transposition. InducTn-seq generates millions of transposon mutants from a single colony, enabling the sensitive detection of subtle fitness defects and transforming binary classifications of gene essentiality into a quantitative fitness measurement across both essential and non-essential genes. Using a mouse model of infectious colitis, we show that InducTn-seq bypasses a highly restrictive host bottleneck to generate a diverse transposon mutant population from the few cells that initiate infection, revealing the role of oxygen-related metabolic plasticity in pathogenesis. Overall, InducTn-seq overcomes the limitations of traditional Tn-seq, unlocking new possibilities for genome-scale forward genetic screens in bacteria.
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Affiliation(s)
- David W. Basta
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ian W. Campbell
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Emily J. Sullivan
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Julia A Hotinger
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Karthik Hullahalli
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
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Vilela C, Araújo B, Soares-Guedes C, Caridade-Silva R, Martins-Macedo J, Teixeira C, Gomes ED, Prudêncio C, Vieira M, Teixeira FG. From the Gut to the Brain: Is Microbiota a New Paradigm in Parkinson's Disease Treatment? Cells 2024; 13:770. [PMID: 38727306 PMCID: PMC11083070 DOI: 10.3390/cells13090770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Parkinson's disease (PD) is recognized as the second most prevalent primary chronic neurodegenerative disorder of the central nervous system. Clinically, PD is characterized as a movement disorder, exhibiting an incidence and mortality rate that is increasing faster than any other neurological condition. In recent years, there has been a growing interest concerning the role of the gut microbiota in the etiology and pathophysiology of PD. The establishment of a brain-gut microbiota axis is now real, with evidence denoting a bidirectional communication between the brain and the gut microbiota through metabolic, immune, neuronal, and endocrine mechanisms and pathways. Among these, the vagus nerve represents the most direct form of communication between the brain and the gut. Given the potential interactions between bacteria and drugs, it has been observed that the therapies for PD can have an impact on the composition of the microbiota. Therefore, in the scope of the present review, we will discuss the current understanding of gut microbiota on PD and whether this may be a new paradigm for treating this devastating disease.
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Affiliation(s)
- Cristiana Vilela
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Bruna Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (B.A.); (J.M.-M.)
- ICVS/3B’s Associate Lab, PT Government Associated Lab, 4710-057/4805-017 Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Carla Soares-Guedes
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Rita Caridade-Silva
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Joana Martins-Macedo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (B.A.); (J.M.-M.)
- ICVS/3B’s Associate Lab, PT Government Associated Lab, 4710-057/4805-017 Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Catarina Teixeira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Eduardo D. Gomes
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Cristina Prudêncio
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Mónica Vieira
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Fábio G. Teixeira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (B.A.); (J.M.-M.)
- ICVS/3B’s Associate Lab, PT Government Associated Lab, 4710-057/4805-017 Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
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Duodu S, Ayiku ANA, Adelani AA, Daah DA, Amoako EK, Jansen MD, Cudjoe KS. Serotype distribution, virulence and antibiotic resistance of Streptococcus agalactiae isolated from cultured tilapia Oreochromis niloticus in Lake Volta, Ghana. DISEASES OF AQUATIC ORGANISMS 2024; 158:27-36. [PMID: 38661135 DOI: 10.3354/dao03780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Streptococcus agalactiae infection is one of the major factors limiting the expansion of tilapia farming globally. In this study, we investigated the serotype distribution, virulence and antimicrobial resistance of S. agalactiae isolates from tilapia farmed in Lake Volta, Ghana. Isolates from 300 moribund fish were characterised by Gram staining, MALDI-TOF/MS and 16S rRNA sequencing. Serotype identification was based on multiplex polymerase chain reaction (PCR) amplification of the capsular polysaccharide genes. Detection of virulence genes (cfb, fbsA and cspA) and histopathology were used to infer the pathogenicity of the isolates. The susceptibility of isolates to antibiotics was tested using the Kirby-Bauer disk diffusion assay. All 32 isolates identified as S. agalactiae were of serotype Ia. This was notably different from isolates previously collected from the farms in 2017, which belonged to serotype Ib, suggesting a possible serotype replacement. The prevalence of the pathogen was related to the scale of farm operation, with large-scale farms showing higher S. agalactiae positivity. Data from histopathological analysis and PCR amplification of targeted virulence genes confirmed the virulence potential and ability of the isolates to cause systemic infection in tilapia. Except for gentamicin, the majority of the isolates were less resistant to the tested antibiotics. All isolates were fully sensitive to oxytetracycline, erythromycin, florfenicol, enrofloxacin, ampicillin and amoxicillin. This study has improved our understanding of the specific S. agalactiae serotypes circulating in Lake Volta and demonstrates the need for continuous monitoring to guide the use of antimicrobials and vaccines against streptococcal infections in Ghanaian aquaculture systems.
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Affiliation(s)
- Samuel Duodu
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
| | - Angela N A Ayiku
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
| | - Abigail A Adelani
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
| | - Derrick A Daah
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
| | - Enock K Amoako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
| | - Mona D Jansen
- Norwegian Veterinary Institute, Elizabeth Stephansons vei 1, 1433 Ås, Norway
| | - Kofitsyo S Cudjoe
- Norwegian Veterinary Institute, Elizabeth Stephansons vei 1, 1433 Ås, Norway
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Guo Z, Huang L, Lai S. Global knowledge mapping and emerging research trends in the microbiome and asthma: A bibliometric and visualized analysis using VOSviewer and CiteSpace. Heliyon 2024; 10:e24528. [PMID: 38304829 PMCID: PMC10831755 DOI: 10.1016/j.heliyon.2024.e24528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
Background Numerous prior studies have extensively highlighted the significance of the microbiome in association with asthma. While several studies have concentrated on the asthma microbiome in previous research, there is currently a lack of publications that employ bibliometric methods to assess this area. Methods In this study, the Web of Science Core Collection database was utilized as the data source, and the SCI-EXPANDED index was employed to ensure that the retrieved data were comprehensive and accurate. All original research articles and review articles related to the correlation between asthma and the microbiome were systematically searched from the inception of the database until June 20, 2023. These articles were subsequently visualized and analyzed using VOSviewer and CiteSpace software. Results A total of 1366 relevant publications were acquired, indicating a consistent annual increase in global publications in the field. The United States and China emerged as the top two contributors to international publications. Among prolific authors, Susan V. Lynch achieved the highest publication record, with Hans Bisgaard and Jakob Stokholm sharing the second position. The majority of publications concentrated on allergy-related and microbiome areas, with a few comprehensive journals standing out. Journals with 40 or more publications included the Journal of Allergy and Clinical Immunology, Allergy, Frontiers in Immunology, and PLOS One. The top 5 cited journals were the Journal of Allergy and Clinical Immunology, PLOS One, American Journal of Respiratory and Critical Care Medicine, Clinical and Experimental Allergy, and Nature. Upon analyzing keywords, high-frequency terms, such as asthma, gut microbiota, microbiome, children, childhood asthma, allergy, risk, exposure, inflammation, diversity, and chain fatty acids emerged as representative terms in the field. Conclusion This study systematically presented a comprehensive overview of the literature regarding the association between asthma and the microbiome over the last two decades. Through a bibliometric perspective, the findings may assist researchers with a better understanding of the essential information in the field.
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Affiliation(s)
- ZhiFeng Guo
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian Province, China
| | - LingHong Huang
- Department of Endocrinology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian Province, China
| | - SuMei Lai
- Stem Cell Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian Province, China
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Liang Y, Dou S, Zhao G, Shen J, Fu G, Fu L, Li S, Cong B, Dong C. Prediction of BMI traits in the Chinese population based on the gut metagenome. Microb Cell Fact 2023; 22:250. [PMID: 38066544 PMCID: PMC10704812 DOI: 10.1186/s12934-023-02255-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Identifying individual characteristics based on trace evidence left at a crime scene is crucial in forensic identification. Microbial communities found in fecal traces have high individual specificity and could serve as potential markers for forensic characterization. Previous research has established that predicting body type based on the relative abundance of the gut microbiome is relatively accurate. However, the long-term stability and high individual specificity of the gut microbiome are closely linked to changes at the genome level of the microbiome. No studies have been conducted to deduce body shape from genetic traits. Therefore, in this study, the vital role of gut bacterial community characteristics and genetic traits in predicting body mass index (BMI) was investigated using gut metagenomic data from a healthy Chinese population. RESULTS Regarding the gut microbial community, the underweight group displayed increased α-diversity in comparison to the other BMI groups. There were significant differences in the relative abundances of 19 species among these three BMI groups. The BMI prediction model, based on the 31 most significant species, showed a goodness of fit (R2) of 0.56 and a mean absolute error (MAE) of 2.09 kg/m2. The overweight group exhibited significantly higher α-diversity than the other BMI groups at the level of gut microbial genes. Furthermore, there were significant variations observed in the single-nucleotide polymorphism (SNP) density of 732 contigs between these three BMI groups. The BMI prediction model, reliant on the 62 most contributing contigs, exhibited a model R2 of 0.72 and an MAE of 1.56 kg/m2. The model predicting body type from 44 contigs correctly identified the body type of 93.55% of the study participants. CONCLUSION Based on metagenomic data from a healthy Chinese population, we demonstrated the potential of genetic traits of gut bacteria to predict an individual's BMI. The findings of this study suggest the effectiveness of a novel method for determining the body type of suspects in forensic applications using the genetic traits of the gut microbiome and holds great promise for forensic individual identification.
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Affiliation(s)
- Yu Liang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Shujie Dou
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Guangzhong Zhao
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Jie Shen
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Guangping Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Lihong Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Chunnan Dong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China.
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, 050017, Hebei, China.
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Bader AC, Van Zuylen EM, Handsley-Davis M, Alegado RA, Benezra A, Pollet RM, Ehau-Taumaunu H, Weyrich LS, Anderson MZ. A relational framework for microbiome research with Indigenous communities. Nat Microbiol 2023; 8:1768-1776. [PMID: 37770743 DOI: 10.1038/s41564-023-01471-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 07/26/2023] [Indexed: 09/30/2023]
Abstract
Ethical practices in human microbiome research have failed to keep pace with scientific advances in the field. Researchers seeking to 'preserve' microbial species associated with Indigenous groups, but absent from industrialized populations, have largely failed to include Indigenous people in knowledge co-production or benefit, perpetuating a legacy of intellectual and material extraction. We propose a framework centred on relationality among Indigenous peoples, researchers and microbes, to guide ethical microbiome research. Our framework centres accountability to flatten historical power imbalances that favour researcher perspectives and interests to provide space for Indigenous worldviews in pursuit of Indigenous research sovereignty. Ethical inclusion of Indigenous communities in microbiome research can provide health benefits for all populations and reinforce mutually beneficial partnerships between researchers and the public.
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Affiliation(s)
- Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada.
| | - Essie M Van Zuylen
- Department of Microbiology and Immunology, University of Otago, Dunedin North, Dunedin, New Zealand
- School of Product Design, University of Canterbury, Christchurch, New Zealand
| | - Matilda Handsley-Davis
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Wollongong, Wollongong, New South Wales, Australia
| | - Rosanna A Alegado
- Department of Oceanography, University of Hawai'i Mānoa, Honolulu, HI, USA
| | - Amber Benezra
- Department of Science and Technology Studies, Stevens Institute of Technology, Hoboken, NJ, USA
| | | | - Hanareia Ehau-Taumaunu
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA, USA
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Wollongong, Wollongong, New South Wales, Australia
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA.
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Bénard MV, Arretxe I, Wortelboer K, Harmsen HJM, Davids M, de Bruijn CMA, Benninga MA, Hugenholtz F, Herrema H, Ponsioen CY. Anaerobic Feces Processing for Fecal Microbiota Transplantation Improves Viability of Obligate Anaerobes. Microorganisms 2023; 11:2238. [PMID: 37764082 PMCID: PMC10535047 DOI: 10.3390/microorganisms11092238] [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: 07/31/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is under investigation for several indications, including ulcerative colitis (UC). The clinical success of FMT depends partly on the engraftment of viable bacteria. Because the vast majority of human gut microbiota consists of anaerobes, the currently used aerobic processing protocols of donor stool may diminish the bacterial viability of transplanted material. This study assessed the effect of four processing techniques for donor stool (i.e., anaerobic and aerobic, both direct processing and after temporary cool storage) on bacterial viability. By combining anaerobic culturing on customized media for anaerobes with 16S rRNA sequencing, we could successfully culture and identify the majority of the bacteria present in raw fecal suspensions. We show that direct anaerobic processing of donor stool is superior to aerobic processing conditions for preserving the bacterial viability of obligate anaerobes and butyrate-producing bacteria related to the clinical response to FMT in ulcerative colitis patients, including Faecalibacterium, Eubacterium hallii, and Blautia. The effect of oxygen exposure during stool processing decreased when the samples were stored long-term. Our results confirm the importance of sample conditioning to preserve the bacterial viability of oxygen-sensitive gut bacteria. Anaerobic processing of donor stool may lead to increased clinical success of FMT, which should further be investigated in clinical trials.
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Affiliation(s)
- Mèlanie V. Bénard
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.V.B.); (I.A.); (C.M.A.d.B.); (M.A.B.)
- Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Iñaki Arretxe
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.V.B.); (I.A.); (C.M.A.d.B.); (M.A.B.)
| | - Koen Wortelboer
- Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (K.W.); (M.D.); (H.H.)
| | - Hermie J. M. Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands;
| | - Mark Davids
- Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (K.W.); (M.D.); (H.H.)
| | - Clara M. A. de Bruijn
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.V.B.); (I.A.); (C.M.A.d.B.); (M.A.B.)
- Pediatric Gastroenterology, Hepatology and Nutrition, Emma Children’s Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Emma Children’s Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Marc A. Benninga
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.V.B.); (I.A.); (C.M.A.d.B.); (M.A.B.)
- Pediatric Gastroenterology, Hepatology and Nutrition, Emma Children’s Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Emma Children’s Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Floor Hugenholtz
- Center for Experimental and Molecular Medicine, Amsterdam Medical Center, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (K.W.); (M.D.); (H.H.)
| | - Cyriel Y. Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.V.B.); (I.A.); (C.M.A.d.B.); (M.A.B.)
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Kazura W, Michalczyk K, Stygar D. The Relationship between the Source of Dietary Animal Fats and Proteins and the Gut Microbiota Condition and Obesity in Humans. Nutrients 2023; 15:3082. [PMID: 37513500 PMCID: PMC10385089 DOI: 10.3390/nu15143082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The relationship between gut microbiota and obesity is well documented in humans and animal models. Dietary factors can change the intestinal microbiota composition and influence obesity development. However, knowledge of how diet, metabolism, and intestinal microbiota interact and modulate energy metabolism and obesity development is still limited. Epidemiological studies show a link between consuming dietary proteins and fats from specific sources and obesity. Animal studies confirm that proteins and fats of different origins differ in their ability to prevent or induce obesity. Protein sources, such as meat, dairy products, vegetables, pulses, and seafood, vary in their amino acid composition. In addition, the type and level of other factors, such as fatty acids or persistent organic pollutants, vary depending on the source of dietary protein. All these factors can modulate the intestinal microbiota composition and, thus, may influence obesity development. This review summarizes selected evidence of how proteins and fats of different origins affect energy efficiency, obesity development, and intestinal microbiota, linking protein and fat-dependent changes in the intestinal microbiota with obesity.
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Affiliation(s)
- Wojciech Kazura
- Department of Physiology, Faculty of Medical Sciences, Medical University of Silesia, Jordana Street 19, 41-808 Zabrze, Poland
| | - Katarzyna Michalczyk
- Department of Physiology, Faculty of Medical Sciences, Medical University of Silesia, Jordana Street 19, 41-808 Zabrze, Poland
| | - Dominika Stygar
- Department of Physiology, Faculty of Medical Sciences, Medical University of Silesia, Jordana Street 19, 41-808 Zabrze, Poland
- SLU University Animal Hospital, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
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Fernandez-Cantos MV, Garcia-Morena D, Yi Y, Liang L, Gómez-Vázquez E, Kuipers OP. Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products. Front Microbiol 2023; 14:1219272. [PMID: 37469430 PMCID: PMC10352776 DOI: 10.3389/fmicb.2023.1219272] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023] Open
Abstract
The Bacteroidales order, widely distributed among diverse human populations, constitutes a key component of the human microbiota. Members of this Gram-negative order have been shown to modulate the host immune system, play a fundamental role in the gut's microbial food webs, or be involved in pathogenesis. Bacteria inhabiting such a complex environment as the human microbiome are expected to display social behaviors and, hence, possess factors that mediate cooperative and competitive interactions. Different types of molecules can mediate interference competition, including non-ribosomal peptides (NRPs), polyketides, and bacteriocins. The present study investigates the potential of Bacteroidales bacteria to biosynthesize class I bacteriocins, which are ribosomally synthesized and post-translationally modified peptides (RiPPs). For this purpose, 1,136 genome-sequenced strains from this order were mined using BAGEL4. A total of 1,340 areas of interest (AOIs) were detected. The most commonly identified enzymes involved in RiPP biosynthesis were radical S-adenosylmethionine (rSAM), either alone or in combination with other biosynthetic enzymes such as YcaO. A more comprehensive analysis of a subset of 9 biosynthetic gene clusters (BGCs) revealed a consistent association in Bacteroidales BGCs between peptidase-containing ATP-binding transporters (PCATs) and precursor peptides with GG-motifs. This finding suggests a possibly shared mechanism for leader peptide cleavage and transport of mature products. Notably, human metagenomic studies showed a high prevalence and abundance of the RiPP BGCs from Phocaeicola vulgatus and Porphyromonas gulae. The mature product of P. gulae BGC is hypothesized to display γ-thioether linkages and a C-terminal backbone amidine, a potential new combination of post-translational modifications (PTM). All these findings highlight the RiPP biosynthetic potential of Bacteroidales bacteria, as a rich source of novel peptide structures of possible relevance in the human microbiome context.
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Affiliation(s)
- Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Diego Garcia-Morena
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Yunhai Yi
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | | | - Emilio Gómez-Vázquez
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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10
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Songtanin B, Chen JN, Nugent K. Microscopic Colitis: Pathogenesis and Diagnosis. J Clin Med 2023; 12:4442. [PMID: 37445477 DOI: 10.3390/jcm12134442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Microscopic colitis is a type of inflammatory bowel disease and is classified as either collagenous colitis or lymphocytic colitis. The typical presentation is chronic watery diarrhea. The disease occurs more frequently in women aged 60-65 years and is increasing in incidence. The pathophysiology of microscopic colitis remains poorly understood and has not been well-described with possible several pathogeneses. To date, the diagnosis of microscopic colitis depends on histological tissue obtained during colonoscopy. Other non-invasive biomarkers, such as inflammatory markers and fecal biomarkers, have been studied in microscopic colitis, but the results remains inconclusive. The approach to chronic diarrhea is important and being able to differentiate chronic diarrhea in patients with microscopic colitis from other diseases, such as inflammatory bowel disease, functional diarrhea, and malignancy, by using non-invasive biomarkers would facilitate patient management. The management of microscopic colitis should be based on each individual's underlying pathogenesis and involves budesonide, bile acid sequestrants, or immunosuppressive drugs in refractory cases. Cigarette smoking and certain medications, especially proton pump inhibitors, should be eliminated, when possible, after the diagnosis is made.
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Affiliation(s)
- Busara Songtanin
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Jason N Chen
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Kenneth Nugent
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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11
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Fernandes A, Oliveira A, Carvalho AL, Soares R, Barata P. Faecalibacterium prausnitzii in Differentiated Thyroid Cancer Patients Treated with Radioiodine. Nutrients 2023; 15:2680. [PMID: 37375584 DOI: 10.3390/nu15122680] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Faecalibacterium prausnitzii, one of the most important bacteria of the human gut microbiota, produces butyrate (a short-chain fatty acid). Short-chain fatty acids are known to influence thyroid physiology and thyroid cancer's response to treatment. We aimed to analyze the relative abundance of Faecalibacterium prausnitzii on the gut microbiota of differentiated thyroid cancer patients compared to controls and its variation after radioiodine therapy (RAIT). METHODS Fecal samples were collected from 37 patients diagnosed with differentiated thyroid cancer before and after radioiodine therapy and from 10 volunteers. The abundance of F. prausnitzii was determined using shotgun metagenomics. RESULTS Our study found that the relative abundance of F. prausnitzii is significantly reduced in thyroid cancer patients compared to volunteers. We also found that there was a mixed response to RAIT, with an increase in the relative and absolute abundances of this bacterium in most patients. CONCLUSIONS Our study confirms that thyroid cancer patients present a dysbiotic gut microbiota, with a reduction in F. prausnitzii's relative abundance. In our study, radioiodine did not negatively affect F. prausnitzii, quite the opposite, suggesting that this bacterium might play a role in resolving radiation aggression issues.
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Affiliation(s)
- Ana Fernandes
- Department of Nuclear Medicine, Centro Hospitalar Universitário de São João, E.P.E., 4200-319 Porto, Portugal
| | - Ana Oliveira
- Department of Nuclear Medicine, Centro Hospitalar Universitário de São João, E.P.E., 4200-319 Porto, Portugal
| | - Ana Luísa Carvalho
- Department of Nuclear Medicine, Centro Hospitalar Universitário de São João, E.P.E., 4200-319 Porto, Portugal
| | - Raquel Soares
- Department of Biomedicine, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Pedro Barata
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Department of Pharmaceutical Science, Faculdade de Ciências da Saúde da Universidade Fernando Pessoa, 4249-004 Porto, Portugal
- Department of Pathology, Centro Hospitalar Universitário do Porto, 4099-001 Porto, Portugal
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12
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Al-Bayati L, Fasaei BN, Merat S, Bahonar A, Ghoddusi A. Quantitative analysis of the three gut microbiota in UC and non-UC patients using real-time PCR. Microb Pathog 2023:106198. [PMID: 37295481 DOI: 10.1016/j.micpath.2023.106198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND and study aims: Gastrointestinal microbiota are closely related to the pathogenesis of ulcerative colitis (UC). This study aimed at quantification of F. prausnitzii, Provetella, and Peptostreptococcus in UC and non-UC patients using Real-Time PCR and a new set of primers were also validated for this purpose. MATERIALS AND METHODS In this study, the relative abundance of microbial populations between the UC and non-UC subjects were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). DNA extraction from biopsies and polymerase chain reaction (PCR) amplification of bacterial 16S rRNA gene-targeted species-specific primers was performed to detect the anaerobic bacterial species. The qRT-PCR was used to show the relative change in the bacterial populations of F. prausnitzii, Provetella, and Peptostreptococcus in the UC and non-UC subjects. RESULTS Our data for detection of the anaerobic intestinal flora showed Faecalibacterium prausnitzii, Provetella and Peptostreptococcus were the predominant microflora in the controls and showed significant differences (p = 0.002, 0.025 and 0.039, respectively). The qRT-PCR analyses of F. prausnitzii, Provetella and Peptostreptococcus were 8.69-, 9.38- and 5.77-higher, respectively, in the control group than in the UC group. CONCLUSION The results of this study showed decreased abundance of F. prausnitzii, Provetella and Peptostreptococcus in the intestine of UC patients in comparison to non-UC patients. Quantitative RT-PCR, as a progressive and sensitive method, could be useful for evaluation of bacterial populations in patients with inflammatory bowel diseases to attain appropriate therapeutic strategies.
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Affiliation(s)
- Luma Al-Bayati
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran; Department of Microbiology, Faculty of Medicine, University of Wassit, Iraq
| | - Bahar Nayeri Fasaei
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Shahin Merat
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Bahonar
- Department of Food Hygiene, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Arefeh Ghoddusi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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13
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Zhang Y, Wang Y, Tang M, Zhou J, Zhang T. The microbial dark matter and "wanted list" in worldwide wastewater treatment plants. MICROBIOME 2023; 11:59. [PMID: 36973807 PMCID: PMC10045942 DOI: 10.1186/s40168-023-01503-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Wastewater treatment plants (WWTPs) are one of the largest biotechnology applications in the world and are of critical importance to modern urban societies. An accurate evaluation of the microbial dark matter (MDM, microorganisms whose genomes remain uncharacterized) proportions in WWTPs is of great value, while there is no such research yet. This study conducted a global meta-analysis of MDM in WWTPs with 317,542 prokaryotic genomes from the Genome Taxonomy Database and proposed a "wanted list" for priority targets in further investigations of activated sludge. RESULTS Compared with the Earth Microbiome Project data, WWTPs had relatively lower genome-sequenced proportions of prokaryotes than other ecosystems, such as the animal related environments. Analysis showed that the median proportions of the genome-sequenced cells and taxa (100% identity and 100% coverage in 16S rRNA gene region) in WWTPs reached 56.3% and 34.5% for activated sludge, 48.6% and 28.5% for aerobic biofilm, and 48.3% and 28.5% for anaerobic digestion sludge, respectively. This result meant MDM had high proportions in WWTPs. Besides, all of the samples were occupied by a few predominant taxa, and the majority of the sequenced genomes were from pure cultures. The global-scale "wanted list" for activated sludge contained four phyla that have few representatives and 71 operational taxonomic units with the majority of them having no genome or isolate yet. Finally, several genome mining methods were verified to successfully recover genomes from activated sludge such as hybrid assembly of the second- and third-generation sequencing. CONCLUSIONS This work elucidated the proportion of MDM in WWTPs, defined the "wanted list" of activated sludge for future investigations, and certified potential genome recovery methods. The proposed methodology of this study can be applied to other ecosystems and improve understanding of ecosystem structure across diverse habitats. Video Abstract.
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Affiliation(s)
- Yulin Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Mingxi Tang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Shenzhen Bay Laboratory, Shenzhen, China.
- Peking University Shenzhen Graduate School, Shenzhen, China.
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China.
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14
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Zhang H, Chong H, Yu Q, Zha Y, Cheng M, Ning K. Tracing human life trajectory using gut microbial communities by context-aware deep learning. Brief Bioinform 2023; 24:6984796. [PMID: 36631408 DOI: 10.1093/bib/bbac629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/15/2022] [Accepted: 12/25/2022] [Indexed: 01/13/2023] Open
Abstract
The gut microbial communities are highly plastic throughout life, and the human gut microbial communities show spatial-temporal dynamic patterns at different life stages. However, the underlying association between gut microbial communities and time-related factors remains unclear. The lack of context-awareness, insufficient data, and the existence of batch effect are the three major issues, making the life trajection of the host based on gut microbial communities problematic. Here, we used a novel computational approach (microDELTA, microbial-based deep life trajectory) to track longitudinal human gut microbial communities' alterations, which employs transfer learning for context-aware mining of gut microbial community dynamics at different life stages. Using an infant cohort, we demonstrated that microDELTA outperformed Neural Network for accurately predicting the age of infant with different delivery mode, especially for newborn infants of vaginal delivery with the area under the receiver operating characteristic curve of microDELTA and Neural Network at 0.811 and 0.436, respectively. In this context, we have discovered the influence of delivery mode on infant gut microbial communities. Along the human lifespan, we also applied microDELTA to a Chinese traveler cohort, a Hadza hunter-gatherer cohort and an elderly cohort. Results revealed the association between long-term dietary shifts during travel and adult gut microbial communities, the seasonal cycling of gut microbial communities for the Hadza hunter-gatherers, and the distinctive microbial pattern of elderly gut microbial communities. In summary, microDELTA can largely solve the issues in tracing the life trajectory of the human microbial communities and generate accurate and flexible models for a broad spectrum of microbial-based longitudinal researches.
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Affiliation(s)
- Haohong Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Hui Chong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qingyang Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yuguo Zha
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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15
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Ghaddar B, Biswas A, Harris C, Omary MB, Carpizo DR, Blaser MJ, De S. Tumor microbiome links cellular programs and immunity in pancreatic cancer. Cancer Cell 2022; 40:1240-1253.e5. [PMID: 36220074 PMCID: PMC9556978 DOI: 10.1016/j.ccell.2022.09.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 07/01/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022]
Abstract
Microorganisms are detected in multiple cancer types, including in putatively sterile organs, but the contexts in which they influence oncogenesis or anti-tumor responses in humans remain unclear. We recently developed single-cell analysis of host-microbiome interactions (SAHMI), a computational pipeline to recover and denoise microbial signals from single-cell sequencing of host tissues. Here we use SAHMI to interrogate tumor-microbiome interactions in two human pancreatic cancer cohorts. We identify somatic-cell-associated bacteria in a subset of tumors and their near absence in nonmalignant tissues. These bacteria predominantly pair with tumor cells, and their presence is associated with cell-type-specific gene expression and pathway activities, including cell motility and immune signaling. Modeling results indicate that tumor-infiltrating lymphocytes closely resemble T cells from infected tissue. Finally, using multiple independent datasets, a signature of cell-associated bacteria predicts clinical prognosis. Tumor-microbiome crosstalk may modulate tumorigenesis in pancreatic cancer with implications for clinical management.
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Affiliation(s)
- Bassel Ghaddar
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Albany St., New Brunswick, NJ 08901, USA
| | - Antara Biswas
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Albany St., New Brunswick, NJ 08901, USA
| | - Chris Harris
- Department of Surgery, University of Rochester Medical Center, 601 Elmwood Avenue, Box SURG, Rochester, NY 14642, USA
| | - M Bishr Omary
- Center for Advanced Biotechnology and Medicine, Rutgers University, 679 Hoes Lane West, Piscataway, NJ 08854, USA
| | - Darren R Carpizo
- Department of Surgery, University of Rochester Medical Center, 601 Elmwood Avenue, Box SURG, Rochester, NY 14642, USA
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, 679 Hoes Lane West, Piscataway, NJ 08854, USA.
| | - Subhajyoti De
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Albany St., New Brunswick, NJ 08901, USA.
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16
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Changes in the quality and microbial compositions of ground beef packaged on food absorbent pads incorporated with levulinic acid and sodium dodecyl sulfate. Int J Food Microbiol 2022; 376:109771. [DOI: 10.1016/j.ijfoodmicro.2022.109771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/07/2022] [Accepted: 05/30/2022] [Indexed: 11/18/2022]
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17
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Kumar T, Dutta RR, Velagala VR, Ghosh B, Mudey A. Analyzing the Complicated Connection Between Intestinal Microbiota and Cardiovascular Diseases. Cureus 2022; 14:e28165. [PMID: 36148181 PMCID: PMC9482761 DOI: 10.7759/cureus.28165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/19/2022] [Indexed: 12/12/2022] Open
Abstract
Relentless human curiosity to understand the basis of every aspect of medical science has led humanity to unlock the deepest secrets about the physiology of human existence and, in the process, has reached milestones that a century ago could only be imagined. Recent ground-breaking breakthroughs have helped scientists and physicians all over the world to update the scientific basis of diseases and hence further improve treatment outcomes. According to recent studies, scientists have found a link between intestinal flora and the pathogenesis of diseases, including cardiovascular diseases. Any change in the typical habitat of gut microbiota has been shown to result in the culmination of various metabolic and cardiac diseases. Therefore, gut microbiota can be credited for influencing the course of the development of a disease. Any change in the composition and function of bacterial species living in the gut can result in both beneficial and harmful effects on the body. Gut microbiota achieves this role by numerous mechanisms. Generations of various metabolites like TMAO (trimethylamine N-oxide), increased receptibility of various bacterial antigens, and disruption of the enzyme action in various metabolic pathways like the bile acids pathway may result in the development of metabolic as well as cardiovascular diseases. Even if they may not be the only etiological factor in the pathogenesis of a disease, they may very well serve as a contributing factor in worsening the outcome of the condition. Studies have shown that they actively play a role in the progression of cardiovascular diseases like atherosclerotic plaque formation and rising blood pressure. The focus of this review article is to establish a relation between various cardiovascular diseases and gut microbiota. This could prove beneficial for clinicians, health care providers, and scientists to develop novel therapeutic algorithms while treating cardiac patients.
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18
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Baxa DV, Nehring RB. Effect of substrate on the proliferation of Myxobolus cerebralis in the mitochondrial lineages of the Tubifex tubifex host. Parasitol Res 2022; 121:2503-2516. [PMID: 35895112 PMCID: PMC9378325 DOI: 10.1007/s00436-022-07587-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 06/24/2022] [Indexed: 10/31/2022]
Abstract
The study goal was to examine the effects of sand and mud on the propagation of Myxobolus cerebralis, the whirling disease agent, in four mitochondrial 16S ribosomal DNA lineages (I, III, V, VI) of its oligochaete host, Tubifex tubifex (Tt). In all the lineage groups held continuously in either substrate (non-shifted) or transferred from sand to mud (shifted), substrate influenced parasite proliferation only in lineage III. Sporogenesis and release of triactinomyxon spores (TAMs) were more prevalent in lineage III Tt in mud compared to sand. Low-infection prevalence and lack of parasite development in lineage I is associated with the greater number of resistant worms and were not affected by substrate type. Substrate did not impact Tt from lineages V and VI that failed to develop any parasite stages in either substrate even after shifting from sand to mud. The relationship between the microbial community in the substrate and parasite proliferation in lineage III was described but not analyzed due to small sample size. Substrate-associated bacteria were hypothesized as essential dietary source for the oligochaete host feeding selectively on fine (mud)-microflora. Progeny was produced by all lineage groups shifted to mud with disparate survival profiles in lineage V and VI and high mortalities in lineage III. Our study demonstrates that substrate type can alter parasite proliferation in lineage III. Conversely, parasite development and infectivity were not altered in lineage V and VI that are refractory to the parasite nor among the more resistant phenotypes (I), regardless of substrate type.
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Affiliation(s)
- Dolores V Baxa
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA. .,Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
| | - R Barry Nehring
- Colorado Division of Parks and Wildlife, 2300 South Townsend Avenue, Montrose, CO, 81401, USA
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19
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The gut microbiome, immune check point inhibition and immune-related adverse events in non-small cell lung cancer. Cancer Metastasis Rev 2022; 41:347-366. [PMID: 35876944 PMCID: PMC9388426 DOI: 10.1007/s10555-022-10039-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/07/2022] [Indexed: 11/04/2022]
Abstract
Systemic treatment options for patients with lung cancer have expanded in recent years, with a number of immunotherapeutic strategies now in our treatment armamentarium. Toxicity of and resistance to treatment hold a major stake in lung cancer morbidity and mortality. Herein, we summarise the background, current evidence and potential mechanisms underlying the role of the commensal gut microbiota in immunotherapy outcomes such as response and toxicity in patients with non-small cell lung cancer (NSCLC).
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20
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Tonneau M, Nolin-Lapalme A, Kazandjian S, Auclin E, Panasci J, Benlaifaoui M, Ponce M, Al-Saleh A, Belkaid W, Naimi S, Mihalcioiu C, Watson I, Bouin M, Miller W, Hudson M, Wong MK, Pezo RC, Turcotte S, Bélanger K, Jamal R, Oster P, Velin D, Richard C, Messaoudene M, Elkrief A, Routy B. Helicobacter pylori serology is associated with worse overall survival in patients with melanoma treated with immune checkpoint inhibitors. Oncoimmunology 2022; 11:2096535. [PMID: 35832043 PMCID: PMC9272833 DOI: 10.1080/2162402x.2022.2096535] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The microbiome is now regarded as one of the hallmarks of cancer and several strategies to modify the gut microbiota to improve immune checkpoint inhibitor (ICI) activity are being evaluated in clinical trials. Preliminary data regarding the upper gastro-intestinal microbiota indicated that Helicobacter pylori seropositivity was associated with a negative prognosis in patients amenable to ICI. In 97 patients with advanced melanoma treated with ICI, we assessed the impact of H. pylori on outcomes and microbiome composition. We performed H. pylori serology and profiled the fecal microbiome with metagenomics sequencing. Among the 97 patients, 22% were H. pylori positive (Pos). H. pylori Pos patients had a significantly shorter overall survival (p = .02) compared to H. pylori negative (Neg) patients. In addition, objective response rate and progression-free survival were decreased in H. pylori Pos patients. Metagenomics sequencing did not reveal any difference in diversity indexes between the H. pylori groups. At the taxa level, Eubacterium ventriosum, Mediterraneibacter (Ruminococcus) torques, and Dorea formicigenerans were increased in the H. pylori Pos group, while Alistipes finegoldii, Hungatella hathewayi and Blautia producta were over-represented in the H. pylori Neg group. In a second independent cohort of patients with NSCLC, diversity indexes were similar in both groups and Bacteroides xylanisolvens was increased in H. pylori Neg patients. Our results demonstrated that the negative impact of H. pylori on outcomes seem to be independent from the fecal microbiome composition. These findings warrant further validation and development of therapeutic strategies to eradicate H. pylori in immuno-oncology arena.
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Affiliation(s)
- Marion Tonneau
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Université de Médecine, Lille, France
| | - Alexis Nolin-Lapalme
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | | | - Edouard Auclin
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Justin Panasci
- Department of Oncology, McGill University Health Center, QC, Canada
| | - Myriam Benlaifaoui
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Mayra Ponce
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Afnan Al-Saleh
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Wiam Belkaid
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Sabrine Naimi
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | | | - Ian Watson
- Rosalind and Morris Goodman Cancer Institute, Montréal, QC, Canada
| | - Mickael Bouin
- Department of Gastroenterology, Centre Hospitalier de l’Université de Montréal, Montreal, QC, Canada
| | - Wilson Miller
- Lady Davis Institute of the Jewish General Hospital, Montreal, QC, Canada
| | - Marie Hudson
- Lady Davis Institute of the Jewish General Hospital, Montreal, QC, Canada
| | - Matthew K. Wong
- Division of Medical Oncology, Sunnybrook Health Sciences Center, Odette Cancer Center, QC, Canada
| | - Rossanna C. Pezo
- Division of Medical Oncology, Sunnybrook Health Sciences Center, Odette Cancer Center, QC, Canada
| | - Simon Turcotte
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Department of Surgery, Centre Hospitalier de l’Université de Montréal, QC, Canada
| | - Karl Bélanger
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Division of Hemato-Oncology, Centre Hospitalier de l’Université de Montréal (CHUM)Montreal, QC, Canada
| | - Rahima Jamal
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Division of Hemato-Oncology, Centre Hospitalier de l’Université de Montréal (CHUM)Montreal, QC, Canada
| | - Paul Oster
- Service of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Dominique Velin
- Service of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Corentin Richard
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Meriem Messaoudene
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Arielle Elkrief
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Bertrand Routy
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Division of Hemato-Oncology, Centre Hospitalier de l’Université de Montréal (CHUM)Montreal, QC, Canada
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21
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Kubovčiak J, Schmiedová L, Albrecht T, Těšický M, Tomášek O, Kauzálová T, Kreisinger J. Within-community variation of interspecific divergence patterns in passerine gut microbiota. Ecol Evol 2022; 12:e9071. [PMID: 35813907 PMCID: PMC9251858 DOI: 10.1002/ece3.9071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 12/11/2022] Open
Abstract
Gut microbiota (GM) often exhibit variation between different host species and co-divergence with hosts' phylogeny. Identifying these patterns is a key for understanding the mechanisms that shaped symbiosis between GM and its hosts. Therefore, both GM-host species specificity and GM-host co-divergence have been investigated by numerous studies. However, most of them neglected a possibility that different groups of bacteria within GM can vary in the tightness of their association with the host. Consequently, unlike most of these studies, we aimed to directly address how the strength of GM-host species specificity and GM-host co-divergence vary across different GM clades. We decomposed GM communities of 52 passerine species (394 individuals), characterized by 16S rRNA amplicon sequence variant (ASV) profiles, into monophyletic Binned Taxonomic units (BTUs). Subsequently, we analyzed strength of host species specificity and correlation with host phylogeny separately for resulting BTUs. We found that most BTUs exhibited significant host-species specificity in their composition. Notably, BTUs exhibiting high host-species specificity comprised bacterial taxa known to impact host's physiology and immune system. However, BTUs rarely displayed significant co-divergence with host phylogeny, suggesting that passerine GM evolution is not shaped primarily through a shared evolutionary history between the host and its gut microbes.
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Affiliation(s)
- Jan Kubovčiak
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Oldřich Tomášek
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Tereza Kauzálová
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
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22
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D'Angelo G. Microbiota and Hematological Diseases. Int J Hematol Oncol Stem Cell Res 2022; 16:164-173. [PMID: 36694706 PMCID: PMC9831866 DOI: 10.18502/ijhoscr.v16i3.10139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/28/2021] [Indexed: 01/27/2023] Open
Abstract
The microbiota is directly involved in the host metabolic process, as well as in immune response modulation and recruitment of different cells typology in the inflammatory site. Human microbiota modification (dysbiosis) is a condition which could be correlated with various pathologies. The short-chain fatty acids produced by the metabolic process have an important role as immune mediators. In hematology field, dysbiosis can represent a predisposing condition for triggering and/or conditioning both non-neoplastic (iron deficiency anemia, thrombosis, thrombocytosis or thrombocytopenia) and neoplastic disorders (lymphomas, leukemias, myeloma). Dysbiosis may also interfere on therapy efficacy (iron supplementation, chemotherapy, immunotherapy, and hematopoietic stem cell transplantation), impacting on patient's outcome.
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Affiliation(s)
- Guido D'Angelo
- Laboratory of Clinical-Chemistry, Hematology and Microbiology, (ASST-Valle Olona) Gallarate Hospital, Gallarate, Varese, Italy
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23
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Ye L, Dong N, Xiong W, Li J, Li R, Heng H, Chan EWC, Chen S. High-Resolution Metagenomics of Human Gut Microbiota Generated by Nanopore and Illumina Hybrid Metagenome Assembly. Front Microbiol 2022; 13:801587. [PMID: 35633679 PMCID: PMC9134245 DOI: 10.3389/fmicb.2022.801587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/11/2022] [Indexed: 11/15/2022] Open
Abstract
Metagenome assembly is a core yet methodologically challenging step for taxonomic classification and functional annotation of a microbiome. This study aims to generate the high-resolution human gut metagenome using both Illumina and Nanopore platforms. Assembly was achieved using four assemblers, including Flye (Nanopore), metaSPAdes (Illumina), hybridSPAdes (Illumina and Nanopore), and OPERA-MS (Illumina and Nanopore). Hybrid metagenome assembly was shown to generate contigs with almost same sizes comparable to those produced using Illumina reads alone, but was more contiguous, informative, and longer compared with those assembled with Illumina reads only. In addition, hybrid metagenome assembly enables us to obtain complete plasmid sequences and much more AMR gene-encoding contigs than the Illumina method. Most importantly, using our workflow, 58 novel high-quality metagenome bins were obtained from four assembly algorithms, particularly hybrid assembly (47/58), although metaSPAdes could provide 11 high-quality bins independently. Among them, 29 bins were currently uncultured bacterial metagenome-assembled genomes. These findings were highly consistent and supported by mock community data tested. In the analysis of biosynthetic gene clusters (BGCs), the number of BGCs in the contigs from hybridSPAdes (241) is higher than that of contigs from metaSPAdes (233). In conclusion, hybrid metagenome assembly could significantly enhance the efficiency of contig assembly, taxonomic binning, and genome construction compared with procedures using Illumina short-read data alone, indicating that nanopore long reads are highly useful in metagenomic applications. This technique could be used to create high-resolution references for future human metagenome studies.
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Affiliation(s)
- Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ning Dong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Wenguang Xiong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Heng Heng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Edward Wai Chi Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- *Correspondence: Sheng Chen,
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24
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The relationship between the gut microbiota, benign prostatic hyperplasia, and erectile dysfunction. Int J Impot Res 2022:10.1038/s41443-022-00569-1. [PMID: 35418604 DOI: 10.1038/s41443-022-00569-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/12/2022]
Abstract
Microbiota is defined as the group of commensal microorganisms that inhabit a specific human body site. The composition of each individual's gastrointestinal microbiota is influenced by several factors such as age, diet, lifestyle, and drug intake, but an increasing number of studies have shown that the differences between a healthy microbiota and a dysbiotic one can be related to different diseases such as benign prostatic hyperplasia (BPH) and erectile dysfunction (ED). The aim of this review is to give an overview of the role of the gut microbiota on BPH and ED. Gut microbiota modifications can influence prostate health indirectly by the activation of the immune system and the production of proinflammatory cytokines such as IL-17, IL-23, TNF-alpha, and IFN-gamma, which are able to promote an inflammatory state. Gut dysbiosis may lead to the onset of ED by the alteration of hormone levels and metabolic profiles, the modulation of stress/anxiety-mediated sexual dysfunction, the development of altered metabolic conditions such as obesity and diabetes mellitus, and the development of hypertension. In conclusion, much evidence suggests that the intestinal microbiota has an influence on various pathologies including BPH and ED.
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25
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Mavima L, Beukes CW, Palmer M, De Meyer SE, James EK, Maluk M, Muasya MA, Avontuur JR, Yin Chan W, Venter SN, Steenkamp ET. Delineation of Paraburkholderia tuberum sensu stricto and description of Paraburkholderia podalyriae sp. nov. nodulating the South African legume Podalyria calyptrata. Syst Appl Microbiol 2022; 45:126316. [DOI: 10.1016/j.syapm.2022.126316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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26
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Bellali S, Lagier JC, Million M, Anani H, Haddad G, Francis R, Kuete Yimagou E, Khelaifia S, Levasseur A, Raoult D, Bou Khalil J. Running after ghosts: are dead bacteria the dark matter of the human gut microbiota? Gut Microbes 2022; 13:1-12. [PMID: 33757378 PMCID: PMC7993147 DOI: 10.1080/19490976.2021.1897208] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The human gut microbiota has been explored by a wide range of culture-dependent and culture-independent methods, revealing that many microbes remain uncharacterized and uncultured. In this work, we aimed to confirm the hypothesis that some of the species present in the human gut microbiota remain uncultured not because of culture limitations, but because all members of such species are dead before reaching the end of the gastro-intestinal tract.We evaluate this phenomenon by studying the microbial viability and culturability of the human gut microbiota from the fresh fecal materials of eight healthy adults. For the first time, we applied fluorescence-activated cell sorting (FACS) combined with 16S metagenomics analysis and microbial culturomics.We identified a total of 1,020 bacterial OTUs and 495 bacterial isolates through metagenomics and culturomics, respectively. Among the FACS metagenomics results, only 735 bacterial OTUs were alive, comprising on average 42% of known species and 87% of relative abundance per individual. The remaining uncultured bacteria were rare, dead, or injured.Our strategy allowed us to shed light on the dark matter of the human gut microbiota and revealed that both metagenomics and culturomics approaches are needed for greater insight into the diversity and richness of bacteria in the human gut microbiota. Further work on culture is needed to enhance the repertoire of cultured gut bacteria by targeting low abundance bacteria and optimizing anaerobic sample conditioning and processing to preserve the viability of bacteria.
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Affiliation(s)
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France,Aix-Marseille Université, IRD, MEPHI, Marseille, France, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, Marseille, France,Aix-Marseille Université, IRD, MEPHI, Marseille, France, Marseille, France
| | | | - Gabriel Haddad
- IHU Méditerranée Infection, Marseille, France,Aix-Marseille Université, IRD, MEPHI, Marseille, France, Marseille, France
| | - Rania Francis
- IHU Méditerranée Infection, Marseille, France,Aix-Marseille Université, IRD, MEPHI, Marseille, France, Marseille, France
| | | | | | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France,Aix-Marseille Université, IRD, MEPHI, Marseille, France, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France,CONTACT Didier Raoult
| | - Jacques Bou Khalil
- IHU Méditerranée Infection, Marseille, France,Jacques Bou Khalil IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
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27
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Zhu C, Wang X, Li J, Jiang R, Chen H, Chen T, Yang Y. Determine independent gut microbiota-diseases association by eliminating the effects of human lifestyle factors. BMC Microbiol 2022; 22:4. [PMID: 34979898 PMCID: PMC8722223 DOI: 10.1186/s12866-021-02414-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/06/2021] [Indexed: 02/08/2023] Open
Abstract
Lifestyle and physiological variables on human disease risk have been revealed to be mediated by gut microbiota. Low concordance between case-control studies for detecting disease-associated microbe existed due to limited sample size and population-wide bias in lifestyle and physiological variables. To infer gut microbiota-disease associations accurately, we propose to build machine learning models by including both human variables and gut microbiota. When the model's performance with both gut microbiota and human variables is better than the model with just human variables, the independent gut microbiota -disease associations will be confirmed. By building models on the American Gut Project dataset, we found that gut microbiota showed distinct association strengths with different diseases. Adding gut microbiota into human variables enhanced the classification performance of IBD significantly; independent associations between occurrence information of gut microbiota and irritable bowel syndrome, C. difficile infection, and unhealthy status were found; adding gut microbiota showed no improvement on models' performance for diabetes, small intestinal bacterial overgrowth, lactose intolerance, cardiovascular disease. Our results suggested that although gut microbiota was reported to be associated with many diseases, a considerable proportion of these associations may be very weak. We proposed a list of microbes as biomarkers to classify IBD and unhealthy status. Further functional investigations of these microbes will improve understanding of the molecular mechanism of human diseases.
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Affiliation(s)
- Congmin Zhu
- School of Biomedical Engineering, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Xin Wang
- Department of Ultrasound, Peking Union Medical College Hospital, Beijing, China
| | - Jianchu Li
- Department of Ultrasound, Peking Union Medical College Hospital, Beijing, China
| | - Rui Jiang
- Bioinformatics Division and Center for Synthetic & Systems Biology, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing, China
| | - Hui Chen
- School of Biomedical Engineering, Capital Medical University, Beijing, China
| | - Ting Chen
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing, China.
| | - Yuqing Yang
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, China.
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28
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A randomized double-blind placebo controlled pilot study of probiotics in adolescents with severe obesity. J Diabetes Metab Disord 2021; 20:1289-1300. [PMID: 34900780 DOI: 10.1007/s40200-021-00855-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Purpose The purpose of the study is to assess the effect of probiotic supplementation on gut microbiota and insulin resistance in adolescents with severe obesity. Methods Through a randomized, double blind, placebo-controlled, 12-week pilot clinical trial, 15 adolescents with severe obesity received either an oral probiotic 'Visbiome®' (n = 8) or placebo (n = 7). Anthropometry, fasting glucose, insulin, hs-CRP and stool for microbiome and calprotectin were collected at baseline (week 0) and 12 weeks after intervention. Results Among completers (n = 4 in each of the two groups), mean change in fasting glucose was significantly lower in the probiotic group (0 ± 4 mg/dL) as compared to the placebo group (6.3 ± 1.7 mg/dL) (p = 0.028). Gut microbial Firmicutes to Bacteroidetes (F/B) ratio had a greater decline from week 0 to week 12 in the probiotic group (mean 17.7 ± 25.1 to 2.39 ± 2.0, respectively) but was not statistically significant (p = 0.06) as compared to in the placebo group (mean 12.8 ± 18.2 to 6.9 ± 5.61, respectively) (p = 0.89). Weight and BMI (mean ± SD) trended to remain stable in the treatment group (-1.07 ± 6.1 kg and -0.3 ± 2.2 kg/m2 respectively) as compared to the placebo group (3.9 ± 5.1 kg, 1.0 ± 1.6 kg/m2) but was not significant (p = 0.12 for weight and 0.38 for BMI). No significant change in the fasting insulin, HOMA-IR, or serum and stool inflammatory markers were noted between the two groups (p > 0.05). One participant in the treatment arm reported adverse effects of gastrointestinal intolerance. Conclusion Probiotic therapy with Visbiome® may improve the fasting glucose and possibly decrease the gut microbial F/B ratio as compared to placebo in adolescents with severe obesity. Future larger studies are required to confirm these findings.U.S. Clinical Trial Registry number: NCT03109587. Supplementary Information The online version contains supplementary material available at 10.1007/s40200-021-00855-7.
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29
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Sandlund N, Johansen R, Fiksdal IU, Einen ACB, Modahl I, Gjerset B, Bergh Ø. Susceptibility and Pathology in Juvenile Atlantic Cod Gadus morhua to a Marine Viral Haemorrhagic Septicaemia Virus Isolated from Diseased Rainbow Trout Oncorhynchus mykiss. Animals (Basel) 2021; 11:ani11123523. [PMID: 34944298 PMCID: PMC8698066 DOI: 10.3390/ani11123523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/26/2021] [Accepted: 12/08/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary VHSV (viral haemorrhagic septicaemia virus) is a globally important group of viruses, infecting a wide range of fish species, in both marine and freshwater. New initiatives are now being taken to re-establish Atlantic cod as an aquaculture species. Any susceptibility to diseases would be relevant for this industry. Atlantic cod was experimentally infected with a strain of VHSV originating from a disease outbreak of farmed rainbow trout in Norway. The fish infected by injection did develop the disease, as verified by investigations of tissue samples. However, no transmission of the virus to cohabitant fish (i.e., individuals sharing the tank with infected fish) was found. This indicates that, despite the fact that the virus is capable of causing disease in Atlantic cod, the degree and ability to infect the fish is limited. Abstract The first known outbreak caused by a viral haemorrhagic septicaemia virus (VHSV) strain of genotype III in rainbow trout occurred in 2007 at a marine farm in Storfjorden, Norway. The source of the virus is unknown, and cod and other marine fish around the farms are suspected as a possible reservoir. The main objective of this study was to test the susceptibility of juvenile Atlantic cod to the VHSV isolate from Storfjorden. As the pathology of VHS in cod is sparsely described, an additional aim of the study was to give a histopathological description of the disease. Two separate challenge experiments were carried out, using both intra peritoneal (ip) injection and cohabitation as challenge methods. Mortality in the ip injection experiment leveled at approximately 50% three weeks post challenge. Both immunohistochemical and rRT-PCR analysis of organs sampled from diseased and surviving fish confirmed VHSV infection. No VHSV was detected in the cohabitants. The results indicate that Atlantic cod has a low natural susceptibility to this VHSV genotype III strain. One of the most extensive pathological changes was degeneration of cardiac myocytes. Immunohistochemistry confirmed that the lesions were related to VHSV. In some fish, the hematopoietic tissue of spleen and kidney showed degeneration and immunostaining, classical signs of VHS, as described in rainbow trout. Positive immunostaining of the capillaries of the gills, suggests this organ as a useful alternative when screening for VHSV.
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Affiliation(s)
- Nina Sandlund
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817 Bergen, Norway; (N.S.); (I.U.F.); (A.C.B.E.)
| | - Renate Johansen
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway; (R.J.); (I.M.); (B.G.)
| | - Ingrid U. Fiksdal
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817 Bergen, Norway; (N.S.); (I.U.F.); (A.C.B.E.)
| | - Ann Cathrine B. Einen
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817 Bergen, Norway; (N.S.); (I.U.F.); (A.C.B.E.)
| | - Ingebjørg Modahl
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway; (R.J.); (I.M.); (B.G.)
| | - Britt Gjerset
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway; (R.J.); (I.M.); (B.G.)
| | - Øivind Bergh
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817 Bergen, Norway; (N.S.); (I.U.F.); (A.C.B.E.)
- Correspondence:
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30
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D’Anna SE, Maniscalco M, Cappello F, Carone M, Motta A, Balbi B, Ricciardolo FLM, Caramori G, Di Stefano A. Bacterial and viral infections and related inflammatory responses in chronic obstructive pulmonary disease. Ann Med 2021; 53:135-150. [PMID: 32997525 PMCID: PMC7877965 DOI: 10.1080/07853890.2020.1831050] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/25/2020] [Indexed: 12/24/2022] Open
Abstract
In chronic obstructive pulmonary disease (COPD) patients, bacterial and viral infections play a relevant role in worsening lung function and, therefore, favour disease progression. The inflammatory response to lung infections may become a specific indication of the bacterial and viral infections. We here review data on the bacterial-viral infections and related airways and lung parenchyma inflammation in stable and exacerbated COPD, focussing our attention on the prevalent molecular pathways in these different clinical conditions. The roles of macrophages, autophagy and NETosis are also briefly discussed in the context of lung infections in COPD. Controlling their combined response may restore a balanced lung homeostasis, reducing the risk of lung function decline. KEY MESSAGE Bacteria and viruses can influence the responses of the innate and adaptive immune system in the lung of chronic obstructive pulmonary disease (COPD) patients. The relationship between viruses and bacterial colonization, and the consequences of the imbalance of these components can modulate the inflammatory state of the COPD lung. The complex actions involving immune trigger cells, which activate innate and cell-mediated inflammatory responses, could be responsible for the clinical consequences of irreversible airflow limitation, lung remodelling and emphysema in COPD patients.
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Affiliation(s)
| | - Mauro Maniscalco
- Divisione di Pneumologia, Istituti Clinici Scientifici Maugeri, IRCCS, Telese, Italy
| | - Francesco Cappello
- Dipartimento di Biomedicina, Neuroscienze e Diagnostica avanzata (BIND), Istituto di Anatomia Umana e Istologia Università degli Studi di Palermo, Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Mauro Carone
- UOC Pulmonology and Pulmonary Rehabilitation, Istituti Clinici Scientifici Maugeri, IRCCS di Bari, Bari, Italy
| | - Andrea Motta
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Italy
| | - Bruno Balbi
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell’Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, IRCCS, Veruno, Italy
| | - Fabio L. M. Ricciardolo
- Dipartimento di Scienze Cliniche e Biologiche, Università di Torino, AOU San Luigi Gonzaga, Torino, Italy
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini morfologiche e funzionali (BIOMORF), Università degli studi di Messina, Italy
| | - Antonino Di Stefano
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell’Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, IRCCS, Veruno, Italy
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31
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Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota. Animals (Basel) 2021; 11:ani11113280. [PMID: 34828011 PMCID: PMC8614244 DOI: 10.3390/ani11113280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotics are major disruptors of the gastrointestinal microbiota, depleting bacterial species beneficial for the host health and favoring the emergence of potential pathogens. Furthermore, the intestine is a reactor of antibiotic resistance emergence, and the presence of antibiotics exacerbates the selection of resistant bacteria that can disseminate in the environment and propagate to further hosts. We reviewed studies analyzing the effect of antibiotics on the intestinal microbiota and antibiotic resistance conducted on animals, focusing on the main food-producing and companion animals. Irrespective of antibiotic classes and animal hosts, therapeutic dosage decreased species diversity and richness favoring the bloom of potential enteropathogens and the selection of antibiotic resistance. These negative effects of antibiotic therapies seem ineluctable but often were mitigated when an antibiotic was administered by parenteral route. Sub-therapeutic dosages caused the augmentation of taxa involved in sugar metabolism, suggesting a link with weight gain. This result should not be interpreted positively, considering that parallel information on antibiotic resistance selection was rarely reported and selection of antibiotic resistance is known to occur also at low antibiotic concentration. However, studies on the effect of antibiotics as growth promoters put the basis for understanding the gut microbiota composition and function in this situation. This knowledge could inspire alternative strategies to antibiotics, such as probiotics, for improving animal performance. This review encompasses the analysis of the main animal hosts and all antibiotic classes, and highlights the future challenges and gaps of knowledge that should be filled. Further studies are necessary for elucidating pharmacodynamics in animals in order to improve therapy duration, antibiotic dosages, and administration routes for mitigating negative effects of antibiotic therapies. Furthermore, this review highlights that studies on aminoglycosides are almost inexistent, and they should be increased, considering that aminoglycosides are the first most commonly used antibiotic family in companion animals. Harmonization of experimental procedures is necessary in this research field. In fact, current studies are based on different experimental set-up varying for antibiotic dosage, regimen, administration, and downstream microbiota analysis. In the future, shotgun metagenomics coupled with long-reads sequencing should become a standard experimental approach enabling to gather comprehensive knowledge on GIM in terms of composition and taxonomic functions, and of ARGs. Decorticating GIM in animals will unveil revolutionary strategies for medication and improvement of animals' health status, with positive consequences on global health.
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Arora T, Tremaroli V. Therapeutic Potential of Butyrate for Treatment of Type 2 Diabetes. Front Endocrinol (Lausanne) 2021; 12:761834. [PMID: 34737725 PMCID: PMC8560891 DOI: 10.3389/fendo.2021.761834] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/23/2021] [Indexed: 12/18/2022] Open
Abstract
Metagenomics studies have shown that type 2 diabetes (T2D) is associated with an altered gut microbiota. Whereas different microbiota patterns have been observed in independent human cohorts, reduction of butyrate-producing bacteria has consistently been found in individuals with T2D, as well as in those with prediabetes. Butyrate is produced in the large intestine by microbial fermentations, particularly of dietary fiber, and serves as primary fuel for colonocytes. It also acts as histone deacetylase inhibitor and ligand to G-protein coupled receptors, affecting cellular signaling in target cells, such as enteroendocrine cells. Therefore, butyrate has become an attractive drug target for T2D, and treatment strategies have been devised to increase its intestinal levels, for example by supplementation of butyrate-producing bacteria and dietary fiber, or through fecal microbiota transplant (FMT). In this review, we provide an overview of current literature indicating that these strategies have yielded encouraging results and short-term benefits in humans, but long-term improvements of glycemic control have not been reported so far. Further studies are required to find effective approaches to restore butyrate-producing bacteria and butyrate levels in the human gut, and to investigate their impact on glucose regulation in T2D.
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Affiliation(s)
- Tulika Arora
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Valentina Tremaroli
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Hasani A, Ebrahimzadeh S, Hemmati F, Khabbaz A, Hasani A, Gholizadeh P. The role of Akkermansia muciniphila in obesity, diabetes and atherosclerosis. J Med Microbiol 2021; 70. [PMID: 34623232 DOI: 10.1099/jmm.0.001435] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Alteration in the composition of the gut microbiota can lead to a number of chronic clinical diseases. Akkermansia muciniphila is an anaerobic bacteria constituting 3-5% of the gut microbial community in healthy adults. This bacterium is responsible for degenerating mucin in the gut; its scarcity leads to diverse clinical disorders. In this review, we focus on the role of A. muciniphila in diabetes, obesity and atherosclerosis, as well as the use of this bacterium as a next-generation probiotic. In regard to obesity and diabetes, human and animal trials have shown that A. muciniphila controls the essential regulatory system of glucose and energy metabolism. However, the underlying mechanisms by which A. muciniphila alleviates the complications of obesity, diabetes and atherosclerosis are unclear. At the same time, its abundance suggests improved metabolic disorders, such as metabolic endotoxemia, adiposity insulin resistance and glucose tolerance. The role of A. muciniphila is implicated in declining aortic lesions and atherosclerosis. Well-characterized virulence factors, antigens and cell wall extracts of A. muciniphila may act as effector molecules in these diseases. These molecules may provide novel mechanisms and strategies by which this bacterium could be used as a probiotic for the treatment of obesity, diabetes and atherosclerosis.
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Affiliation(s)
- Alka Hasani
- Clinical Research Development Unit, Sina Educational, Research and Treatment Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saba Ebrahimzadeh
- Department of Food Science and Technology, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Fatemeh Hemmati
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Aytak Khabbaz
- Clinical Research Development Unit, Sina Educational, Research and Treatment Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Akbar Hasani
- Department of Clinical Biochemistry and Laboratory Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Abstract
INTRODUCTION Obesity is a major public health concern with an increasing prevalence. Recent studies suggest an influence of gastrointestinal microbiota on obesity. Consequently, microbiota restoration therapies are being considered as potential management. We present data on microbiome markers and the future of microbiota therapeutics for obesity. AREAS COVERED We summarize the pathogenesis of obesity, relationship between gut microbiota and obesity, use of microbiota-based therapies. Data were gathered by a literature search of articles in PubMed from the date of inception till August 2020. Keywords used were 'gut microbiota,' 'gut microbiome,' 'microbiota,' 'microbiome,' 'obesity,' and 'obesity and fecal microbiota transplantation' as MeSH terms. EXPERT OPINION The direct relationship of gut microbiota in causing obesity needs exploration. Because of the scarcity of human studies, the utility of microbiota-based therapies as treatment remains uncertain and the use of microbiome restoration for obesity should be restricted to research settings. To evaluate the efficacy of microbiota restoration, studies using these therapies as an adjunct with diet and lifestyle should be conducted. Once relationships between bacterial strains and the human metabolic profile are determined, these strains could be cultured for transfer to obese patients. Such advancement could help in tailoring personalized therapies for obese persons.
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Affiliation(s)
- Kanika Sehgal
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sahil Khanna
- Mayo Clinic School of Graduate Medical Education, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
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Nouri R, Hasani A, Shirazi KM, Aliand MR, Sepehri B, Sotoodeh S, Hemmati F, Rezaee MA. Escherichia coli and colorectal cancer: Unfolding the enigmatic relationship. Curr Pharm Biotechnol 2021; 23:1257-1268. [PMID: 34514986 DOI: 10.2174/1389201022666210910094827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/21/2021] [Accepted: 06/07/2021] [Indexed: 11/22/2022]
Abstract
Colorectal cancer (CRC) is one of the deadliest cancers in the world. Specific strains of intestinal Escherichia coli (E. coli) may influence the initiation and development of CRC by exploiting virulence factors and inflammatory pathways. Mucosa-associated E. coli strains are more prevalent in CRC biopsies in comparison to healthy controls. Moreover, these strains can survive and replicate within macrophages and induce a pro-inflammatory response. Chronic exposure to inflammatory mediators can lead to increased cell proliferation and cancer. Production of colobactin toxin by the majority of mucosa-associated E. coli isolated from CRC patients is another notable finding. Colibactin-producing E. coli strains, in particular, induce double-strand DNA breaks, stop the cell cycle, involve in chromosomal rearrangements of mammalian cells and are implicated in carcinogenic effects in animal models. Moreover, some enteropathogenic E. coli (EPEC) strains are able to survive and replicate in colon cells as chronic intracellular pathogens and may promote susceptibility to CRC by downregulation of DNA Mismatch Repair (MMR) proteins. In this review, we discuss current evidence and focus on the mechanisms by which E. coli can influence the development of CRC.
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Affiliation(s)
- Rogayeh Nouri
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Alka Hasani
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Kourosh Masnadi Shirazi
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Mohammad Reza Aliand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Bita Sepehri
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Simin Sotoodeh
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Fatemeh Hemmati
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz. Iran
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Terrisse S, Derosa L, Iebba V, Ghiringhelli F, Vaz-Luis I, Kroemer G, Fidelle M, Christodoulidis S, Segata N, Thomas AM, Martin AL, Sirven A, Everhard S, Aprahamian F, Nirmalathasan N, Aarnoutse R, Smidt M, Ziemons J, Caldas C, Loibl S, Denkert C, Durand S, Iglesias C, Pietrantonio F, Routy B, André F, Pasolli E, Delaloge S, Zitvogel L. Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment. Cell Death Differ 2021; 28:2778-2796. [PMID: 33963313 PMCID: PMC8408230 DOI: 10.1038/s41418-021-00784-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/05/2021] [Accepted: 04/12/2021] [Indexed: 02/03/2023] Open
Abstract
The prognosis of early breast cancer (BC) relies on cell autonomous and immune parameters. The impact of the intestinal microbiome on clinical outcome has not yet been evaluated. Shotgun metagenomics was used to determine the composition of the fecal microbiota in 121 specimens from 76 early BC patients, 45 of whom were paired before and after chemotherapy. These patients were enrolled in the CANTO prospective study designed to record the side effects associated with the clinical management of BC. We analyzed associations between baseline or post-chemotherapy fecal microbiota and plasma metabolomics with BC prognosis, as well as with therapy-induced side effects. We examined the clinical relevance of these findings in immunocompetent mice colonized with BC patient microbiota that were subsequently challenged with histo-compatible mouse BC and chemotherapy. We conclude that specific gut commensals that are overabundant in BC patients compared with healthy individuals negatively impact BC prognosis, are modulated by chemotherapy, and may influence weight gain and neurological side effects of BC therapies. These findings obtained in adjuvant and neoadjuvant settings warrant prospective validation.
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Affiliation(s)
- Safae Terrisse
- Gustave Roussy Cancer Center, Villejuif, France
- INSERM U1015, Equipe Labellisée par la ligue Contre le Cancer, Villejuif, France
- University Paris Saclay, School of Medicine, Le Kremlin-Bicêtre, France
- Department of Medical Oncology, Saint Louis Hospital, Paris, France
| | - Lisa Derosa
- Gustave Roussy Cancer Center, Villejuif, France
- INSERM U1015, Equipe Labellisée par la ligue Contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT), Villejuif, France
| | - Valerio Iebba
- Gustave Roussy Cancer Center, Villejuif, France
- INSERM U1015, Equipe Labellisée par la ligue Contre le Cancer, Villejuif, France
| | - François Ghiringhelli
- Research Platform in Biological Oncology, Dijon, France
- GIMI Genetic and Immunology Medical Institute, Dijon, France
- University of Burgundy-Franche Comté, Dijon, France
- Department of Medical Oncology, Center GF Leclerc, Dijon, France
| | - Ines Vaz-Luis
- INSERM U 981, Gustave Roussy, Villejuif, Île-de-France, France
- Department of Medicine, Breast Cancer committee, Gustave Roussy, Villejuif, France
| | - Guido Kroemer
- INSERM U1138, Equipe Labelisée par la ligue Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Université de Paris, Paris, France
- Sorbonne Université, Paris, France
| | - Marine Fidelle
- Gustave Roussy Cancer Center, Villejuif, France
- INSERM U1015, Equipe Labellisée par la ligue Contre le Cancer, Villejuif, France
- University Paris Saclay, School of Medicine, Le Kremlin-Bicêtre, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT), Villejuif, France
| | - Stergios Christodoulidis
- University Paris Saclay, Saint-Aubain, France
- Prism Precision Medicine Center, Gustave Roussy, Villejuif, France
| | - Nicola Segata
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | | | - Fanny Aprahamian
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | | | - Romy Aarnoutse
- Faculty of Health, Medicine & Life Sciences, Department of Surgery, Maastricht, The Netherlands
- GROW School for Oncology & Developmental Biology, Maastricht, The Netherlands
- Maastricht University, Maastricht, The Netherlands
| | - Marjolein Smidt
- Faculty of Health, Medicine & Life Sciences, Department of Surgery, Maastricht, The Netherlands
- GROW School for Oncology & Developmental Biology, Maastricht, The Netherlands
- Maastricht University, Maastricht, The Netherlands
| | - Janine Ziemons
- Faculty of Health, Medicine & Life Sciences, Department of Surgery, Maastricht, The Netherlands
- GROW School for Oncology & Developmental Biology, Maastricht, The Netherlands
- Maastricht University, Maastricht, The Netherlands
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Sibylle Loibl
- Goethe University Frankfurt, Frankfurt, Germany
- Clinical Consultant Centre for Haematology and Oncology, Frankfurt, Germany
| | - Carsten Denkert
- Philipps-University Marburg and University Hospital Marburg (UKGM), Marburg, Germany
| | - Sylvere Durand
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Claudia Iglesias
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | | | - Bertrand Routy
- Division d'hémato-oncologie, Département de Médicine, Centre Hospitalier de l'université de Montréal (CHUM), Montréal, Québec, Canada
| | - Fabrice André
- Gustave Roussy Cancer Center, Villejuif, France
- INSERM U 981, Gustave Roussy, Villejuif, Île-de-France, France
- Department of Medicine, Breast Cancer committee, Gustave Roussy, Villejuif, France
- University Paris Saclay, Saint-Aubain, France
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Suzette Delaloge
- Gustave Roussy Cancer Center, Villejuif, France
- Department of Medicine, Breast Cancer committee, Gustave Roussy, Villejuif, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Center, Villejuif, France.
- INSERM U1015, Equipe Labellisée par la ligue Contre le Cancer, Villejuif, France.
- University Paris Saclay, School of Medicine, Le Kremlin-Bicêtre, France.
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT), Villejuif, France.
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Hwang J, Thompson A, Jaros J, Blackcloud P, Hsiao J, Shi VY. Updated understanding of Staphylococcus aureus in atopic dermatitis: From virulence factors to commensals and clonal complexes. Exp Dermatol 2021; 30:1532-1545. [PMID: 34293242 DOI: 10.1111/exd.14435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/18/2021] [Accepted: 07/20/2021] [Indexed: 12/22/2022]
Abstract
Atopic dermatitis (AD) is a common inflammatory dermatosis that has multiple contributing factors including genetic, immunologic and environmental. Staphylococcus aureus (SA) has long been associated with exacerbation of AD. SA produces many virulence factors that interact with the human skin and immune system. These superantigens and toxins have been shown to contribute to adhesion, inflammation and skin barrier destruction. Recent advances in genome sequencing techniques have led to a broadened understanding of the multiple ways SA interacts with the cutaneous environment in AD hosts. For example, temporal shifts in the microbiome, specifically in clonal complexes of SA, have been identified during AD flares and remission. Herein, we review mechanisms of interaction between the cutaneous microbiome and SA and highlight known differences in SA clonal complexes that contribute to AD pathogenesis. Detailed knowledge of the genetic strains of SA and cutaneous dysbiosis is becoming increasingly relevant in paving the way for microbiome-modulating and precision therapies for AD.
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Affiliation(s)
- Jonwei Hwang
- University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Alyssa Thompson
- College of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Joanna Jaros
- John H. Stroger Hospital Cook County Health Dermatology, Chicago, Illinois, USA
| | - Paul Blackcloud
- Division of Dermatology, University of California, Los Angeles, Los Angeles, California, USA
| | - Jennifer Hsiao
- Division of Dermatology, University of California, Los Angeles, Los Angeles, California, USA
| | - Vivian Y Shi
- Department of Dermatology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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38
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Zhang L, Qing P, Yang H, Wu Y, Liu Y, Luo Y. Gut Microbiome and Metabolites in Systemic Lupus Erythematosus: Link, Mechanisms and Intervention. Front Immunol 2021; 12:686501. [PMID: 34335588 PMCID: PMC8319742 DOI: 10.3389/fimmu.2021.686501] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/21/2021] [Indexed: 02/05/2023] Open
Abstract
Systemic lupus erythematosus (SLE), often considered the prototype of autoimmune diseases, is characterized by over-activation of the autoimmune system with abnormal functions of innate and adaptive immune cells and the production of a large number of autoantibodies against nuclear components. Given the highly complex and heterogeneous nature of SLE, the pathogenesis of this disease remains incompletely understood and is presumed to involve both genetic and environmental factors. Currently, disturbance of the gut microbiota has emerged as a novel player involved in the pathogenesis of SLE. With in-depth research, the understanding of the intestinal bacteria-host interaction in SLE is much more comprehensive. Recent years have also seen an increase in metabolomics studies in SLE with the attempt to identify potential biomarkers for diagnosis or disease activity monitoring. An intricate relationship between gut microbiome changes and metabolic alterations could help explain the mechanisms by which gut bacteria play roles in the pathogenesis of SLE. Here, we review the role of microbiota dysbiosis in the aetiology of SLE and how intestinal microbiota interact with the host metabolism axis. A proposed treatment strategy for SLE based on gut microbiome (GM) regulation is also discussed in this review. Increasing our understanding of gut microbiota and their function in lupus will provide us with novel opportunities to develop effective and precise diagnostic strategies and to explore potential microbiota-based treatments for patients with lupus.
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Affiliation(s)
- Lingshu Zhang
- Department of Rheumatology and Immunology, Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Pingying Qing
- Department of Rheumatology and Immunology, Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Hang Yang
- Department of Rheumatology and Immunology, Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yongkang Wu
- Department of Laboratory Medicine and Outpatient, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Liu
- Department of Rheumatology and Immunology, Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yubin Luo
- Department of Rheumatology and Immunology, Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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Reitmeier S, Hitch TCA, Treichel N, Fikas N, Hausmann B, Ramer-Tait AE, Neuhaus K, Berry D, Haller D, Lagkouvardos I, Clavel T. Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling. ISME COMMUNICATIONS 2021; 1:31. [PMID: 37938227 PMCID: PMC9723555 DOI: 10.1038/s43705-021-00033-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 04/23/2023]
Abstract
16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.
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Affiliation(s)
- Sandra Reitmeier
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany
| | - Nicole Treichel
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany
| | - Nikolaos Fikas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Klaus Neuhaus
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - David Berry
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dirk Haller
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Ilias Lagkouvardos
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany.
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece.
| | - Thomas Clavel
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany.
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany.
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Dong Q, Chen ES, Zhao C, Jin C. Host-Microbiome Interaction in Lung Cancer. Front Immunol 2021; 12:679829. [PMID: 34108973 PMCID: PMC8183378 DOI: 10.3389/fimmu.2021.679829] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/07/2021] [Indexed: 12/18/2022] Open
Abstract
Commensal microbiota has emerged as an essential biomarker and regulator of both tumorigenesis and response to cancer therapy. However, our current knowledge about microbiota in cancer has been largely limited to intestinal microbiota. As a mucosal organ harboring one of the largest surface areas in the body, the lung is exposed to a variety of microbes through inhalation and micro-aspiration, and is colonized by a diverse bacterial community in both physiological and pathological conditions. Importantly, increasing evidence has linked the lung microbiome to cancer development. Studies in lung cancer patients and mouse models have revealed tumor-associated dysregulation of the local microbiome in the lung, which in turn impacts cancer progression by shaping the tumor microenvironment and modulating the activity of tumor-infiltrating immune cells. These findings not only provide novel mechanistic insight into the biology of lung cancer but also shed light on new therapeutic targets and strategies for lung cancer prevention and treatment. The goal of this review is to discuss the key findings, remaining questions, and future directions in this new and exciting field.
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Affiliation(s)
- Qiang Dong
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Eric S Chen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Chen Zhao
- Thoracic and Gastrointestinal Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Chengcheng Jin
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Yang XJ, Liu D, Ren HY, Zhang XY, Zhang J, Yang XJ. Effects of sepsis and its treatment measures on intestinal flora structure in critical care patients. World J Gastroenterol 2021; 27:2376-2393. [PMID: 34040329 PMCID: PMC8130038 DOI: 10.3748/wjg.v27.i19.2376] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/23/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sepsis is a common disease in intensive care units, with high morbidity and mortality. Intestinal microecology plays a vital part in the development and progression of this disease, possibly because sepsis and its treatment cause specific changes in the composition of the intestinal flora.
AIM To investigate the characteristics of intestinal flora disturbance in sepsis patients treated with antibiotics.
METHODS In this prospective comparative study, we enrolled ten patients with sepsis (sepsis group), hospitalized in the Department of Critical Care Medicine of the General Hospital, Ningxia Medical University, China (a class IIIa general hospital) from February 2017 to June 2017; ten patients without sepsis hospitalized in the same period (non-sepsis group) and ten healthy individuals (control group) were also enrolled. Fecal samples collected from the three groups were subjected to 16S rRNA gene sequencing and the intestinal flora diversity, structure, and composition were determined. Additionally, the dynamics of the intestinal flora diversity, structure, and composition in sepsis patients were investigated via 16S rRNA gene sequencing of samples collected 0 d, 3 d, and 7 d after admittance to the intensive care unit. Correlations between the serum levels of procalcitonin, endotoxin, diamine oxidase, and D-lactic acid and the intestinal flora composition of sepsis patients were also investigated.
RESULTS Compared with the healthy control group, sepsis and non-sepsis patients showed reduced intestinal flora α-diversity and a distinct flora structure, with Firmicutes as the dominant phylum, and significantly decreased proportions of Bacteroidetes, as well as Prevotella and Lachnospira, among other genera. Of note, the proportion of Enterococcus was significantly increased in the intestinal tract of sepsis patients. Interestingly, the α-diversity in the sepsis group decreased gradually, from days 1 to 7 of treatment. However, pairwise comparisons showed that both the diversity and structure of the intestinal flora were not significantly different considering the three different time points studied. Curiously, the serum levels of procalcitonin, endotoxin, diamine oxidase, and D-lactic acid in sepsis patients correlated with the prevalence of various bacterial genera. For example, the prevalence of Ruminococcus was positively correlated with serum procalcitonin, endotoxins, and diamine oxidase; similarly, the prevalence of Roseburia was positively correlated with serum procalcitonin, endotoxins, and D-lactic acid.
CONCLUSION Sepsis patients in intensive care units show dysbiosis, lasting for at least 1 wk.
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Affiliation(s)
- Xiao-Juan Yang
- Department of Critical Care Medicine, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Dan Liu
- Department of Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei Province, China
| | - Hong-Yan Ren
- Shanghai Mobio Biomedical Technology Co., Shanghai 201318, China
| | - Xiao-Ya Zhang
- Department of Critical Care Medicine, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Jun Zhang
- Department of Critical Care Medicine, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Xiao-Jun Yang
- Department of Critical Care Medicine, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
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42
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Hollingsworth BA, Cassatt DR, DiCarlo AL, Rios CI, Satyamitra MM, Winters TA, Taliaferro LP. Acute Radiation Syndrome and the Microbiome: Impact and Review. Front Pharmacol 2021; 12:643283. [PMID: 34084131 PMCID: PMC8167050 DOI: 10.3389/fphar.2021.643283] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/04/2021] [Indexed: 12/12/2022] Open
Abstract
Study of the human microbiota has been a centuries-long endeavor, but since the inception of the National Institutes of Health (NIH) Human Microbiome Project in 2007, research has greatly expanded, including the space involving radiation injury. As acute radiation syndrome (ARS) is multisystemic, the microbiome niches across all areas of the body may be affected. This review highlights advances in radiation research examining the effect of irradiation on the microbiome and its potential use as a target for medical countermeasures or biodosimetry approaches, or as a medical countermeasure itself. The authors also address animal model considerations for designing studies, and the potential to use the microbiome as a biomarker to assess radiation exposure and predict outcome. Recent research has shown that the microbiome holds enormous potential for mitigation of radiation injury, in the context of both radiotherapy and radiological/nuclear public health emergencies. Gaps still exist, but the field is moving forward with much promise.
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Affiliation(s)
- Brynn A Hollingsworth
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - David R Cassatt
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - Andrea L DiCarlo
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - Carmen I Rios
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - Merriline M Satyamitra
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - Thomas A Winters
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - Lanyn P Taliaferro
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
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43
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Diet-induced dysbiosis of the maternal gut microbiome in early life programming of neurodevelopmental disorders. Neurosci Res 2021; 168:3-19. [PMID: 33992660 DOI: 10.1016/j.neures.2021.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022]
Abstract
The maternal gut microbiome plays a critical role in fetal and early postnatal development, shaping fundamental processes including immune maturation and brain development, among others. Consequently, it also contributes to fetal programming of health and disease. Over the last decade, epidemiological studies and work in preclinical animal models have begun to uncover a link between dysbiosis of the maternal gut microbiome and neurodevelopmental disorders in offspring. Neurodevelopmental disorders are caused by both genetic and environmental factors, and their interactions; however, clinical heterogeneity, phenotypic variability, and comorbidities make identification of underlying mechanisms difficult. Among environmental factors, exposure to maternal obesity in utero confers a significant increase in risk for neurodevelopmental disorders. Obesogenic diets in humans, non-human primates, and rodents induce functional modifications in maternal gut microbiome composition, which animal studies suggest are causally related to adverse mental health outcomes in offspring. Here, we review evidence linking maternal diet-induced gut dysbiosis to neurodevelopmental disorders and discuss how it could affect pre- and early postnatal brain development. We are hopeful that this burgeoning field of research will revolutionize antenatal care by leading to accessible prophylactic strategies, such as prenatal probiotics, to improve mental health outcomes in children affected by maternal diet-induced obesity.
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44
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Chandra S, Harvey E, Emery D, Holmes EC, Šlapeta J. Unbiased Characterization of the Microbiome and Virome of Questing Ticks. Front Microbiol 2021; 12:627327. [PMID: 34054743 PMCID: PMC8153229 DOI: 10.3389/fmicb.2021.627327] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/16/2021] [Indexed: 11/30/2022] Open
Abstract
Due to their vector capacity, ticks are ectoparasites of medical and veterinary significance. Modern sequencing tools have facilitated tick-associated microbiota studies, but these have largely focused on bacterial pathogens and symbionts. By combining 16S rRNA gene sequencing with total RNA-sequencing methods, we aimed to determine the complete microbiome and virome of questing, female Ixodes holocyclus recovered from coastal, north-eastern New South Wales (NSW), Australia. We present, for the first time, a robust and unbiased method for the identification of novel microbes in ticks that enabled us to identify bacteria, viruses, fungi and eukaryotic pathogens. The dominant bacterial endosymbionts were Candidatus Midichloria sp. Ixholo1 and Candidatus Midichloria sp. Ixholo2. Candidatus Neoehrlichia australis and Candidatus Neoehrlichia arcana were also recovered, confirming that these bacteria encompass I. holocyclus’ core microbiota. In addition, seven virus species were detected—four previously identified in I. holocyclus and three novel species. Notably, one of the four previously identified virus species has pathogenic potential based on its phylogenetic relationship to other tick-associated pathogens. No known pathogenic eukaryotes or fungi were identified. This study has revealed the microbiome and virome of female I. holocyclus from the environment in north-eastern NSW. We propose that future tick microbiome and virome studies utilize equivalent methods to provide an improved representation of the microbial diversity in ticks globally.
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Affiliation(s)
- Shona Chandra
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Erin Harvey
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - David Emery
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
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45
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Goubet AG, Wheeler R, Fluckiger A, Qu B, Lemaître F, Iribarren K, Mondragón L, Tidjani Alou M, Pizzato E, Durand S, Derosa L, Aprahamian F, Bossut N, Moya-Nilges M, Derrien D, Chen G, Leduc M, Joseph A, Pons N, Le Chatelier E, Segata N, Yonekura S, Iebba V, Kepp O, Raoult D, André F, Kroemer G, Boneca IG, Zitvogel L, Daillère R. Multifaceted modes of action of the anticancer probiotic Enterococcus hirae. Cell Death Differ 2021; 28:2276-2295. [PMID: 33976389 DOI: 10.1038/s41418-021-00753-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
A deviated repertoire of the gut microbiome predicts resistance to cancer immunotherapy. Enterococcus hirae compensated cancer-associated dysbiosis in various tumor models. However, the mechanisms by which E. hirae restored the efficacy of cyclophosphamide administered with concomitant antibiotics remain ill defined. Here, we analyzed the multifaceted modes of action of this anticancer probiotic. Firstly, E. hirae elicited emigration of thymocytes and triggered systemic and intratumoral IFNγ-producing and CD137-expressing effector memory T cell responses. Secondly, E. hirae activated the autophagy machinery in enterocytes and mediated ATG4B-dependent anticancer effects, likely as a consequence of its ability to increase local delivery of polyamines. Thirdly, E. hirae shifted the host microbiome toward a Bifidobacteria-enriched ecosystem. In contrast to the live bacterium, its pasteurized cells or membrane vesicles were devoid of anticancer properties. These pleiotropic functions allow the design of optimal immunotherapies combining E. hirae with CD137 agonistic antibodies, spermidine, or Bifidobacterium animalis. We surmise that immunological, metabolic, epithelial, and microbial modes of action of the live E. hirae cooperate to circumvent primary resistance to therapy.
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Affiliation(s)
- Anne-Gaëlle Goubet
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Villejuif, France.,Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
| | - Richard Wheeler
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut Pasteur Paris, Unit Biology and Genetics of the Bacterial Cell Wall, CNRS UMR 2001, Paris, France
| | - Aurélie Fluckiger
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Villejuif, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Bo Qu
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Villejuif, France.,Department of Rheumatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fabien Lemaître
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,EverImmune, Gustave Roussy Cancer Center, Villejuif, France
| | - Kristina Iribarren
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,EverImmune, Gustave Roussy Cancer Center, Villejuif, France
| | - Laura Mondragón
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France.,Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Maryam Tidjani Alou
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Villejuif, France
| | - Eugénie Pizzato
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Villejuif, France
| | - Sylvère Durand
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Lisa Derosa
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Villejuif, France.,Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
| | - Fanny Aprahamian
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Noélie Bossut
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | | | - Diane Derrien
- Institut Pasteur Paris, Unit Biology and Genetics of the Bacterial Cell Wall, CNRS UMR 2001, Paris, France
| | - Guo Chen
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Marion Leduc
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Adrien Joseph
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Nicolas Pons
- MetaGenoPolis, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Satoru Yonekura
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Villejuif, France
| | - Valerio Iebba
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Villejuif, France
| | - Oliver Kepp
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Didier Raoult
- Aix Marseille Université, IHU Méditerranée Infection, MEPHI, Marseille, France
| | - Fabrice André
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France.,Department of Medical Oncology, Gustave Roussy, Villejuif, France.,INSERM, U981, Gustave Roussy, Villejuif, France
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Université de Paris, Paris, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France.,Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden.,Suzhou Institute for Systems Biology, Chinese Academy of Medical Sciences, Suzhou, China
| | - Ivo Gomperts Boneca
- Institut Pasteur Paris, Unit Biology and Genetics of the Bacterial Cell Wall, CNRS UMR 2001, Paris, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France. .,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Villejuif, France. .,Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France. .,Center of Clinical Investigations BIOTHERIS, Villejuif, France.
| | - Romain Daillère
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France. .,EverImmune, Gustave Roussy Cancer Center, Villejuif, France.
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Abstract
Microbiology began as a unified science using the principles of chemistry to understand living systems. The unified view quickly split into the subdisciplines of medical microbiology, molecular biology, and environmental microbiology. The advent of a universal phylogeny and culture-independent approaches have helped tear down the boundaries separating the subdisciplines. The vision for the future is that the study of the fundamental roles of microbes in ecology and evolution will lead to an integrated biology with no boundary between microbiology and macrobiology. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Roberto Kolter
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA;
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47
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Cvetkovic L, Régis C, Richard C, Derosa L, Leblond A, Malo J, Messaoudene M, Desilets A, Belkaid W, Elkrief A, Routy B, Juneau D. Physiologic colonic uptake of 18F-FDG on PET/CT is associated with clinical response and gut microbiome composition in patients with advanced non-small cell lung cancer treated with immune checkpoint inhibitors. Eur J Nucl Med Mol Imaging 2021; 48:1550-1559. [PMID: 33128571 DOI: 10.1007/s00259-020-05081-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Immune checkpoint inhibitors (ICI) represent the backbone treatment for advanced non-small cell lung cancer (NSCLC). Emerging data suggest that increased gut microbiome diversity is associated with favorable response to ICI and that antibiotic-induced dysbiosis is associated with deleterious outcomes. 18F-FDG physiologic colonic uptake on PET/CT increases following treatment with antibiotics (ATB) and could act as a surrogate marker for microbiome composition and predict prognosis. The aim of this study was to determine if 18F-FDG physiologic colonic uptake prior to ICI initiation correlates with gut microbiome profiling and clinical outcomes in patients with advanced NSCLC. METHODS Seventy-one patients with advanced NSCLC who underwent a PET/CT prior to ICI were identified. Blinded colonic contouring was performed for each colon segment and patients were stratified according to the median of the average colon SUVmax as well as for each segment in low vs. high SUVmax groups. Response rate, progression-free survival (PFS), and overall survival (OS) were compared in the low vs. high SUVmax groups. Gut microbiome composition was analyzed for 23 patients using metagenomics sequencing. RESULTS The high colon SUVmax group had a higher proportion of non-responders (p = 0.033) and significantly shorter PFS (4.1 vs. 11.3 months, HR 1.94, 95% CI 1.11-3.41, p = 0.005). High caecum SUVmax correlated with numerically shorter OS (10.8 vs. 27.6 months, HR 1.85, 95% CI 0.97-3.53, p = 0.058). Metagenomics sequencing revealed distinctive microbiome populations in each group. Patients with low caecum SUVmax had higher microbiome diversity (p = 0.046) and were enriched with Bifidobacteriaceae, Lachnospiraceae, and Bacteroidaceae. CONCLUSIONS Lower colon physiologic 18F-FDG uptake on PET/CT prior to ICI initiation was associated with better clinical outcomes and higher gut microbiome diversity in patients with advanced NSCLC. Here, we propose that 18F-FDG physiologic colonic uptake on PET/CT could serve as a potential novel marker of gut microbiome composition and may predict clinical outcomes in this population.
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Affiliation(s)
- Lena Cvetkovic
- Department of Hematology and Oncology, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, Québec, Canada
| | - Claudine Régis
- Department of Radiology and Nuclear Medicine, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
- Department of Radiology and Nuclear Medicine, Institut de Cardiologie de Montréal, Montréal, Québec, Canada
| | - Corentin Richard
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, Québec, Canada
| | - Lisa Derosa
- Department of Tumor Immunology and Immunotherapy INSERM U1015, Gustave Roussy Cancer Center, Villejuif, France
| | - Antoine Leblond
- Department of Radiology and Nuclear Medicine, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
- Department of Radiology and Nuclear Medicine, Centre Hospitalier Affilié Universitaire Régional (CHAUR), Trois-Rivières, Québec, Canada
| | - Julie Malo
- Department of Hematology and Oncology, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, Québec, Canada
| | - Meriem Messaoudene
- Department of Hematology and Oncology, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, Québec, Canada
| | - Antoine Desilets
- Department of Hematology and Oncology, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, Québec, Canada
| | - Wiam Belkaid
- Department of Hematology and Oncology, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, Québec, Canada
| | - Arielle Elkrief
- Department of Hematology and Oncology, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, Québec, Canada
| | - Bertrand Routy
- Department of Hematology and Oncology, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, Québec, Canada.
| | - Daniel Juneau
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, Québec, Canada.
- Department of Radiology and Nuclear Medicine, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada.
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48
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Steinum TM, Turgay E, Yardımcı RE, Småge SB, Karataş S. Tenacibaculum maritimum CRISPR loci analysis and evaluation of isolate spoligotyping. J Appl Microbiol 2021; 131:1848-1857. [PMID: 33905598 DOI: 10.1111/jam.15116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Indexed: 11/27/2022]
Abstract
AIMS We performed in silico analysis of CRISPRcas loci from Tenacibaculum maritimum, evaluated spoligotyping as a subtyping method and genotyped uncharacterized Turkish isolates from European sea bass by multilocus sequence typing (MLST). METHODS AND RESULTS Spoligotyping was performed with primers designed to allow amplification and sequencing of whole CRISPR-arrays from 23 T. maritimum isolates. Twenty-three completed/draft genomes were also downloaded from the NCBI database and analysed. MLST of Turkish isolates was achieved with a well-established 7-gene scheme. Tenacibaculum maritimum genomes carry a structurally complete but partially defective class II CRISPRcas locus due to known amino acid substitutions in encoded Cas9 proteins. Our spacer identification suggests that the host range of bacteriophage P2559Y and Vibrio phage nt-1 include T. maritimum and that the most recurrent infection recorded by isolates has been with Tenacibaculum phage PTm5. Thirty-eight isolates with this CRISPRcas locus belonged to 25 spoligotypes and to 24 sequence types by MLST, respectively. According to MLST, T. maritimum isolates from Turkey are most related to previously defined sequence types ST3, ST40 and ST41 isolates from Spain, Malta and France. CONCLUSIONS The evaluated spoligotyping offers discriminatory power comparable to MLST. SIGNIFICANCE AND IMPACT OF THE STUDY Spoligotyping has potential as a quick, easy and cheap tool for subtyping of T. maritimum isolates.
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Affiliation(s)
- T M Steinum
- Department of Molecular Biology and Genetics, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | - E Turgay
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
| | - R E Yardımcı
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
| | | | - S Karataş
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
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Künili İE, Ertürk Gürkan S, Aksu A, Turgay E, Çakir F, Gürkan M, Altinağaç U. Mass mortality in endangered fan mussels Pinna nobilis (Linnaeus 1758) caused by co-infection of Haplosporidium pinnae and multiple Vibrio infection in Çanakkale Strait, Turkey. Biomarkers 2021; 26:450-461. [PMID: 33899623 DOI: 10.1080/1354750x.2021.1910344] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE Pinna nobilis (fan mussel) is one of the most important endemic bivalve molluscs in the Mediterranean and mass mortality events were observed in these mussels in recent years. In this study, we report mass mortalities caused by Haplosporidium pinnae, which has been spreading in the Mediterranean for 3 years, and reached the Çanakkale Strait, which is the entrance of the Marmara and the Black Sea. MATERIAL AND METHODS Field observations during sampling and subsequent histopathological, biochemical, genetic, and microbiological analyses were carried out. RESULTS These analyses showed that H. pinnae infection spread among the natural beds of P. nobilis, causing severe tissue damage and oxidative stress. Our phylogenetic analyses suggested that the parasite spread through the Mediterranean much faster than thought. The results showed that vibriosis originating from Vibrio coralliilyticus, Vibrio tubiashii, Vibrio mediterranei, and Vibrio hispanicus, acted together with H. pinnae in infected individuals and caused death. CONCLUSION It is highly probable that the spread of H. pinnae to the Sea of Marmara and the Black Sea may occur earlier than expected, and it was concluded that mass deaths were caused by co-infection with H. pinnae and a geographically specific marine pathogen that can infect P. nobilis populations.
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Affiliation(s)
- İbrahim Ender Künili
- Faculty of Marine Science and Technology, Department of Fishing and Processing Technology, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Selin Ertürk Gürkan
- Faculty of Arts and Sciences, Department of Biology, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Ata Aksu
- Gedik Vocational School, Department of Motor Vehicles and Transportation Technologies, Underwater Technology, İstanbul Gedik University, Istanbul, Turkey
| | - Emre Turgay
- Faculty of Aquatic Sciences, Department of Aquaculture and Fish Diseases, İstanbul University, Istanbul, Turkey
| | - Fikret Çakir
- Faculty of Marine Science and Technology, Department of Fishing and Processing Technology, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Mert Gürkan
- Faculty of Arts and Sciences, Department of Biology, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Uğur Altinağaç
- Faculty of Marine Science and Technology, Department of Fishing and Processing Technology, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
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Role of Microbiota-Derived Extracellular Vesicles in Gut-Brain Communication. Int J Mol Sci 2021; 22:ijms22084235. [PMID: 33921831 PMCID: PMC8073592 DOI: 10.3390/ijms22084235] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 12/11/2022] Open
Abstract
Human intestinal microbiota comprise of a dynamic population of bacterial species and other microorganisms with the capacity to interact with the rest of the organism and strongly influence the host during homeostasis and disease. Commensal and pathogenic bacteria coexist in homeostasis with the intestinal epithelium and the gastrointestinal tract’s immune system, or GALT (gut-associated lymphoid tissue), of the host. However, a disruption to this homeostasis or dysbiosis by different factors (e.g., stress, diet, use of antibiotics, age, inflammatory processes) can cause brain dysfunction given the communication between the gut and brain. Recently, extracellular vesicles (EVs) derived from bacteria have emerged as possible carriers in gut-brain communication through the interaction of their vesicle components with immune receptors, which lead to neuroinflammatory immune response activation. This review discusses the critical role of bacterial EVs from the gut in the neuropathology of brain dysfunctions by modulating the immune response. These vesicles, which contain harmful bacterial EV contents such as lipopolysaccharide (LPS), peptidoglycans, toxins and nucleic acids, are capable of crossing tissue barriers including the blood-brain barrier and interacting with the immune receptors of glial cells (e.g., Toll-like receptors) to lead to the production of cytokines and inflammatory mediators, which can cause brain impairment and behavioral dysfunctions.
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