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Liao J, Shenhav L, Urban JA, Serrano M, Zhu B, Buck GA, Korem T. Microdiversity of the vaginal microbiome is associated with preterm birth. Nat Commun 2023; 14:4997. [PMID: 37591872 PMCID: PMC10435516 DOI: 10.1038/s41467-023-40719-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield insights into these associations. Here, we analyze metagenomic data from 705 vaginal samples collected during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative. We find that the vaginal microbiome of pregnancies that ended preterm exhibited unique genetic profiles. It was more genetically diverse at the species level, a result which we validate in an additional cohort, and harbored a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species drove this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. underwent more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our population genetics analyses reveal associations between the vaginal microbiome and PTB and suggest that evolutionary processes acting on vaginal microbes may play a role in adverse pregnancy outcomes such as PTB.
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Affiliation(s)
- Jingqiu Liao
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA.
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA
| | - Julia A Urban
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Myrna Serrano
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Bin Zhu
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Gregory A Buck
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA.
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, ON, Canada.
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2
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Liao J, Shenhav L, Urban JA, Serrano M, Zhu B, Buck GA, Korem T. Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523991. [PMID: 36711990 PMCID: PMC9882146 DOI: 10.1101/2023.01.13.523991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield new insights into these associations. To this end, we analyzed metagenomic data from 705 vaginal samples collected longitudinally during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative (MOMS-PI). We find that the vaginal microbiome of pregnancies that ended preterm exhibits unique genetic profiles. It is more genetically diverse at the species level, a result which we validate in an additional cohort, and harbors a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species, a group of central vaginal pathobionts, are driving this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. undergoes more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our results reveal novel associations between the vaginal microbiome and PTB using population genetics analyses, and suggest that evolutionary processes acting on the vaginal microbiome may play a vital role in adverse pregnancy outcomes such as preterm birth.
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Affiliation(s)
- Jingqiu Liao
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA
| | - Julia A. Urban
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Myrna Serrano
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Bin Zhu
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Gregory A. Buck
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, Canada
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3
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Inchingolo AM, Patano A, Di Pede C, Inchingolo AD, Palmieri G, de Ruvo E, Campanelli M, Buongiorno S, Carpentiere V, Piras F, Settanni V, Viapiano F, Hazballa D, Rapone B, Mancini A, Di Venere D, Inchingolo F, Fatone MC, Palermo A, Minetti E, Lorusso F, Scarano A, Sauro S, Tartaglia GM, Bordea IR, Dipalma G, Malcangi G. Autologous Tooth Graft: Innovative Biomaterial for Bone Regeneration. Tooth Transformer® and the Role of Microbiota in Regenerative Dentistry. A Systematic Review. J Funct Biomater 2023; 14:jfb14030132. [PMID: 36976056 PMCID: PMC10058341 DOI: 10.3390/jfb14030132] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/05/2023] Open
Abstract
Different biomaterials, from synthetic products to autologous or heterologous grafts, have been suggested for the preservation and regeneration of bone. The aim of this study is to evaluate the effectiveness of autologous tooth as a grafting material and examine the properties of this material and its interactions with bone metabolism. PubMed, Scopus, Cochrane Library, and Web of Science were searched to find articles addressing our topic published from 1 January 2012 up to 22 November 2022, and a total of 1516 studies were identified. Eighteen papers in all were considered in this review for qualitative analysis. Demineralized dentin can be used as a graft material, since it shows high cell compatibility and promotes rapid bone regeneration by striking an ideal balance between bone resorption and production; it also has several benefits, such as quick recovery times, high-quality newly formed bone, low costs, no risk of disease transmission, the ability to be performed as an outpatient procedure, and no donor-related postoperative complications. Demineralization is a crucial step in the tooth treatment process, which includes cleaning, grinding, and demineralization. Since the presence of hydroxyapatite crystals prevents the release of growth factors, demineralization is essential for effective regenerative surgery. Even though the relationship between the bone system and dysbiosis has not yet been fully explored, this study highlights an association between bone and gut microbes. The creation of additional scientific studies to build upon and enhance the findings of this study should be a future objective of scientific research.
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Affiliation(s)
| | - Assunta Patano
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Chiara Di Pede
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | | | - Giulia Palmieri
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Elisabetta de Ruvo
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Merigrazia Campanelli
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Silvio Buongiorno
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Vincenzo Carpentiere
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Fabio Piras
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Vito Settanni
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Fabio Viapiano
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Denisa Hazballa
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Biagio Rapone
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Antonio Mancini
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Daniela Di Venere
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
- Correspondence: (F.I.); (M.C.F.); Tel.: +39-331-211-1104 (F.I.); +39-3479914635 (M.C.F.)
| | - Maria Celeste Fatone
- PTA Trani-ASL BT, Viale Padre Pio, 76125 Trani, Italy
- Correspondence: (F.I.); (M.C.F.); Tel.: +39-331-211-1104 (F.I.); +39-3479914635 (M.C.F.)
| | - Andrea Palermo
- College of Medicine and Dentistry Birmingham, University of Birmingham, Birmingham B4 6BN, UK
| | - Elio Minetti
- Department of Biomedical, Surgical, and Dental Science, Università Degli Studi di Milano, 20122 Milan, Italy
| | - Felice Lorusso
- Department of Innovative Technologies in Medicine and Dentistry, University of Chieti-Pescara, 66100 Chieti, Italy
| | - Antonio Scarano
- Department of Innovative Technologies in Medicine and Dentistry, University of Chieti-Pescara, 66100 Chieti, Italy
| | - Salvatore Sauro
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
- Dental Biomaterials and Minimally Invasive Dentistry, Department of Dentistry, Cardenal Herrera-CEU University, CEU Universities, C/Santiago Ramón y Cajal, s/n., Alfara del Patriarca, 46115 Valencia, Spain
| | - Gianluca Martino Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, University of Milan, 20100 Milan, Italy
- UOC Maxillo-Facial Surgery and Dentistry Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Ioana Roxana Bordea
- Department of Oral Rehabilitation, Faculty of Dentistry, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Giuseppina Malcangi
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
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Wan L, Li H, Sun G, Zhang L, Xu H, Su F, He S, Xiao F. Mutational Pattern Induced by 5-Fluorouracil and Oxaliplatin in the Gut Microbiome. Front Microbiol 2022; 13:841458. [PMID: 35572679 PMCID: PMC9101311 DOI: 10.3389/fmicb.2022.841458] [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: 12/22/2021] [Accepted: 02/17/2022] [Indexed: 11/17/2022] Open
Abstract
Chemotherapeutic agents, such as 5-fluorouracil (5-FU) and oxaliplatin (Oxi), can not only kill the cancer cell but also influence the proliferation of gut microbiota; however, the interaction between these drugs and gut microbiota remains poorly understood. In this study, we developed a powerful framework for taxonomy composition and genomic variation analysis to investigate the mutagenesis effect and proliferation influence of chemotherapeutic agents, such as 5-FU and Oxi, on gut microbiota and the interaction between these drugs and gut microbiota during chemotherapy. Using the gut microbiome data, we detected 1.45 million variations among the chemotherapy groups and found the drugs significantly affected mutation signatures of gut microbiota. Oxi notably increased transversion rate, whereas 5-FU reduced the rate. Traits related to cell division and nutrient mobilization showed evidence of strong selection pressure from chemotherapeutic agents. In addition, drug-associated bacteriome shift patterns and functional alterations were found: the metabolism changes in the 5-FU group implied that gut microbiota could provide additional nicotinamide adenine dinucleotide (NAD+) to inhibit cancer cell autophagy; in the Oxi group, the ribosome and lysine biosynthesis genes were obviously enriched. Our study provides a blueprint for characterizing the role of microbes and drug–microbe interaction in the gut microbiota response to chemotherapy.
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Affiliation(s)
- Li Wan
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Beijing Institute of Geriatrics, Chinese Academy of Medical Sciences, Beijing, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Gaoyuan Sun
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongtao Xu
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fei Xiao
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Beijing Institute of Geriatrics, Chinese Academy of Medical Sciences, Beijing, China
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5
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Strain identification and quantitative analysis in microbial communities. J Mol Biol 2022; 434:167582. [DOI: 10.1016/j.jmb.2022.167582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 12/14/2022]
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Bozzi Cionci N, Lucaccioni L, Pietrella E, Ficara M, Spada C, Torelli P, Bedetti L, Lugli L, Di Gioia D, Berardi A. Antibiotic Exposure, Common Morbidities and Main Intestinal Microbial Groups in Very Preterm Neonates: A Pilot Study. Antibiotics (Basel) 2022; 11:antibiotics11020237. [PMID: 35203839 PMCID: PMC8868158 DOI: 10.3390/antibiotics11020237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023] Open
Abstract
Prematurity exposes newborns to increased risks of infections and it is associated with critical morbidities. Preterm infants often require antibiotic therapies that can affect the correct establishment of gut microbiota. The aim of this study was to investigate targeted intestinal bacteria in preterm neonates with common morbidities and receiving antibiotic treatments of variable duration. Stool samples were collected after birth, at 15, 30 and 90 days of life. qPCR quantification of selected microbial groups (Bifidobacterium spp., Bacteroides fragilis group, Enterobacteriaceae, Clostridium cluster I and total bacteria) was performed and correlation between their levels, the duration of antibiotic treatment and different clinical conditions was studied. An increasing trend over time was observed for all microbial groups, especially for Bifdobacterium spp. Prolonged exposure to antibiotics in the first weeks of life affected Clostridium and B. fragilis levels, but these changes no longer persisted at 90 days of life. Variations of bacterial counts were associated with the length of hospital stay, feeding and mechanical ventilation. Late-onset sepsis and patent ductus arteriosus reduced the counts of Bifidobacterium, whereas B. fragilis was influenced by compromised respiratory conditions. This study can be a start point for the identification of microbial biomarkers associated with some common morbidities and tailored strategies for a healthy microbial development.
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Affiliation(s)
- Nicole Bozzi Cionci
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (N.B.C.); (D.D.G.)
| | - Laura Lucaccioni
- Pediatric Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, 41124 Modena, Italy
- Correspondence:
| | - Elisa Pietrella
- Pediatric Unit, Department of Medical for Mothers and Children, Ramazzini Hospital, 41012 Carpi, Italy;
| | - Monica Ficara
- Pediatric Unit, Department of Medical for Mothers and Children, Bufalini Hospital, 47521 Cesena, Italy;
| | - Caterina Spada
- Neonatal Intensive Care Unit, Department of Medical for Mothers and Children, Bufalini Hospital, 47521 Cesena, Italy;
| | - Paola Torelli
- Neonatal Intensive Care Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, 41124 Modena, Italy; (P.T.); (L.B.); (L.L.); (A.B.)
| | - Luca Bedetti
- Neonatal Intensive Care Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, 41124 Modena, Italy; (P.T.); (L.B.); (L.L.); (A.B.)
- PhD Program in Clinical and Experimental Medicine, University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - Licia Lugli
- Neonatal Intensive Care Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, 41124 Modena, Italy; (P.T.); (L.B.); (L.L.); (A.B.)
| | - Diana Di Gioia
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (N.B.C.); (D.D.G.)
| | - Alberto Berardi
- Neonatal Intensive Care Unit, Department of Medical and Surgical Sciences for Mothers, Children and Adults, University of Modena and Reggio Emilia, 41124 Modena, Italy; (P.T.); (L.B.); (L.L.); (A.B.)
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Inchingolo F, Hazballa D, Inchingolo AD, Malcangi G, Marinelli G, Mancini A, Maggiore ME, Bordea IR, Scarano A, Farronato M, Tartaglia GM, Lorusso F, Inchingolo AM, Dipalma G. Innovative Concepts and Recent Breakthrough for Engineered Graft and Constructs for Bone Regeneration: A Literature Systematic Review. MATERIALS 2022; 15:ma15031120. [PMID: 35161065 PMCID: PMC8839672 DOI: 10.3390/ma15031120] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023]
Abstract
Background: For decades, regenerative medicine and dentistry have been improved with new therapies and innovative clinical protocols. The aim of the present investigation was to evaluate through a critical review the recent innovations in the field of bone regeneration with a focus on the healing potentials and clinical protocols of bone substitutes combined with engineered constructs, growth factors and photobiomodulation applications. Methods: A Boolean systematic search was conducted by PubMed/Medline, PubMed/Central, Web of Science and Google scholar databases according to the PRISMA guidelines. Results: After the initial screening, a total of 304 papers were considered eligible for the qualitative synthesis. The articles included were categorized according to the main topics: alloplastic bone substitutes, autologous teeth derived substitutes, xenografts, platelet-derived concentrates, laser therapy, microbiota and bone metabolism and mesenchymal cells construct. Conclusions: The effectiveness of the present investigation showed that the use of biocompatible and bio-resorbable bone substitutes are related to the high-predictability of the bone regeneration protocols, while the oral microbiota and systemic health of the patient produce a clinical advantage for the long-term success of the regeneration procedures and implant-supported restorations. The use of growth factors is able to reduce the co-morbidity of the regenerative procedure ameliorating the post-operative healing phase. The LLLT is an adjuvant protocol to improve the soft and hard tissues response for bone regeneration treatment protocols.
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Affiliation(s)
- Francesco Inchingolo
- Department of Interdisciplinary Medicine, University of Medicine Aldo Moro, 70124 Bari, Italy; (D.H.); (A.D.I.); (G.M.); (G.M.); (A.M.); (M.E.M.); (A.M.I.)
- Correspondence: (F.I.); (F.L.); (G.D.); Tel.: +39-3312111104 (F.I.); +39-3282132586 (F.L.); +39-3396989939 (G.D.)
| | - Denisa Hazballa
- Department of Interdisciplinary Medicine, University of Medicine Aldo Moro, 70124 Bari, Italy; (D.H.); (A.D.I.); (G.M.); (G.M.); (A.M.); (M.E.M.); (A.M.I.)
- Kongresi Elbasanit, Rruga: Aqif Pasha, 3001 Elbasan, Albania
| | - Alessio Danilo Inchingolo
- Department of Interdisciplinary Medicine, University of Medicine Aldo Moro, 70124 Bari, Italy; (D.H.); (A.D.I.); (G.M.); (G.M.); (A.M.); (M.E.M.); (A.M.I.)
| | - Giuseppina Malcangi
- Department of Interdisciplinary Medicine, University of Medicine Aldo Moro, 70124 Bari, Italy; (D.H.); (A.D.I.); (G.M.); (G.M.); (A.M.); (M.E.M.); (A.M.I.)
| | - Grazia Marinelli
- Department of Interdisciplinary Medicine, University of Medicine Aldo Moro, 70124 Bari, Italy; (D.H.); (A.D.I.); (G.M.); (G.M.); (A.M.); (M.E.M.); (A.M.I.)
| | - Antonio Mancini
- Department of Interdisciplinary Medicine, University of Medicine Aldo Moro, 70124 Bari, Italy; (D.H.); (A.D.I.); (G.M.); (G.M.); (A.M.); (M.E.M.); (A.M.I.)
| | - Maria Elena Maggiore
- Department of Interdisciplinary Medicine, University of Medicine Aldo Moro, 70124 Bari, Italy; (D.H.); (A.D.I.); (G.M.); (G.M.); (A.M.); (M.E.M.); (A.M.I.)
| | - Ioana Roxana Bordea
- Department of Oral Rehabilitation, Faculty of Dentistry, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Antonio Scarano
- Department of Innovative Technologies in Medicine and Dentistry, University of Chieti-Pescara, 66100 Chieti, Italy;
| | - Marco Farronato
- UOC Maxillo-Facial Surgery and Dentistry, Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, University of Milan, 20100 Milan, Italy; (M.F.); (G.M.T.)
| | - Gianluca Martino Tartaglia
- UOC Maxillo-Facial Surgery and Dentistry, Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, University of Milan, 20100 Milan, Italy; (M.F.); (G.M.T.)
| | - Felice Lorusso
- Department of Innovative Technologies in Medicine and Dentistry, University of Chieti-Pescara, 66100 Chieti, Italy;
- Correspondence: (F.I.); (F.L.); (G.D.); Tel.: +39-3312111104 (F.I.); +39-3282132586 (F.L.); +39-3396989939 (G.D.)
| | - Angelo Michele Inchingolo
- Department of Interdisciplinary Medicine, University of Medicine Aldo Moro, 70124 Bari, Italy; (D.H.); (A.D.I.); (G.M.); (G.M.); (A.M.); (M.E.M.); (A.M.I.)
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine, University of Medicine Aldo Moro, 70124 Bari, Italy; (D.H.); (A.D.I.); (G.M.); (G.M.); (A.M.); (M.E.M.); (A.M.I.)
- Correspondence: (F.I.); (F.L.); (G.D.); Tel.: +39-3312111104 (F.I.); +39-3282132586 (F.L.); +39-3396989939 (G.D.)
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8
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Lee CC, Feng Y, Yeh YM, Lien R, Chen CL, Zhou YL, Chiu CH. Gut Dysbiosis, Bacterial Colonization and Translocation, and Neonatal Sepsis in Very-Low-Birth-Weight Preterm Infants. Front Microbiol 2021; 12:746111. [PMID: 34690993 PMCID: PMC8529156 DOI: 10.3389/fmicb.2021.746111] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/08/2021] [Indexed: 01/14/2023] Open
Abstract
Gut dysbiosis may precede neonatal sepsis, but the association is still not well-understood. The goal of this study is to investigate the association between gut microbiota and neonatal sepsis, and to seek the evidence of colonization of pathogenic bacteria in the gut before evolving into an invasive infection. A prospective cohort study examined fecal microbiota composition in preterm infants with and without sepsis. Thirty-two very-low-birth-weight (VLBW) preterm infants and 10 healthy term infants as controls were enrolled. The fecal samples collected from the participants at the first, fourth, and seventh weeks of life underwent 16S rRNA amplicon sequencing for measurement of the diversity and composition of the microbiota. The bacterial isolates causing neonatal sepsis were genome sequenced. PCR was performed to confirm the translocation of the bacteria from the gut to the blood. The results showed that VLBW preterm infants with sepsis had lower microbial diversity in the gut at birth compared to preterm infants without sepsis and term infants. The composition of gut microbiome in preterm infants was similar to healthy terms at birth but evolved toward dysbiosis with increasing Proteobacteria and decreasing Firmicutes weeks later. The strain-specific PCR confirmed the presence of causative pathogens in the gut in 4 (40%) out of 10 VLBW preterms with sepsis before or at onset of sepsis, and persistence of the colonization for weeks after antibiotic treatment. The same bacterial strain could horizontally spread to cause infection in other infants. Prolonged antibiotic exposure significantly reduced beneficial Bifidobacterium and Lactobacillus in the gut. In conclusion, preterm infants with gut dysbiosis are at risk for neonatal sepsis, and the causative pathogens may be from the gut and persist to spread horizontally. The association of increased Proteobacteria abundance and decrease in microbiome diversity suggests the need for interventions targeting the gut microbiome to prevent dysbiosis and sepsis in VLBW preterm infants.
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Affiliation(s)
- Chien-Chung Lee
- Division of Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ye Feng
- Sir Run Run Shaw Hospital, Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Reyin Lien
- Division of Neonatology, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ying-Li Zhou
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
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9
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Buffet-Bataillon S, Bellanger A, Boudry G, Gangneux JP, Yverneau M, Beuchée A, Blat S, Le Huërou-Luron I. New Insights Into Microbiota Modulation-Based Nutritional Interventions for Neurodevelopmental Outcomes in Preterm Infants. Front Microbiol 2021; 12:676622. [PMID: 34177860 PMCID: PMC8232935 DOI: 10.3389/fmicb.2021.676622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022] Open
Abstract
Gut microbiota and the central nervous system have parallel developmental windows during pre and post-natal life. Increasing evidences suggest that intestinal dysbiosis in preterm infants predisposes the neonate to adverse neurological outcomes later in life. Understanding the link between gut microbiota colonization and brain development to tailor therapies aimed at optimizing initial colonization and microbiota development are promising strategies to warrant adequate brain development and enhance neurological outcomes in preterm infants. Breast-feeding has been associated with both adequate cognitive development and healthy microbiota in preterms. Infant formula are industrially produced substitutes for infant nutrition that do not completely recapitulate breast-feeding benefices and could be largely improved by the understanding of the role of breast milk components upon gut microbiota. In this review, we will first discuss the nutritional and bioactive component information on breast milk composition and its contribution to the assembly of the neonatal gut microbiota in preterms. We will then discuss the emerging pathways connecting the gut microbiota and brain development. Finally, we will discuss the promising microbiota modulation-based nutritional interventions (including probiotic and prebiotic supplementation of infant formula and maternal nutrition) for improving neurodevelopmental outcomes.
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Affiliation(s)
- Sylvie Buffet-Bataillon
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
- Department of Clinical Microbiology, CHU Rennes, Rennes, France
| | - Amandine Bellanger
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
- Department of Pediatrics-Neonatology, CHU Rennes, Rennes, France
| | - Gaelle Boudry
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
| | | | | | - Alain Beuchée
- Department of Pediatrics-Neonatology, Univ Rennes, CHU Rennes, LTSI-UMR 1099, Rennes, France
| | - Sophie Blat
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
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10
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Westaway JAF, Huerlimann R, Miller CM, Kandasamy Y, Norton R, Rudd D. Methods for exploring the faecal microbiome of premature infants: a review. Matern Health Neonatol Perinatol 2021; 7:11. [PMID: 33685524 PMCID: PMC7941982 DOI: 10.1186/s40748-021-00131-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
The premature infant gut microbiome plays an important part in infant health and development, and recognition of the implications of microbial dysbiosis in premature infants has prompted significant research into these issues. The approaches to designing investigations into microbial populations are many and varied, each with its own benefits and limitations. The technique used can influence results, contributing to heterogeneity across studies. This review aimed to describe the most common techniques used in researching the preterm infant microbiome, detailing their various limitations. The objective was to provide those entering the field with a broad understanding of available methodologies, so that the likely effects of their use can be factored into literature interpretation and future study design. We found that although many techniques are used for characterising the premature infant microbiome, 16S rRNA short amplicon sequencing is the most common. 16S rRNA short amplicon sequencing has several benefits, including high accuracy, discoverability and high throughput capacity. However, this technique has limitations. Each stage of the protocol offers opportunities for the injection of bias. Bias can contribute to variability between studies using 16S rRNA high throughout sequencing. Thus, we recommend that the interpretation of previous results and future study design be given careful consideration.
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Affiliation(s)
- Jacob A F Westaway
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia.
| | - Roger Huerlimann
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
| | - Catherine M Miller
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia
| | - Yoga Kandasamy
- Townsville University Hospital, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Robert Norton
- Pathology Queensland, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Donna Rudd
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
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11
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The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota. Microorganisms 2021; 9:microorganisms9020278. [PMID: 33572789 PMCID: PMC7911719 DOI: 10.3390/microorganisms9020278] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 12/19/2022] Open
Abstract
The preterm infant gut microbiota is influenced by environmental, endogenous, maternal, and genetic factors. Although siblings share similar gut microbial composition, it is not known how genetic relatedness affects alpha diversity and specific taxa abundances in preterm infants. We analyzed the 16S rRNA gene content of stool samples, ≤ and >3 weeks postnatal age, and clinical data from preterm multiplets and singletons at two Neonatal Intensive Care Units (NICUs), Tampa General Hospital (TGH; FL, USA) and Carle Hospital (IL, USA). Weeks on bovine milk-based fortifier (BMF) and weight gain velocity were significant predictors of alpha diversity. Alpha diversity between siblings were significantly correlated, particularly at ≤3 weeks postnatal age and in the TGH NICU, after controlling for clinical factors. Siblings shared higher gut microbial composition similarity compared to unrelated individuals. After residualizing against clinical covariates, 30 common operational taxonomic units were correlated between siblings across time points. These belonged to the bacterial classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Erysipelotrichia, and Negativicutes. Besides the influence of BMF and weight variables on the gut microbial diversity, our study identified gut microbial similarities between siblings that suggest genetic or shared maternal and environmental effects on the preterm infant gut microbiota.
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12
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A framework for identifying the recent origins of mobile antibiotic resistance genes. Commun Biol 2021; 4:8. [PMID: 33398069 PMCID: PMC7782503 DOI: 10.1038/s42003-020-01545-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Since the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics. Mobile resistance genes, acquired through horizontal gene transfer, play an important role in this process. Understanding from which bacterial taxa these genes were mobilized, and whether their origin taxa share common traits, is critical for predicting which environments and conditions contribute to the emergence of novel resistance genes. This knowledge may prove valuable for limiting or delaying future transfer of novel resistance genes into pathogens. The literature on the origins of mobile resistance genes is scattered and based on evidence of variable quality. Here, we summarize, amend and scrutinize the evidence for 37 proposed origins of mobile resistance genes. Using state-of-the-art genomic analyses, we supplement and evaluate the evidence based on well-defined criteria. Nineteen percent of reported origins did not fulfill the criteria to confidently assign the respective origin. Of the curated origin taxa, >90% have been associated with infection in humans or domestic animals, some taxa being the origin of several different resistance genes. The clinical emergence of these resistance genes appears to be a consequence of antibiotic selection pressure on taxa that are permanently or transiently associated with the human/domestic animal microbiome. Ebmeyer and colleagues developed a genomic framework for identification and scrutiny of the origins of antibiotic resistance genes. Using data scoured from the literature and publicly available genomes, their results indicate that only 81% of previously reported origins are valid, and that the majority of resistance genes of which the origin is known to date emerged in taxa that have been associated with infection in humans and domesticated animals.
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13
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Wang S, Jiang Y, Li S. PStrain: An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data. Bioinformatics 2020; 36:5499-5506. [PMID: 33346799 DOI: 10.1093/bioinformatics/btaa1056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/29/2020] [Accepted: 12/09/2020] [Indexed: 01/21/2023] Open
Abstract
MOTIVATION The microbial community plays an essential role in human diseases and physiological activities. The functions of microbes can differ due to strain-level differences in the genome sequences. Shotgun metagenomic sequencing allows us to profile the strains in microbial communities practically. However, current methods are underdeveloped due to the highly similar sequences among strains. We observe that strains genotypes at the same single nucleotide variant (SNV) locus can be speculated by the genotype frequencies. Also, the variants in different loci covered by the same reads can provide evidence that they reside on the same strain. RESULTS These insights inspire us to design PStrain, an optimization method that utilizes genotype frequencies and the reads which cover multiple SNV loci to profile strains iteratively based on SNVs in a set of MetaPhlAn2 marker genes. Compared to the state-of-art methods, PStrain, on average, improved the performance of inferring strains abundances and genotypes by 87.75% and 59.45%, respectively. We have applied the PStrain package to the dataset with two cohorts of colorectal cancer (CRC) and found that the sequences of Bacteroides coprocola strains are significantly different between CRC and control samples, which is the first time to report the potential role of B. coprocola in the gut microbiota of CRC. AVAILABILITY https://github.com/wshuai294/PStrain. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shuai Wang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Yiqi Jiang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong
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14
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Kumar PS, Dabdoub SM, Ganesan SM. Probing periodontal microbial dark matter using metataxonomics and metagenomics. Periodontol 2000 2020; 85:12-27. [PMID: 33226714 DOI: 10.1111/prd.12349] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Our view of the periodontal microbial community has been shaped by a century or more of cultivation-based and microscopic investigations. While these studies firmly established the infection-mediated etiology of periodontal diseases, it was apparent from the very early days that periodontal microbiology suffered from what Staley and Konopka described as the "great plate count anomaly", in that these culturable bacteria were only a minor part of what was visible under the microscope. For nearly a century, much effort has been devoted to finding the right tools to investigate this uncultivated majority, also known as "microbial dark matter". The discovery that DNA was an effective tool to "see" microbial dark matter was a significant breakthrough in environmental microbiology, and oral microbiologists were among the earliest to capitalize on these advances. By identifying the order in which nucleotides are arranged in a stretch of DNA (DNA sequencing) and creating a repository of these sequences, sequence databases were created. Computational tools that used probability-driven analysis of these sequences enabled the discovery of new and unsuspected species and ascribed novel functions to these species. This review will trace the development of DNA sequencing as a quantitative, open-ended, comprehensive approach to characterize microbial communities in their native environments, and explore how this technology has shifted traditional dogmas on how the oral microbiome promotes health and its role in disease causation and perpetuation.
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Affiliation(s)
- Purnima S Kumar
- Department of Periodontology, College of Dentistry, The Ohio State University, Columbus, Ohio, USA
| | - Shareef M Dabdoub
- Department of Periodontology, College of Dentistry, The Ohio State University, Columbus, Ohio, USA
| | - Sukirth M Ganesan
- Department of Periodontics, College of Dentistry and Dental Clinics, The University of Iowa, Iowa City, Iowa, USA
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15
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Yadav M, Pandey R, Chauhan NS. Catabolic Machinery of the Human Gut Microbes Bestow Resilience Against Vanillin Antimicrobial Nature. Front Microbiol 2020; 11:588545. [PMID: 33193247 PMCID: PMC7605359 DOI: 10.3389/fmicb.2020.588545] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022] Open
Abstract
Vanillin is a phenolic food additive commonly used for flavor, antimicrobial, and antioxidant properties. Though it is one of the widely used food additives, strategies of the human gut microbes to evade its antimicrobial activity await extensive elucidation. The current study explores the human gut microbiome with a multi-omics approach to elucidate its composition and metabolic machinery to counter vanillin bioactivity. A combination of SSU rRNA gene diversity, metagenomic RNA features diversity, phylogenetic affiliation of metagenome encoded proteins, uniformly (R = 0.99) indicates the abundance of Bacteroidetes followed by Firmicutes and Proteobacteria. Manual curation of metagenomic dataset identified gene clusters specific for the vanillin metabolism (ligV, ligK, and vanK) and intermediary metabolic pathways (pca and cat operon). Metagenomic dataset comparison identified the omnipresence of vanillin catabolic features across diverse populations. The metabolomic analysis brings forth the functionality of the vanillin catabolic pathway through the Protocatechuate branch of the beta-ketoadipate pathway. These results highlight the human gut microbial features and metabolic bioprocess involved in vanillin catabolism to overcome its antimicrobial activity. The current study advances our understanding of the human gut microbiome adaption toward changing dietary habits.
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Affiliation(s)
- Monika Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Rajesh Pandey
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
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16
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Kingkaw A, Nakphaichit M, Suratannon N, Nitisinprasert S, Wongoutong C, Chatchatee P, Krobthong S, Charoenlappanit S, Roytrakul S, Vongsangnak W. Analysis of the infant gut microbiome reveals metabolic functional roles associated with healthy infants and infants with atopic dermatitis using metaproteomics. PeerJ 2020; 8:e9988. [PMID: 33033661 PMCID: PMC7521340 DOI: 10.7717/peerj.9988] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022] Open
Abstract
The infant gut microbiome consists of a complex and diverse microbial community. Comprehensive taxonomic and metabolic functional knowledge about microbial communities supports medical and biological applications, such as fecal diagnostics. Among the omics approaches available for the investigation of microbial communities, metaproteomics-based analysis is a very powerful approach; under this method, the activity of microbial communities is explored by investigating protein expression within a sample. Through use of metaproteomics, this study aimed to investigate the microbial community composition of the infant gut to identify different key proteins playing metabolic functional roles in the microbiome of healthy infants and infants with atopic dermatitis in a Thai population-based birth cohort. Here, 18 fecal samples were analyzed by liquid chromatography-tandem mass spectrometry to conduct taxonomic, functional, and pathway-based protein annotation. Accordingly, 49,973 annotated proteins out of 68,232 total proteins were investigated in gut microbiome samples and compared between the healthy and atopic dermatitis groups. Through differentially expressed proteins (DEPs) analysis, 130 significant DEPs were identified between the healthy and atopic dermatitis groups. Among these DEPs, eight significant proteins were uniquely expressed in the atopic dermatitis group. For instance, triosephosphate isomerase (TPI) in Bifidobacteriaceae in the genus Alloscardovia and demethylmenaquinone methyltransferase (DMM) in Bacteroides were shown to potentially play metabolic functional roles related to disease. PPI network analysis revealed seven reporter proteins showing metabolic alterations between the healthy and disease groups associated with the biosynthesis of ubiquinone and other quinones as well as the energy supply. This study serves as a scaffold for microbial community-wide metabolic functional studies of the infant gut microbiome in relation to allergic disease.
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Affiliation(s)
- Amornthep Kingkaw
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Narissara Suratannon
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Sunee Nitisinprasert
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Chantha Wongoutong
- Department of Statistics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pantipa Chatchatee
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Sucheewin Krobthong
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sawanya Charoenlappanit
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
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17
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Darcy JL, Washburne AD, Robeson MS, Prest T, Schmidt SK, Lozupone CA. A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome. THE ISME JOURNAL 2020; 14:1359-1368. [PMID: 32076128 PMCID: PMC7242462 DOI: 10.1038/s41396-020-0613-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023]
Abstract
Understanding when and why new species are recruited into microbial communities is a formidable problem with implications for managing microbial systems, for instance by helping us better understand whether a probiotic or pathogen would be expected to colonize a human microbiome. Much theory in microbial temporal dynamics is focused on how phylogenetic relationships between microbes impact the order in which those microbes are recruited; for example, species that are closely related may competitively exclude each other. However, several recent human microbiome studies have observed closely related bacteria being recruited into microbial communities in short succession, suggesting that microbial community assembly is historically contingent, but competitive exclusion of close relatives may not be important. To address this, we developed a mathematical model that describes the order in which new species are detected in microbial communities over time within a phylogenetic framework. We use our model to test three hypothetical assembly modes: underdispersion (species recruitment is more likely if a close relative was previously detected), overdispersion (recruitment is more likely if a close relative has not been previously detected), and the neutral model (recruitment likelihood is not related to phylogenetic relationships among species). We applied our model to longitudinal human microbiome data, and found that for the individuals we analyzed, the human microbiome generally follows the underdispersion (i.e., nepotism) hypothesis. Exceptions were oral communities and the fecal communities of two infants that had undergone heavy antibiotic treatment. None of the datasets we analyzed showed statistically significant phylogenetic overdispersion.
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Affiliation(s)
- John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Alex D Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Michael S Robeson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Tiffany Prest
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Catherine A Lozupone
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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18
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Valentine G, Prince A, Aagaard KM. The Neonatal Microbiome and Metagenomics: What Do We Know and What Is the Future? Neoreviews 2020; 20:e258-e271. [PMID: 31261078 DOI: 10.1542/neo.20-5-e258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The human microbiota includes the trillions of microorganisms living in the human body whereas the human microbiome includes the genes and gene products of this microbiota. Bacteria were historically largely considered to be pathogens that inevitably led to human disease. However, because of advances in both cultivation-based methods and the advent of metagenomics, bacteria are now recognized to be largely beneficial commensal organisms and thus, key to normal and healthy human development. This relatively new area of medical research has elucidated insights into diseases such as inflammatory bowel disease and obesity, as well as metabolic and atopic disorders. However, much remains unknown about the complexity of microbe-microbe and microbe-host interactions. Future efforts aimed at answering key questions pertaining to the early establishment of the microbiome, alongside what defines its dysbiosis, will likely lead to long-term health and mitigation of disease. Here, we review the relevant literature pertaining to modulations in the perinatal and neonatal microbiome, the impact of environmental and maternal factors in shaping the neonatal microbiome, and future questions and directions in the exciting emerging arena of metagenomic medicine.
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Affiliation(s)
- Gregory Valentine
- Department of Pediatrics.,Division of Neonatology at Texas Children's Hospital, Houston, TX
| | - Amanda Prince
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine
| | - Kjersti M Aagaard
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine.,Center for Microbiome and Metagenomics Research, and Departments of.,Molecular & Human Genetics and.,Molecular & Cell Biology, Baylor College of Medicine, Houston, TX
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19
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Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Brief Bioinform 2020; 20:1140-1150. [PMID: 28968737 DOI: 10.1093/bib/bbx098] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/13/2017] [Indexed: 01/09/2023] Open
Abstract
Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation.
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20
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Newberry E, Bhandari R, Kemble J, Sikora E, Potnis N. Genome-resolved metagenomics to study co-occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations. Environ Microbiol 2020; 22:2693-2708. [PMID: 32207218 DOI: 10.1111/1462-2920.14989] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/09/2020] [Accepted: 03/18/2020] [Indexed: 01/12/2023]
Abstract
Assessment of pathogen diversity in agricultural fields is essential for informing management decisions and the development of resistant plant varieties. However, many population genomic studies have relied on culture-based approaches that do not provide quantitative assessment of pathogen populations at the field-level or the associated host microbiome. Here, we applied whole-genome shotgun sequencing of microbial DNA extracted directly from the washings of pooled leaf samples, collected from individual tomato and pepper fields in Alabama that displayed the classical symptoms of bacterial spot disease caused by Xanthomonas spp. Our results revealed that while the occurrence of both X. perforans and X. euvesicatoria within fields was limited, evidence of co-occurrence of up to three distinct X. perforans genotypes was obtained in 7 of 10 tomato fields sampled. These population dynamics were accompanied by the corresponding type 3 secreted effector repertoires associated with the co-occurring X. perforans genotypes, indicating that metapopulation structure within fields should be considered when assessing the adaptive potential of X. perforans. Finally, analysis of microbial community composition revealed that co-occurrence of the bacterial spot pathogens Pseudomonas cichorii and Xanthomonas spp. is common in Alabama fields and provided evidence for the non-random association of several other human and plant opportunists.
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Affiliation(s)
- Eric Newberry
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Joseph Kemble
- Department of Horticulture, Auburn University, Auburn, AL, USA
| | - Edward Sikora
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA.,Alabama Cooperative Extension System, Auburn, AL, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
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21
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Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut. PLoS One 2020; 15:e0229537. [PMID: 32130257 PMCID: PMC7055874 DOI: 10.1371/journal.pone.0229537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 02/09/2020] [Indexed: 12/29/2022] Open
Abstract
Microbes alter their transcriptomic profiles in response to the environment. The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. However, this analysis requires accurate reference genomes to identify the specific genes from which RNA reads originate. In addition, such an analysis should avoid biases in transcript counts related to differences in organism abundance. In this study we describe an approach to address these difficulties. Sample-specific meta-genomic assembled genomes (MAGs) were used as reference genomes to accurately identify the origin of RNA reads, and transcript ratios of genes with opposite transcription responses were compared to eliminate biases related to differences in organismal abundance, an approach hereafter named the “diametric ratio” method. We used this approach to probe the environmental conditions experienced by Escherichia spp. in the gut of 4 premature infants, 2 of whom developed necrotizing enterocolitis (NEC), a severe inflammatory intestinal disease. We analyzed twenty fecal samples taken from four premature infants (4–6 time points from each infant), and found significantly higher diametric ratios of genes associated with low oxygen levels in samples of infants later diagnosed with NEC than in samples without NEC. We also show this method can be used for examining other physiological conditions, such as exposure to nitric oxide and osmotic pressure. These study results should be treated with caution, due to the presence of confounding factors that might also distinguish between NEC and control infants. Nevertheless, together with benchmarking analyses, we show here that the diametric ratio approach can be applied for evaluating the physiological conditions experienced by microbes in situ. Results from similar studies can be further applied for designing diagnostic methods to detect NEC in its early developmental stages.
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22
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Fundora JB, Guha P, Shores DR, Pammi M, Maheshwari A. Intestinal dysbiosis and necrotizing enterocolitis: assessment for causality using Bradford Hill criteria. Pediatr Res 2020; 87:235-248. [PMID: 31238334 PMCID: PMC7224339 DOI: 10.1038/s41390-019-0482-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 02/08/2023]
Abstract
In recent years, several studies have shown that premature infants who develop NEC frequently display enteric dysbiosis with increased Gram-negative bacteria for several days to weeks prior to NEC onset. The importance of these findings, for the possibility of a causal role of these bacteria in NEC pathogenesis, and for potential value of gut dysbiosis as a biomarker of NEC, is well-recognized. In this review, we present current evidence supporting the association between NEC in premature infants and enteric dysbiosis, and its evaluation using the Bradford Hill criteria for causality. To provide an objective appraisal, we developed a novel scoring system for causal inference. Despite important methodological and statistical limitations, there is support for the association from several large studies and a meta-analysis. The association draws strength from strong biological plausibility of a role of Gram-negative bacteria in NEC and from evidence for temporality, that dysbiosis may antedate NEC onset. The weakness of the association is in the low level of consistency across studies, and the lack of specificity of effect. There is a need for an improved definition of dysbiosis, either based on a critical threshold of relative abundances or at higher levels of taxonomic resolution.
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Affiliation(s)
- Jennifer B Fundora
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pallabi Guha
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Darla R Shores
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mohan Pammi
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Akhil Maheshwari
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Spencer SP, Fragiadakis GK, Sonnenburg JL. Pursuing Human-Relevant Gut Microbiota-Immune Interactions. Immunity 2019; 51:225-239. [PMID: 31433970 DOI: 10.1016/j.immuni.2019.08.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The gut microbiota is a complex and plastic network of diverse organisms intricately connected with human physiology. Recent advances in profiling approaches of both the microbiota and the immune system now enable a deeper exploration of immunity-microbiota connections. An important next step is to elucidate a human-relevant "map" of microbial-immune wiring while focusing on animal studies to probe a prioritized subset of interactions. Here, we provide an overview of this field's current status and discuss two approaches for establishing priorities for detailed investigation: (1) longitudinal intervention studies in humans probing the dynamics of both the microbiota and the immune system and (2) the study of traditional populations to assess lost features of human microbial identity whose absence may be contributing to the rise of immunological disorders. These human-centered approaches offer a judicious path forward to understand the impact of the microbiota in immune development and function.
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Affiliation(s)
- Sean P Spencer
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA.
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Ali SA, Singh P, Tomar SK, Mohanty AK, Behare P. Proteomics fingerprints of systemic mechanisms of adaptation to bile in Lactobacillus fermentum. J Proteomics 2019; 213:103600. [PMID: 31805390 DOI: 10.1016/j.jprot.2019.103600] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 11/17/2019] [Accepted: 11/28/2019] [Indexed: 12/17/2022]
Abstract
Lactobacillus fermentum is a natural resident of the human GIT and is used as a probiotic. A unique property of L. fermentum is its ability to tolerate, colonize, and survive in the harsh conditions of bile, which facilitates transient colonization of the host colon. In the current study, we investigated the key mechanisms of action involved in bacterial survival in the presence of bile, using high-resolution mass spectrometry. A total of 1071 proteins were identified, among which 378 were up-regulated and 368 down-regulated by ≥2-fold (t-test, p < .05). Differentially regulated proteins comprised both intracellular and surface-exposed (i.e., membrane) proteins (p < .01, t-test for total proteome analysis; p < .05, t-test for membrane proteome analysis). These alterations strengthen the cell envelope and also mediate bile efflux by adjusting carbohydrate metabolic pathways and prevention of protein misfolding. These processes are mainly involved in the active removal of bile salts or amelioration of its adverse effects on cells. Further investigation of mRNA transcript expression levels of selected proteins by quantitative reverse transcriptase-PCR verified the proteomic data. Together, our proteomics findings reveal the roles of post-stress recovery proteins and highlight the interacting pathways responsible for bacterial cell tolerance to bile stress. BIOLOGICAL SIGNIFICANCE: Our intestinal tract is a nutrient-rich milieu crowded with up to 100 trillion (1014) of microbes. The fact that we are born germ-free describes that these microbes must colonize our intestinal tract from outside. However, their survival is also complicated because of hazardous conditions in the gut due to the presence of bile acid and others, which exerts a deleterious effect on the beneficial microbial load. While there was limited information available describing the comprehensive mechanism of survival? Furthermore, the imbalance of these micro floras leads to numerous disease conditions. It explains the need for enhanced understanding of host-microbe interactions in the colon. The present study majorly focuses on identifying "how microbes respond to environmental stressors" in this context, particularly bile acid response. This work addresses a fascinating cellular mechanism involved in the complex changes of bile induction in the microbial system; in this case, L. fermentum NCDC 605 a well established probiotic organism. In this article, we decipher the characteristic adaptation mechanism adjusted by probiotics in the harsh condition of 1.2% bile. The generated new knowledge will also improve the potential therapeutic efficacy of probiotics strains in clinical trials for patients of inflammatory bowel diseases (IBD) and related disorders.
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Affiliation(s)
- Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Haryana, India.
| | - Parul Singh
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Haryana, India
| | - Sudhir K Tomar
- National Collection of Dairy Cultures (NCDC) lab, Dairy Microbiology Division, National Dairy Research Institute, Haryana, India
| | - Ashok K Mohanty
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Haryana, India
| | - Pradip Behare
- National Collection of Dairy Cultures (NCDC) lab, Dairy Microbiology Division, National Dairy Research Institute, Haryana, India.
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25
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Olm MR, Bhattacharya N, Crits-Christoph A, Firek BA, Baker R, Song YS, Morowitz MJ, Banfield JF. Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. SCIENCE ADVANCES 2019; 5:eaax5727. [PMID: 31844663 PMCID: PMC6905865 DOI: 10.1126/sciadv.aax5727] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/30/2019] [Indexed: 05/16/2023]
Abstract
Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids, and growth rates. A machine learning classifier found that samples collected before NEC diagnosis harbored significantly more Klebsiella, bacteria encoding fimbriae, and bacteria encoding secondary metabolite gene clusters related to quorum sensing and bacteriocin production. Notably, replication rates of all bacteria, especially Enterobacteriaceae, were significantly higher 2 days before NEC diagnosis. The findings uncover biomarkers that could lead to early detection of NEC and targets for microbiome-based therapeutics.
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MESH Headings
- Enterobacteriaceae/genetics
- Enterocolitis, Necrotizing/genetics
- Enterocolitis, Necrotizing/microbiology
- Feces/microbiology
- Fimbriae, Bacterial/genetics
- Fimbriae, Bacterial/microbiology
- Gastrointestinal Microbiome/genetics
- Humans
- Infant, Newborn
- Infant, Premature
- Infant, Premature, Diseases/genetics
- Infant, Premature, Diseases/microbiology
- Klebsiella/genetics
- Metagenomics
- Multigene Family/genetics
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Affiliation(s)
- Matthew R. Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | | | - Brian A. Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robyn Baker
- Division of Newborn Medicine, UPMC Magee-Womens Hospital, Pittsburgh, PA, USA
| | - Yun S. Song
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Michael J. Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jillian F. Banfield
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Soman RJ, Swamy MV. A prospective, randomized, double-blind, placebo-controlled, parallel-group study to evaluate the efficacy and safety of SNZ TriBac, a three-strain Bacillus probiotic blend for undiagnosed gastrointestinal discomfort. Int J Colorectal Dis 2019; 34:1971-1978. [PMID: 31686199 DOI: 10.1007/s00384-019-03416-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/24/2019] [Indexed: 02/04/2023]
Abstract
PURPOSE This prospective, randomized, double-blind, placebo-controlled, parallel-group study aimed to determine the efficacy and safety of a multistrain (Bacillus coagulans [SNZ 1969], Bacillus clausii [SNZ 1971], and Bacillus subtilis [SNZ 1972]) probiotic blend (SNZ TriBac) in managing symptoms of gastrointestinal (GI) discomfort in the absence of specific pathologies. METHODS Sixty adults with symptoms of GI discomfort were enrolled (mean age, 34.89 ± 9.95 years) and randomized to receive either SNZ TriBac or placebo. Changes from baseline in Severity of Dyspepsia Assessment (SODA), Gastrointestinal Symptom Rating Scale (GSRS), and Quality of Life (QoL) scales over the course of product use were determined at baseline and on days 30 and 37 as study outcomes. RESULTS On day 30, significant improvement with SNZ TriBac was noted in SODA burping/belching (P = 0.025), bloating (P = 0.048), sour taste (P = 0.025), and total (P = 0.007) scores as well as pain (P = 0.003), non-pain (P = 0.04), and satisfaction (P = 0.03) subscores. Significant improvement with SNZ TriBac was also observed in SODA burping/belching (P = 0.011), sour taste (P = 0.011), and total SODA scores (P < 0.001), and in SODA pain (P = 0.005), non-pain (P = 0.06), and satisfaction (P = 0.004) subscores on day 37. No adverse events were reported. CONCLUSION Significant improvement in final SODA scores and subscores with SNZ TriBac versus placebo indicates improvement in several symptoms of gastrointestinal discomfort. This multistrain probiotic blend was well tolerated and could be an effective option for treatment of GI discomfort. TRIAL REGISTRATION Clinical Trials Registry of India (CTRI/2018/05/014071).
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Affiliation(s)
- Raunak Jay Soman
- Sanzyme Biologics Pvt. Ltd., Plot no. 13, Sagar Society, Road No. 2, Banjara Hills, Hyderabad, 500034, India.
| | - Malisetty Venkat Swamy
- Sanzyme Biologics Pvt. Ltd., Plot no. 13, Sagar Society, Road No. 2, Banjara Hills, Hyderabad, 500034, India
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Björk JR, Dasari M, Grieneisen L, Archie EA. Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research. Am J Primatol 2019; 81:e22970. [PMID: 30941803 PMCID: PMC7193701 DOI: 10.1002/ajp.22970] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/05/2019] [Accepted: 03/07/2019] [Indexed: 12/16/2022]
Abstract
To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross-sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from 1 day to the next, with consequences for host physical functioning, health, and fitness. Hence, the next frontier of microbiome research will require longitudinal perspectives. Here we argue that primatologists, with their traditional focus on tracking the lives of individual animals and familiarity with longitudinal fecal sampling, are well positioned to conduct research at the forefront of gut microbiome dynamics. We begin by reviewing some of the most important ecological processes governing microbiome change over time, and briefly summarizing statistical challenges and approaches to microbiome time series analysis. We then introduce five questions of general interest to microbiome science where we think field-based primate studies are especially well positioned to fill major gaps: (a) Do early life events shape gut microbiome composition in adulthood? (b) Do shifting social landscapes cause gut microbial change? (c) Are gut microbiome phenotypes heritable across variable environments? (d) Does the gut microbiome show signs of host aging? And (e) do gut microbiome composition and dynamics predict host health and fitness? For all of these questions, we highlight areas where primatologists are uniquely positioned to make substantial contributions. We review preliminary evidence, discuss possible study designs, and suggest future directions.
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Affiliation(s)
- Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
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28
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Ezzeldin S, El-Wazir A, Enany S, Muhammad A, Johar D, Osama A, Ahmed E, Shikshaky H, Magdeldin S. Current Understanding of Human Metaproteome Association and Modulation. J Proteome Res 2019; 18:3539-3554. [PMID: 31262181 DOI: 10.1021/acs.jproteome.9b00301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During the last decade, metaproteomics has provided a better understanding and functional characterization of the microbiome. A large body of evidence now reveals interspecies, species of bacteria-host interactions, via the secreted modulatory microbial protein "metaproteome". Although high-throughput state-of-art mass spectrometry has recently empowered metaproteomics, its profile remains unclear, and, most importantly, the exact consequences and underlying mechanism of these protein molecules on the host are insufficiently understood. Here we address the current progress in the study of the human metaproteome, suggesting possible modulation, a metaproteome dysbiotic signature, challenges, and future perspectives.
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Affiliation(s)
- Shahd Ezzeldin
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt
| | - Aya El-Wazir
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine , Suez Canal University , 41522 Ismailia , Egypt.,Center of Excellence of Molecular and Cellular Medicine , Suez Canal University , 41522 Ismailia , Egypt
| | - Shymaa Enany
- Department of Microbiology and Immunology, Faculty of Pharmacy , Suez Canal University , 41522 Ismailia , Egypt
| | - Abdelrahman Muhammad
- Department of Biomedical Engineering , Higher Technological Institute , 44634 Sharqia , Egypt
| | - Dina Johar
- Biomedical Sciences Program, University of Science and Technology , Zewail City of Science and Technology , 12588 Giza , Egypt
| | - Aya Osama
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt
| | - Eman Ahmed
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt.,Department of Pharmacology, Faculty of Veterinary Medicine , Suez Canal University , 41522 Ismailia , Egypt
| | - Hassan Shikshaky
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt
| | - Sameh Magdeldin
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt.,Department of Physiology, Faculty of Veterinary Medicine , Suez Canal University , 41522 Ismailia , Egypt
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29
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Preterm Birth Has Effects on Gut Colonization in Piglets Within the First 4 Weeks of Life. J Pediatr Gastroenterol Nutr 2019; 68:727-733. [PMID: 30633109 DOI: 10.1097/mpg.0000000000002259] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVES Preterm neonates have an immature gastrointestinal tract and show an altered bacterial colonization of the gut. However, it is not clear if such immature gut microbiota (GM) colonization is induced by specific delivery, diet, environment, and/or host factors related to preterm birth. Using piglets as models for infants, we hypothesized that both shortened gestational age (GA) and start of enteral feeding affect GM composition after caesarean delivery and rearing in identical environments. METHODS Caesarean-delivered preterm and term pigs were reared in incubators and fed total parenteral nutrition (TPN) or gradually increasing early enteral feeding (EEF) for 5 days, followed by full enteral feeding with bovine milk until day 26. GM composition was determined by 16S rRNA gene-amplicon sequencing and luminal short-chain fatty acids (SCFAs) by GC-MS. RESULTS Both GA and EEF feeding affected GM composition on day 5, but only the GA effect persisted until day 26. On day 5, Enterobacteriaceae were dominant, with Lachnospiraceae members also being abundant. Enterobacteriaceae still dominated the GM at day 26 but with higher Akkermansia relative abundance in term pigs. Colonic concentrations of acetate and propionate were higher, and formate lower in term pigs, relative to preterm pigs on day 26. CONCLUSIONS Preterm and term piglets, born and reared in similar ways, show differences in GM colonization during the first 4 weeks of life, which may play a role for early and later gut dysfunction resulting from preterm birth.
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30
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Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing. mSphere 2019; 4:4/1/e00529-18. [PMID: 30651402 PMCID: PMC6336080 DOI: 10.1128/msphere.00529-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms. Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail of comprehensive pathogen genome detection from microbiologically complex samples for subsequent forensic analyses remains a challenge. In the context of an investigation of a nosocomial outbreak, we used shotgun metagenomic sequencing of a human fecal sample and a neural network algorithm based on tetranucleotide frequency profiling to reconstruct microbial genomes and tested the same approach using rectal swabs from a second patient. The approach rapidly and readily detected the genome of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in the patient fecal specimen and in the rectal swab sample, achieving a level of strain resolution that was sufficient for confident transmission inference during a highly clonal outbreak. The analysis also detected previously unrecognized colonization of the patient by vancomycin-resistant Enterococcus faecium, another multidrug-resistant bacterium. IMPORTANCE The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms.
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Neu J, Pammi M. Necrotizing enterocolitis: The intestinal microbiome, metabolome and inflammatory mediators. Semin Fetal Neonatal Med 2018; 23:400-405. [PMID: 30172660 DOI: 10.1016/j.siny.2018.08.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Necrotizing enterocolitis (NEC) is a disease of preterm infants and associated with significant mortality and morbidity. Although the pathogenesis of NEC is not clear, microbial dysbiosis, with a bloom of the phylum Proteobacteria, has been reported. Antibiotics and the use of H2 blockers, which affect the gut microbiome, are associated with increased incidence of NEC. In association with dysbiosis, inflammatory processes are upregulated with increased Toll-like receptor signaling, leading to translocation of nuclear factor kappa-β, a transcription factor that induces transcription of various pro-inflammatory cytokines and chemokines. Microbial metabolites, short chain fatty acids including acetate and butyrate, may modulate immunity, inflammation, intestinal integrity and regulate transcription by epigenetic mechanisms. Evaluation of microbiome and metabolome may provide biomarkers for early diagnosis of NEC and microbial therapeutic approaches to correct microbial dysbiosis.
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Affiliation(s)
- Josef Neu
- Section of Neonatology, Department of Pediatrics, University of Florida, Gainesville, FL, USA.
| | - Mohan Pammi
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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32
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Berry D, Loy A. Stable-Isotope Probing of Human and Animal Microbiome Function. Trends Microbiol 2018; 26:999-1007. [PMID: 30001854 PMCID: PMC6249988 DOI: 10.1016/j.tim.2018.06.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/10/2018] [Accepted: 06/20/2018] [Indexed: 12/30/2022]
Abstract
Humans and animals host diverse communities of microorganisms important to their physiology and health. Despite extensive sequencing-based characterization of host-associated microbiomes, there remains a dramatic lack of understanding of microbial functions. Stable-isotope probing (SIP) is a powerful strategy to elucidate the ecophysiology of microorganisms in complex host-associated microbiotas. Here, we suggest that SIP methodologies should be more frequently exploited as part of a holistic functional microbiomics approach. We provide examples of how SIP has been used to study host-associated microbes in vivo and ex vivo. We highlight recent developments in SIP technologies and discuss future directions that will facilitate deeper insights into the function of human and animal microbiomes.
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Affiliation(s)
- David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Althanstrasse 14, Vienna, Austria.
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Althanstrasse 14, Vienna, Austria
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33
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Bering SB. Human Milk Oligosaccharides to Prevent Gut Dysfunction and Necrotizing Enterocolitis in Preterm Neonates. Nutrients 2018; 10:nu10101461. [PMID: 30297668 PMCID: PMC6213229 DOI: 10.3390/nu10101461] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/25/2022] Open
Abstract
This review focuses on the evidence for health benefits of human milk oligosaccharides (HMOs) for preterm infants to stimulate gut adaptation and reduce the incidence of necrotizing enterocolitis (NEC) in early life. The health benefits of breastfeeding are partly explained by the abundant HMOs that serve as prebiotics and immunomodulators. Gut immaturity in preterm infants leads to difficulties in tolerating enteral feeding and bacterial colonization and a high sensitivity to NEC, particularly when breast milk is insufficient. Due to the immaturity of the preterm infants, their response to HMOs could be different from that in term infants. The concentration of HMOs in human milk is highly variable and there is no evidence to support a specifically adapted high concentration in preterm milk. Further, the gut microbiota is not only different but also highly variable after preterm birth. Studies in pigs as models for preterm infants indicate that HMO supplementation to formula does not mature the gut or prevent NEC during the first weeks after preterm birth and the effects may depend on a certain stage of gut maturity. Supplemented HMOs may become more important for gut protection in the preterm infants when the gut has reached a more mature phase.
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Affiliation(s)
- Stine Brandt Bering
- Comparative Paediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1958 Frederiksberg C, Denmark.
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34
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Lee JZ, Everroad RC, Karaoz U, Detweiler AM, Pett-Ridge J, Weber PK, Prufert-Bebout L, Bebout BM. Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat. PLoS One 2018; 13:e0202792. [PMID: 30204767 PMCID: PMC6133358 DOI: 10.1371/journal.pone.0202792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 08/09/2018] [Indexed: 11/19/2022] Open
Abstract
Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.
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Affiliation(s)
- Jackson Z. Lee
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
- Bay Area Environmental Research Institute, Petaluma, CA, United States of America
- * E-mail:
| | - R. Craig Everroad
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Angela M. Detweiler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
- Bay Area Environmental Research Institute, Petaluma, CA, United States of America
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Leslie Prufert-Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
| | - Brad M. Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
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Ho TTB, Groer MW, Kane B, Yee AL, Torres BA, Gilbert JA, Maheshwari A. Dichotomous development of the gut microbiome in preterm infants. MICROBIOME 2018; 6:157. [PMID: 30208950 PMCID: PMC6136210 DOI: 10.1186/s40168-018-0547-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 09/03/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associated Gammaproteobacteria in very low birth weight (VLBW) infants. Fecal microbiome was characterized at ≤ 2 weeks and during the 3rd and 4th weeks after birth, by 16S rRNA amplicon sequencing. Maternal and infant clinical characteristics were extracted from electronic medical records. Data were analyzed by linear mixed modeling and linear regression. RESULTS Clinical data and fecal microbiome profiles of 45 VLBW infants (gestational age 27.9 ± 2.2 weeks; birth weight 1126 ± 208 g) were studied. Three stool samples were analyzed for each infant at mean postnatal ages of 9.9 ± 3, 20.7 ± 4.1, and 29.4 ± 4.9 days. The average relative abundance of Gammaproteobacteria was 42.5% (0-90%) at ≤ 2 weeks, 69.7% (29.9-86.9%) in the 3rd, and 75.5% (54.5-86%) in the 4th week (p < 0.001). Hierarchical and K-means clustering identified two distinct subgroups: cluster 1 started with comparatively low abundance that increased with time, whereas cluster 2 began with a greater abundance at ≤ 2 weeks (p < 0.001) that decreased over time. Both groups resembled each other by the 3rd week. Single variants of Klebsiella and Staphylococcus described variance in community structure between clusters and were shared between all infants, suggesting a common, hospital-derived source. Fecal Gammaproteobacteria was positively associated with vaginal delivery and antenatal steroids. CONCLUSIONS We detected a dichotomy in gut microbiome assembly in preterm infants: some preterm infants started with low relative gammaproteobacterial abundance in stool that increased as a function of postnatal age, whereas others began with and maintained high abundance. Vaginal birth and antenatal steroids were identified as predictors of Gammaproteobacteria abundance in the early (≤ 2 weeks) and later (3rd and 4th weeks) stool samples, respectively. These findings are important in understanding the development of the gut microbiome in premature infants.
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Affiliation(s)
- Thao T. B. Ho
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL USA
| | - Maureen W. Groer
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL USA
- College of Nursing, University of South Florida, Tampa, FL USA
| | - Bradley Kane
- College of Nursing, University of South Florida, Tampa, FL USA
| | - Alyson L. Yee
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL USA
- Microbiome Center, University of Chicago, Chicago, IL USA
- Department of Surgery, University of Chicago, Chicago, IL USA
| | - Benjamin A. Torres
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL USA
| | - Jack A. Gilbert
- Microbiome Center, University of Chicago, Chicago, IL USA
- Department of Surgery, University of Chicago, Chicago, IL USA
- Argonne National Laboratory, Chicago, IL USA
| | - Akhil Maheshwari
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL USA
- Department of Pediatrics, Johns Hopkins University, 1800 Orleans St, JHCC 8530, Baltimore, MD 21287 USA
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Corfield AP. The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human. Microorganisms 2018; 6:microorganisms6030078. [PMID: 30072673 PMCID: PMC6163557 DOI: 10.3390/microorganisms6030078] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/25/2018] [Accepted: 07/30/2018] [Indexed: 02/07/2023] Open
Abstract
Glycoproteins are major players in the mucus protective barrier in the gastrointestinal and other mucosal surfaces. In particular the mucus glycoproteins, or mucins, are responsible for the protective gel barrier. They are characterized by their high carbohydrate content, present in their variable number, tandem repeat domains. Throughout evolution the mucins have been maintained as integral components of the mucosal barrier, emphasizing their essential biological status. The glycosylation of the mucins is achieved through a series of biosynthetic pathways processes, which generate the wide range of glycans found in these molecules. Thus mucins are decorated with molecules having information in the form of a glycocode. The enteric microbiota interacts with the mucosal mucus barrier in a variety of ways in order to fulfill its many normal processes. How bacteria read the glycocode and link to normal and pathological processes is outlined in the review.
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Affiliation(s)
- Anthony P Corfield
- Mucin Research Group, School of Clinical Sciences, Bristol Royal Infirmary, Level 7, Marlborough Street, Bristol BS2 8HW, UK.
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Relationships Between Perinatal Interventions, Maternal-Infant Microbiomes, and Neonatal Outcomes. Clin Perinatol 2018; 45:339-355. [PMID: 29747892 DOI: 10.1016/j.clp.2018.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The human microbiome acquires its vastness and diversity over a relatively short time period during development. Much is unknown, however, about the precise prenatal versus postnatal timing or its sources and determinants. Given early evidence of a role for influences during pregnancy and early neonatal and infant life on the microbiome and subsequent metabolic health, research investigating the development and shaping of the microbiome in the fetus and neonate is an important arena for study. This article reviews the relevant available literature and future questions on what shapes the microbiome during early development and mechanisms for doing so.
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Kumar J, Verma MK, Kumar T, Gupta S, Pandey R, Yadav M, Chauhan NS. S9A Serine Protease Engender Antigenic Gluten Catabolic Competence to the Human Gut Microbe. Indian J Microbiol 2018; 58:294-300. [PMID: 30013273 DOI: 10.1007/s12088-018-0732-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 04/22/2018] [Indexed: 12/13/2022] Open
Abstract
The human gut microbiome has a significant role in host physiology; however its role in gluten catabolism is debatable. Present study explores the role of human gut microbes in gluten catabolism and a native human gut microbe Cellulomonas sp. HM71 was identified. SSU rDNA analysis has described human gut microbiome structure and also confirmed the permanent residentship of Cellulomonas sp. HM71. Catabolic potential of Cellulomonas sp. HM71 to cleave antigenic gluten peptides indicates presence of candidate gene encoding biocatalytic machinery. Genome analysis has identified the presence of gene encoding S9A serine protease family-prolyl endopeptidase, with Ser591, Asp664 and His685 signature residues. Cellulomonas sp. HM71 prolyl endopeptidase activity was found optimal at pH 7.0 and 37 °C with a KM of 35.53 μmol and specifically cleaves at proline residue. Current study describes the gluten catabolism potential of Cellulomonas sp. HM71 depicting possible role of human gut microbes in gluten catabolism to confer resistance mechanisms for the onset of celiac diseases in populations with gluten diet.
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Affiliation(s)
- Jitendra Kumar
- 1Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Manoj Kumar Verma
- 1Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Tarun Kumar
- 1Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Shashank Gupta
- 1Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Rajesh Pandey
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | - Monika Yadav
- 1Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Nar Singh Chauhan
- 1Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana 124001 India
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Ahmed V, Verma MK, Gupta S, Mandhan V, Chauhan NS. Metagenomic Profiling of Soil Microbes to Mine Salt Stress Tolerance Genes. Front Microbiol 2018; 9:159. [PMID: 29472909 PMCID: PMC5809485 DOI: 10.3389/fmicb.2018.00159] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/23/2018] [Indexed: 12/11/2022] Open
Abstract
Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation. 16S rRNA gene sequence analysis has indicated the dominance of halophilic/halotolerant phylotypes affiliated to Proteobacteria, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Acidobacteria. A functional metagenomics approach led to the identification of osmotolerant clones SSR1, SSR4, SSR6, SSR2 harboring BCAA_ABCtp, GSDH, STK_Pknb, and duf3445 genes. Furthermore, transposon mutagenesis, genetic, physiological and functional studies in close association has confirmed the role of these genes in osmotolerance. Enhancement in host osmotolerance possibly though the cytosolic accumulation of amino acids, reducing equivalents and osmolytes involving BCAA-ABCtp, GSDH, and STKc_PknB. Decoding of the genetic elements prevalent within these microbes can be exploited either as such for ameliorating soils or their genetically modified forms can assist crops to resist and survive in saline environment.
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Affiliation(s)
- Vasim Ahmed
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Manoj K Verma
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Shashank Gupta
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Vibha Mandhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Nar S Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
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Xin X, He J, Qiu W. Volatile fatty acid augmentation and microbial community responses in anaerobic co-fermentation process of waste-activated sludge mixed with corn stalk and livestock manure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:4846-4857. [PMID: 29199365 DOI: 10.1007/s11356-017-0834-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/23/2017] [Indexed: 06/07/2023]
Abstract
This study investigated the acidogenic and microbiological perspectives in the anaerobic co-fermentation of waste-activated sludge (WAS) mixed with corn stalk (CS) and pig manure (PM). The volatile fatty acids (VFAs) increased dramatically to over 5000 mg COD/L accumulation just within 4-5 days with the feedstock carbon to nitrogen (C/N) ratio regulation of 20/1. The CS and PM addition enhanced the compressibility of fermentation residuals by increasing the particle distribution spread index (DSI). Moreover, the external carbon addition conduced to bacterial consortia diversity rising and uneven population distribution in the co-fermentation, which contributed to VFAs accumulation potentially. The organic loading rate (OLR) correlated with bacterial community closely at the early stage (days 1-5), while the oxidation-reduction potential (ORP) and pH played more important roles on bacterial consortia at the terminal stage (days 6-10). The C/N ratio adjustment by CS and PM and proper optimizations of OLR, pH, and ORP at various running stages facilitated VFA accumulation during the co-fermentation operation.
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Affiliation(s)
- Xiaodong Xin
- School of Municipal and Environmental Engineering, Harbin Institute of Technology (HIT), Harbin, 150090, China
| | - Junguo He
- School of Municipal and Environmental Engineering, Harbin Institute of Technology (HIT), Harbin, 150090, China
| | - Wei Qiu
- School of Municipal and Environmental Engineering, Harbin Institute of Technology (HIT), Harbin, 150090, China.
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, China.
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Xin X, He J, Li L, Qiu W. Enzymes catalyzing pre-hydrolysis facilitated the anaerobic fermentation of waste activated sludge with acidogenic and microbiological perspectives. BIORESOURCE TECHNOLOGY 2018; 250:69-78. [PMID: 29153652 DOI: 10.1016/j.biortech.2017.09.211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/28/2017] [Accepted: 09/30/2017] [Indexed: 06/07/2023]
Abstract
This study investigated acidogenic and microbiological perspectives in the anaerobic fermentation (AF) of waste activated sludge (WAS) pre-hydrolyzed by enzymes catalysis. The enzymes catalysis boosted WAS biodegradability dramatically with nearly 8500 mg/L soluble chemical oxygen demand (SCOD) increase just within 4 h. The volatile fatty acids (VFAs) in the acidogenesis were accumulated effectively with over 3200 mg COD/L in 12 d, which reached 0.687 kWh/kg VSS electricity conversion efficiency (2.5 times higher than the control test). The fermentation process favored the compression of fermentative sludge with the distribution spread index (DSI) rising. The core populations of bacteria and archaea shifting enlarged the dissimilarity of communities at different fermentation stages. Increase of community diversity contributed to VFAs accumulation stability. Moreover, the intermediate bacterial community evenness favored VFAs accumulation potentially. The enzymes catalysis might be a promising solution for strengthening VFAs accumulation in the WAS fermentation with boosting the electricity conversion potential.
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Affiliation(s)
- Xiaodong Xin
- School of Municipal and Environmental Engineering, Harbin Institute of Technology (HIT), Harbin 150090, China
| | - Junguo He
- School of Municipal and Environmental Engineering, Harbin Institute of Technology (HIT), Harbin 150090, China
| | - Lin Li
- School of Municipal and Environmental Engineering, Harbin Institute of Technology (HIT), Harbin 150090, China
| | - Wei Qiu
- School of Municipal and Environmental Engineering, Harbin Institute of Technology (HIT), Harbin 150090, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, China.
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42
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Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes. Sci Rep 2018; 8:1397. [PMID: 29362424 PMCID: PMC5780487 DOI: 10.1038/s41598-018-19862-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/09/2018] [Indexed: 01/08/2023] Open
Abstract
Every niche in the biosphere is touched by the seemingly endless capacity of microbes to transform the world around them by adapting swiftly and flexibly to the environmental changes, likewise the gastrointestinal tract is no exception. The ability to cope with rapid changes in external osmolarity is an important aspect of gut microbes for their survival and colonization. Identification of these survival mechanisms is a pivotal step towards understanding genomic suitability of a symbiont for successful human gut colonization. Here we highlight our recent work applying functional metagenomics to study human gut microbiome to identify candidate genes responsible for the salt stress tolerance. A plasmid borne metagenomic library of Bacteroidetes enriched human fecal metagenomic DNA led to identification of unique salt osmotolerance clones SR6 and SR7. Subsequent gene analysis combined with functional studies revealed that TLSRP1 within pSR7 and TMSRP1 and ABCTPP of pSR6 are the active loci responsible for osmotolerance through an energy dependent mechanism. Our study elucidates the novel genetic machinery involved in bestowing osmotolerance in Prevotella and Bacteroidetes, the predominant microbial groups in a North Indian population. This study unravels an alternative method for imparting ionic stress tolerance, which may be prevalent in the human gut microbiome.
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43
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Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands. mSystems 2018; 3:mSystems00192-17. [PMID: 29359197 PMCID: PMC5768791 DOI: 10.1128/msystems.00192-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 12/15/2017] [Indexed: 12/18/2022] Open
Abstract
Bacteria live all around us, and we are constantly exposed to them during our everyday lives. Modern standards of hygiene aim to limit exposure to fecal bacteria, and yet bacteria rapidly colonize the gut in early life and following antibacterial treatment. Exposures to fecal and oral microbes provide risk of disease, but are also necessary since commensal microbes play important roles in health. This work establishes that bacteria of both fecal and oral origins are commonly found on hands. It also establishes that the uniqueness of fecal and oral bacterial communities across people can allow for determination of the likely individual from whom the fecal and oral bacteria came. These techniques allow for understanding the hands as a vector for microbial transmission within families and across populations, which has important implications for public health. Modern hygienic practices are applied to avoid exposure to pathogens that spread via fecal-oral transmission. Despite this, the gastrointestinal tract is quickly colonized by fecal microbes. The hands are an important vector for the transmission of microbes, but the frequency at which fecal and oral microbes exist on hands and the source of those microbes have not been extensively described. Using data from a previous study that characterized the fecal, oral, and skin microbiota from 73 families, we found a significant incidence of fecal and oral microbes on hands. Of palms, 48.9% had fecal signal and 67.2% had oral signal. Fecal, oral, and forehead microbes were tracked to family members and an individual’s own palms far more often than to unrelated individuals and showed relationships with age, gender, and parental status. For instance, oral microbes that were specifically sourced to the same individual (oneself) were most common on infant palms; mothers had more infant-child-sourced and oral-sourced microbes on their palms than nonparents. Fecal microbes on palms more often sourced to members of the family than unrelated individuals, but more often to other members of the family than oneself. This study supports that the hands are an important vector for the transfer of fecal and oral microbes within families. IMPORTANCE Bacteria live all around us, and we are constantly exposed to them during our everyday lives. Modern standards of hygiene aim to limit exposure to fecal bacteria, and yet bacteria rapidly colonize the gut in early life and following antibacterial treatment. Exposures to fecal and oral microbes provide risk of disease, but are also necessary since commensal microbes play important roles in health. This work establishes that bacteria of both fecal and oral origins are commonly found on hands. It also establishes that the uniqueness of fecal and oral bacterial communities across people can allow for determination of the likely individual from whom the fecal and oral bacteria came. These techniques allow for understanding the hands as a vector for microbial transmission within families and across populations, which has important implications for public health.
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44
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Peering into the Genetic Makeup of Natural Microbial Populations Using Metagenomics. POPULATION GENOMICS: MICROORGANISMS 2018. [DOI: 10.1007/13836_2018_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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45
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Ximenez C, Torres J. Development of Microbiota in Infants and its Role in Maturation of Gut Mucosa and Immune System. Arch Med Res 2017; 48:666-680. [PMID: 29198451 DOI: 10.1016/j.arcmed.2017.11.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/15/2017] [Indexed: 12/24/2022]
Abstract
Dysbiosis of the gut microbiota has been associated with increasing numbers of diseases, including obesity, diabetes, inflammatory bowel disease, asthma, allergy, cancer and even neurologic or behavioral disorders. The other side of the coin is that a healthy microbiota leads to a healthy human development, to a mature and well trained immune system and to an efficient metabolic machinery. What we have learned in adults is in the end the result of a good start, a programmed, healthy development of the microbiota that must occur in the early years of life, probably even starting during the fetal stage. This review aims to present and discuss reports that helps us understand what we have learned of the development of microbiota during the early times of life, from pregnancy to delivery to the early years after birth. The impact of the establishment of "healthy" bacterial communities on human surfaces in the maturation of epithelia, immune system and metabolism will also be discussed. The right process of maturation of the bacterial communities that establish a symbiosis with human surfaces depends on a number of environmental, genetic and temporal factors that need to be understand in order to have tools to monitor a healthy development and eventually intervene to correct undesired courses.
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Affiliation(s)
- Cecilia Ximenez
- Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, Unidad Médica de Alta Especialidad, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Centro Médico Nacional Siglo XXI, Ciudad de México, México.
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Biswas R, Gao S, Cultraro CM, Maity TK, Venugopalan A, Abdullaev Z, Shaytan AK, Carter CA, Thomas A, Rajan A, Song Y, Pitts S, Chen K, Bass S, Boland J, Hanada KI, Chen J, Meltzer PS, Panchenko AR, Yang JC, Pack S, Giaccone G, Schrump DS, Khan J, Guha U. Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response. Cold Spring Harb Mol Case Stud 2017; 2:a001263. [PMID: 27900369 PMCID: PMC5111000 DOI: 10.1101/mcs.a001263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We used next-generation sequencing to identify somatic alterations in multiple metastatic sites from an “exceptional responder” lung adenocarcinoma patient during his 7-yr course of ERBB2-directed therapies. The degree of heterogeneity was unprecedented, with ∼1% similarity between somatic alterations of the lung and lymph nodes. One novel translocation, PLAG1-ACTA2, present in both sites, up-regulated ACTA2 expression. ERBB2, the predominant driver oncogene, was amplified in both sites, more pronounced in the lung, and harbored an L869R mutation in the lymph node. Functional studies showed increased proliferation, migration, metastasis, and resistance to ERBB2-directed therapy because of L869R mutation and increased migration because of ACTA2 overexpression. Within the lung, a nonfunctional CDK12, due to a novel G879V mutation, correlated with down-regulation of DNA damage response genes, causing genomic instability, and sensitivity to chemotherapy. We propose a model whereby a subclone metastasized early from the primary site and evolved independently in lymph nodes.
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Affiliation(s)
- Romi Biswas
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Shaojian Gao
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Constance M Cultraro
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Tapan K Maity
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Abhilash Venugopalan
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Corey A Carter
- Walter Reed National Military Medical Center, Bethesda, Maryland 20889, USA
| | - Anish Thomas
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Arun Rajan
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Young Song
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Stephanie Pitts
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Kevin Chen
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Sara Bass
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland 20848, USA
| | - Joseph Boland
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, Maryland 20848, USA
| | - Ken-Ichi Hanada
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Jinqiu Chen
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - James C Yang
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Svetlana Pack
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Giuseppe Giaccone
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, D.C. 20057, USA
| | - David S Schrump
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Udayan Guha
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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Tagini F, Greub G. Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review. Eur J Clin Microbiol Infect Dis 2017; 36:2007-2020. [PMID: 28639162 PMCID: PMC5653721 DOI: 10.1007/s10096-017-3024-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 12/11/2022]
Abstract
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.
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Affiliation(s)
- F Tagini
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland
| | - G Greub
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland.
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Papizadeh M, Rohani M, Nahrevanian H, Javadi A, Pourshafie MR. Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends. Microb Pathog 2017; 111:118-131. [DOI: 10.1016/j.micpath.2017.08.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/12/2017] [Accepted: 08/16/2017] [Indexed: 02/07/2023]
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Abstract
Purpose of Review Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. Recent Findings Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species. The scale and scope of species sequenced is rapidly expanding, leveraging technological advances to assemble and annotate genomes with higher precision. By using iteratively improved reference assemblies or those generated de novo for new species, recent studies have compared the sequence of isolates representing populations or clinical cohorts. Whole genome approaches provide the resolution necessary for comparison of closely related isolates, for example, in the analysis of outbreaks or sampled across time within a single host. Summary Genomic analysis of fungal pathogens has enabled both basic research and diagnostic studies. The increased scale of sequencing can be applied across populations, and new metagenomic methods allow direct analysis of complex samples.
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The Human Gut Phage Community and Its Implications for Health and Disease. Viruses 2017; 9:v9060141. [PMID: 28594392 PMCID: PMC5490818 DOI: 10.3390/v9060141] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/23/2017] [Accepted: 06/02/2017] [Indexed: 12/23/2022] Open
Abstract
In this review, we assess our current understanding of the role of bacteriophages infecting the human gut bacterial community in health and disease. In general, bacteriophages contribute to the structure of their microbial communities by driving host and viral diversification, bacterial evolution, and by expanding the functional diversity of ecosystems. Gut bacteriophages are an ensemble of unique and shared phages in individuals, which encompass temperate phages found predominately as prophage in gut bacteria (prophage reservoir) and lytic phages. In healthy individuals, only a small fraction of the prophage reservoir is activated and found as extracellular phages. Phage community dysbiosis is characterized by a shift in the activated prophage community or an increase of lytic phages, and has been correlated with disease, suggesting that a proper balance between lysis and lysogeny is needed to maintain health. Consequently, the concept of microbial dysbiosis might be extended to the phage component of the microbiome as well. Understanding the dynamics and mechanisms to restore balance after dysbiosis is an active area of research. The use of phage transplants to re-establish health suggests that phages can be used as disease treatment. Such advances represent milestones in our understanding of gut phages in human health and should fuel research on their role in health and disease.
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