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Graham AS, Patel F, Little F, van der Kouwe A, Kaba M, Holmes MJ. Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.591068. [PMID: 38798511 PMCID: PMC11118338 DOI: 10.1101/2024.05.13.591068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Introduction Short-read amplicon sequencing studies have typically focused on 1-2 variable regions of the 16S rRNA gene. Species-level resolution is limited in these studies, as each variable region enables the characterisation of a different subsection of the microbiome. Although long-read sequencing techniques take advantage of all 9 variable regions by sequencing the entire 16S rRNA gene, they are substantially more expensive. This work assessed the feasibility of accurate species-level resolution and reproducibility using a relatively new sequencing kit and bioinformatics pipeline developed for short-read sequencing of multiple variable regions of the 16S rRNA gene. In addition, we evaluated the potential impact of different sample collection methods on our outcomes. Methods Using xGen™ 16S Amplicon Panel v2 kits, sequencing of all 9 variable regions of the 16S rRNA gene was carried out on an Illumina MiSeq platform. Mock cells and mock DNA for 8 bacterial species were included as extraction and sequencing controls respectively. Within-run and between-run replicate samples, and pairs of stool and rectal swabs collected at 0-5 weeks from the same participants, were incorporated. Observed relative abundances of each species were compared to theoretical abundances provided by ZymoBIOMICS. Paired Wilcoxon rank sum tests and distance-based intraclass correlation coefficients were used to statistically compare alpha and beta diversity measures, respectively, for pairs of replicates and stool/rectal swab sample pairs. Results Using multiple variable regions of the 16S ribosomal Ribonucleic Acid (rRNA) gene, we found that we could accurately identify taxa to a species level and obtain highly reproducible results at a species level. Yet, the microbial profiles of stool and rectal swab sample pairs differed substantially despite being collected concurrently from the same infants. Conclusion This protocol provides an effective means for studying infant gut microbial samples at a species level. However, sample collection approaches need to be accounted for in any downstream analysis.
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Affiliation(s)
- Amy S Graham
- Imaging Sciences, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Human Biology, Division of Biomedical Engineering, University of Cape Town, Cape Town, South Africa
| | - Fadheela Patel
- Department of Pathology, Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Francesca Little
- Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
| | - Andre van der Kouwe
- Athinoula A. Martinos Centre for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Mamadou Kaba
- Department of Pathology, Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Martha J Holmes
- Imaging Sciences, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Human Biology, Division of Biomedical Engineering, University of Cape Town, Cape Town, South Africa
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- ImageTech, Simon Fraser University, Surrey, BC, Canada
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Vilela C, Araújo B, Soares-Guedes C, Caridade-Silva R, Martins-Macedo J, Teixeira C, Gomes ED, Prudêncio C, Vieira M, Teixeira FG. From the Gut to the Brain: Is Microbiota a New Paradigm in Parkinson's Disease Treatment? Cells 2024; 13:770. [PMID: 38727306 PMCID: PMC11083070 DOI: 10.3390/cells13090770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Parkinson's disease (PD) is recognized as the second most prevalent primary chronic neurodegenerative disorder of the central nervous system. Clinically, PD is characterized as a movement disorder, exhibiting an incidence and mortality rate that is increasing faster than any other neurological condition. In recent years, there has been a growing interest concerning the role of the gut microbiota in the etiology and pathophysiology of PD. The establishment of a brain-gut microbiota axis is now real, with evidence denoting a bidirectional communication between the brain and the gut microbiota through metabolic, immune, neuronal, and endocrine mechanisms and pathways. Among these, the vagus nerve represents the most direct form of communication between the brain and the gut. Given the potential interactions between bacteria and drugs, it has been observed that the therapies for PD can have an impact on the composition of the microbiota. Therefore, in the scope of the present review, we will discuss the current understanding of gut microbiota on PD and whether this may be a new paradigm for treating this devastating disease.
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Affiliation(s)
- Cristiana Vilela
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Bruna Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (B.A.); (J.M.-M.)
- ICVS/3B’s Associate Lab, PT Government Associated Lab, 4710-057/4805-017 Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Carla Soares-Guedes
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Rita Caridade-Silva
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Joana Martins-Macedo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (B.A.); (J.M.-M.)
- ICVS/3B’s Associate Lab, PT Government Associated Lab, 4710-057/4805-017 Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Catarina Teixeira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
| | - Eduardo D. Gomes
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Cristina Prudêncio
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Mónica Vieira
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida 400, 4200-072 Porto, Portugal; (C.V.); (C.S.-G.); (E.D.G.); (C.P.); (M.V.)
| | - Fábio G. Teixeira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (B.A.); (J.M.-M.)
- ICVS/3B’s Associate Lab, PT Government Associated Lab, 4710-057/4805-017 Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (R.C.-S.); (C.T.)
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3
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Spatafora G, Li Y, He X, Cowan A, Tanner ACR. The Evolving Microbiome of Dental Caries. Microorganisms 2024; 12:121. [PMID: 38257948 PMCID: PMC10819217 DOI: 10.3390/microorganisms12010121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Dental caries is a significant oral and public health problem worldwide, especially in low-income populations. The risk of dental caries increases with frequent intake of dietary carbohydrates, including sugars, leading to increased acidity and disruption of the symbiotic diverse and complex microbial community of health. Excess acid production leads to a dysbiotic shift in the bacterial biofilm composition, demineralization of tooth structure, and cavities. Highly acidic and acid-tolerant species associated with caries include Streptococcus mutans, Lactobacillus, Actinomyces, Bifidobacterium, and Scardovia species. The differences in microbiotas depend on tooth site, extent of carious lesions, and rate of disease progression. Metagenomics and metatranscriptomics not only reveal the structure and genetic potential of the caries-associated microbiome, but, more importantly, capture the genetic makeup of the metabolically active microbiome in lesion sites. Due to its multifactorial nature, caries has been difficult to prevent. The use of topical fluoride has had a significant impact on reducing caries in clinical settings, but the approach is costly; the results are less sustainable for high-caries-risk individuals, especially children. Developing treatment regimens that specifically target S. mutans and other acidogenic bacteria, such as using nanoparticles, show promise in altering the cariogenic microbiome, thereby combatting the disease.
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Affiliation(s)
- Grace Spatafora
- Biology and Program in Molecular Biology and Biochemistry, Middlebury College, Middlebury, VT 05753, USA
| | - Yihong Li
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY 14853, USA;
| | - Xuesong He
- ADA-Forsyth Institute, Cambridge, MA 02142, USA;
| | - Annie Cowan
- The Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
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Adrian MA, Ayati BP, Mangalam AK. A mathematical model of Bacteroides thetaiotaomicron, Methanobrevibacter smithii, and Eubacterium rectale interactions in the human gut. Sci Rep 2023; 13:21192. [PMID: 38040895 PMCID: PMC10692322 DOI: 10.1038/s41598-023-48524-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
The human gut microbiota is a complex ecosystem that affects a range of human physiology. In order to explore the dynamics of the human gut microbiota, we used a system of ordinary differential equations to model mathematically the biomass of three microorganism populations: Bacteroides thetaiotaomicron, Eubacterium rectale, and Methanobrevibacter smithii. Additionally, we modeled the concentrations of relevant nutrients necessary to sustain these populations over time. Our model highlights the interactions and the competition among these three species. These three microorganisms were specifically chosen due to the system's end product, butyrate, which is a short chain fatty acid that aids in developing and maintaining the intestinal barrier in the human gut. The basis of our mathematical model assumes the gut is structured such that bacteria and nutrients exit the gut at a rate proportional to its volume, the rate of volumetric flow, and the biomass or concentration of the particular population or nutrient. We performed global sensitivity analyses using Sobol' sensitivities to estimate the relative importance of model parameters on simulation results.
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Affiliation(s)
- Melissa A Adrian
- Department of Mathematics, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Statistics, University of Chicago, Chicago, IL, 60637, USA.
| | - Bruce P Ayati
- Department of Mathematics, University of Iowa, Iowa City, IA, 52242, USA
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Mousavinasab F, Karimi R, Taheri S, Ahmadvand F, Sanaaee S, Najafi S, Halvaii MS, Haghgoo A, Zamany M, Majidpoor J, Khosravifar M, Baniasadi M, Talebi M, Movafagh A, Aghaei-Zarch SM, Khorram N, Farnia P, Kalhor K. Microbiome modulation in inflammatory diseases: Progress to microbiome genetic engineering. Cancer Cell Int 2023; 23:271. [PMID: 37951913 PMCID: PMC10640760 DOI: 10.1186/s12935-023-03095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 10/07/2023] [Indexed: 11/14/2023] Open
Abstract
Recent developments in sequencing technology and analytical approaches have allowed researchers to show that the healthy gut microbiome is very varied and capable of performing a wide range of tasks. The importance of gut microbiota in controlling immunological, neurological, and endocrine function is becoming well-recognized. Thereby, numerous inflammatory diseases, including those that impact the gastrointestinal system, as well as less obvious ones, including Rheumatoid arthritis (RA), cancer, gestational diabetes (GD), type 1 diabetes (T1D), and type 2 diabetes (T2D), have been linked to dysbiotic gut microbiota. Microbiome engineering is a rapidly evolving frontier for solutions to improve human health. Microbiome engineering seeks to improve the function of an ecosystem by manipulating the composition of microbes. Thereby, generating potential therapies against metabolic, inflammatory, and immunological diseases will be possible through microbiome engineering. This essay first provides an overview of the traditional technological instruments that might be used for microbiome engineering, such as Fecal Microbiota Transplantation (FMT), prebiotics, and probiotics. Moreover, we will also discuss experimental genetic methods such as Metagenomic Alteration of Gut microbiome by In situ Conjugation (MAGIC), Bacteriophage, and Conjugative plasmids in manipulating intestinal microbiota.
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Affiliation(s)
| | - Ronika Karimi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sima Taheri
- Department of Microbiology, Shahr Qods Branch, Islamic Azad University, Tehran, Iran
| | | | - Saameh Sanaaee
- Department of New Science, Faculty of Cellular and Molecular biology, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Alireza Haghgoo
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Marzieh Zamany
- Shahid Akbarabadi Clinical Research Development Unit, Iran University of medical Science, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Mina Khosravifar
- Institute of Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mohammad Baniasadi
- Department of Basic Sciences, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Mehrdad Talebi
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Abolfazl Movafagh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Nastaran Khorram
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran.
| | - Poopak Farnia
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Kambiz Kalhor
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, USA
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6
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Georgescu D, Ancusa OE, Azoulay D, Lascu A, Ionita I, Calamar-Popovici D, Ionita M, Rosca CI, Brează GM, Reisz D, Lighezan D. Portal Vein Thrombosis in Patients with Liver Cirrhosis: What Went Wrong? Int J Gen Med 2023; 16:3889-3906. [PMID: 37662503 PMCID: PMC10473422 DOI: 10.2147/ijgm.s413438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
Purpose This study aimed to explore inflammatory biomarkers, stool's functional bacterial groups and their possible link to portal vein thrombosis (PVT) in patients with liver cirrhosis (LC). Materials and Methods An observational study of 300 participants: 200 inhospital cirrhotic patients, who met inclusion criteria, equally assigned into two groups, based on the presence or absence of PVT and 100 healthy controls was carried out. Results The PVT group displayed significant differences related to older age, cigarettes smoking history, emergency admission, higher Child-Pugh score, metabolic related disorders and nonalcoholic fatty liver disease, as well as non-obstructive aspects, with chronic thrombi. The PVT group exhibited significant differences related to biomarkers such as tumor necrosis factor (TNF)-alpha, C-reactive protein (CRP), D-dimers (D-D), as well as gut overall dysbiosis (DB) and alteration of different functional bacterial groups of the gut microbiota. Strong positive correlations were observed between PVT severity, and TNF-alpha, CRP, D-D as well as lipopolysaccharide (LPS) positive bacteria. Esophageal varices, age and abdominal pain were independent predictors for PVT severity as well as CRP, TNF-alpha and D-D. Conclusion Patients with LC and PVT displayed elevation of TNF-alpha, CRP, D-D alterations of the functional gut microbiota, as well as several morphological and clinical particularities. Although the LPS positive gut microbiota was linked to inflammatory biomarkers and PVT severity, it was not proven to be an independent predictor of the PVT severity like CRP, TNF-alpha and D-D.
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Affiliation(s)
- Doina Georgescu
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology, Department of Internal Medicine I, “V Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Oana-Elena Ancusa
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology, Department of Internal Medicine I, “V Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Daniel Azoulay
- Hepato-Biliary Center, Paul-Brousse Hospital, Paris-Saclay University, Villejuif, France
| | - Ana Lascu
- Department of Functional Sciences, “V Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Ioana Ionita
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology, Department of Internal Medicine I, “V Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Despina Calamar-Popovici
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology, Department of Internal Medicine I, “V Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Mihai Ionita
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology, Department of Internal Medicine I, “V Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Ciprian Ilie Rosca
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology, Department of Internal Medicine I, “V Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Gelu-Mihai Brează
- Department IX of Surgery I, Compartment of Hepatic-Biliary-Pancreatic Surgery, “V Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Daniela Reisz
- Department of Neurosciences, “V Babes” University of Medicine and Pharmacy, Timisoara, Romania
| | - Daniel Lighezan
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology, Department of Internal Medicine I, “V Babes” University of Medicine and Pharmacy, Timisoara, Romania
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Klos B, Steinbach C, Ketel J, Lambert C, Penders J, Doré J, Enck P, Mack I. Effects of isolation and confinement on gastrointestinal microbiota-a systematic review. Front Nutr 2023; 10:1214016. [PMID: 37492598 PMCID: PMC10364611 DOI: 10.3389/fnut.2023.1214016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/21/2023] [Indexed: 07/27/2023] Open
Abstract
Purpose The gastrointestinal (GI) microbiota is a complex and dynamic ecosystem whose composition and function are influenced by many internal and external factors. Overall, the individual GI microbiota composition appears to be rather stable but can be influenced by extreme shifts in environmental exposures. To date, there is no systematic literature review that examines the effects of extreme environmental conditions, such as strict isolation and confinement, on the GI microbiota. Methods We conducted a systematic review to examine the effects of isolated and confined environments on the human GI microbiota. The literature search was conducted according to PRISMA criteria using PubMed, Web of Science and Cochrane Library. Relevant studies were identified based on exposure to isolated and confined environments, generally being also antigen-limited, for a minimum of 28 days and classified according to the microbiota analysis method (cultivation- or molecular based approaches) and the isolation habitat (space, space- or microgravity simulation such as MARS-500 or natural isolation such as Antarctica). Microbial shifts in abundance, alpha diversity and community structure in response to isolation were assessed. Results Regardless of the study habitat, inconsistent shifts in abundance of 40 different genera, mainly in the phylum Bacillota (formerly Firmicutes) were reported. Overall, the heterogeneity of studies was high. Reducing heterogeneity was neither possible by differentiating the microbiota analysis methods nor by subgrouping according to the isolation habitat. Alpha diversity evolved non-specifically, whereas the microbial community structure remained dissimilar despite partial convergence. The GI ecosystem returned to baseline levels following exposure, showing resilience irrespective of the experiment length. Conclusion An isolated and confined environment has a considerable impact on the GI microbiota composition in terms of diversity and relative abundances of dominant taxa. However, due to a limited number of studies with rather small sample sizes, it is important to approach an in-depth conclusion with caution, and results should be considered as a preliminary trend. The risk of dysbiosis and associated diseases should be considered when planning future projects in extreme environments. Systematic review registration https://www.crd.york.ac.uk/prospero/, identifier CRD42022357589.
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Affiliation(s)
- Bea Klos
- Department of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany
| | - Christina Steinbach
- Department of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany
| | - Jasmin Ketel
- Department of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany
| | - Claude Lambert
- CIRI–Immunology Lab University Hospital, Saint-Étienne, France
- LCOMS/ENOSIS Université de Lorraine, Metz, France
| | - John Penders
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, Maastricht University Medical Center, CAPHRI Care and Public Health Research Institute, Maastricht, Netherlands
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, Maastricht University Medical Center, School of Nutrition and Translational Research in Metabolism, Maastricht, Netherlands
| | - Joël Doré
- UMR Micalis Institut, INRA, Paris-Saclay University, Jouy-En-Josas, France
| | - Paul Enck
- Department of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany
| | - Isabelle Mack
- Department of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany
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Dunn T, Cosgun E. A cloud-based pipeline for analysis of FHIR and long-read data. BIOINFORMATICS ADVANCES 2023; 3:vbac095. [PMID: 36726729 PMCID: PMC9872570 DOI: 10.1093/bioadv/vbac095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/02/2022] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Motivation As genome sequencing becomes cheaper and more accurate, it is becoming increasingly viable to merge this data with electronic health information to inform clinical decisions. Results In this work, we demonstrate a full pipeline for working with both PacBio sequencing data and clinical FHIR® data, from initial data to tertiary analysis. The electronic health records are stored in FHIR® (Fast Healthcare Interoperability Resource) format, the current leading standard for healthcare data exchange. For the genomic data, we perform variant calling on long-read PacBio HiFi data using Cromwell on Azure. Both data formats are parsed, processed and merged in a single scalable pipeline which securely performs tertiary analyses using cloud-based Jupyter notebooks. We include three example applications: exporting patient information to a database, clustering patients and performing a simple pharmacogenomic study. Availability and implementation https://github.com/microsoft/genomicsnotebook/tree/main/fhirgenomics. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Tim Dunn
- To whom correspondence should be addressed.
| | - Erdal Cosgun
- Biomedical Platforms and Genomics, Microsoft Research, Redmond, WA 98052, USA
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Thriene K, Michels KB. Human Gut Microbiota Plasticity throughout the Life Course. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1463. [PMID: 36674218 PMCID: PMC9860808 DOI: 10.3390/ijerph20021463] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 06/02/2023]
Abstract
The role of the gut microbiota in human health and disease has garnered heightened attention over the past decade. A thorough understanding of microbial variation over the life course and possible ways to influence and optimize the microbial pattern is essential to capitalize on the microbiota's potential to influence human health. Here, we review our current understanding of the concept of plasticity of the human gut microbiota throughout the life course. Characterization of the plasticity of the microbiota has emerged through recent research and suggests that the plasticity in the microbiota signature is largest at birth when the microbial colonization of the gut is initiated and mode of birth imprints its mark, then decreases postnatally continuously and becomes less malleable and largely stabilized with advancing age. This continuing loss of plasticity has important implication for the impact of the exposome on the microbiota and health throughout the life course and the identification of susceptible 'windows of opportunity' and methods for interventions.
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Affiliation(s)
- Kerstin Thriene
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79110 Freiburg, Germany
| | - Karin B. Michels
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79110 Freiburg, Germany
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
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Chatterjee G, Negi S, Basu S, Faintuch J, O'Donovan A, Shukla P. Microbiome systems biology advancements for natural well-being. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155915. [PMID: 35568180 DOI: 10.1016/j.scitotenv.2022.155915] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Throughout the years all data from epidemiological, physiological and omics have suggested that the microbial communities play a considerable role in modulating human health. The population of microorganisms residing in the human intestine collectively known as microbiota presents a genetic repertoire that is higher in magnitude than the human genome. They play an essential role in host immunity and neuronal signaling. Rapid enhancement of sequence based screening and development of humanized gnotobiotic model has sparked a great deal of interest among scientists to probe the dynamic interactions of the commensal bacteria. This review focuses on systemic analysis of the gut microbiome to decipher the complexity of the host-microbe intercommunication and gives a special emphasis on the evolution of targeted precision medicine through microbiome engineering. In addition, we have also provided a comprehensive description of how interconnection between metabolism and biochemical reactions in a specific organism can be obtained from a metabolic network or a flux balance analysis and combining multiple datasets helps in the identification of a particular metabolite. The review highlights how genetic modification of the critical components and programming the resident microflora can be employed for targeted precision medicine. Inspite of the ongoing debate on the utility of gut microbiome we have explored on the probable new therapeutic avenues like FMT (Fecal microbiota transplant) can be utilized. This review also recapitulates integrating human-relevant 3D cellular models coupled with computational models and the metadata obtained from interventional and epidemiological studies may decipher the complex interactome of diet-microbiota-disease pathophysiology. In addition, it will also open new avenues for the development of therapeutics derived from microbiome or implementation of personalized nutrition. In addition, the identification of biomarkers can also help towards the development of new diagnostic tools and eventually will lead to strategic management of the disease. Inspite of the ongoing debate on the utility of the gut microbiome we have explored how probable new therapeutic avenues like FMT (Fecal microbiota transplant) can be utilized. This review also summarises integrating human-relevant 3D cellular models coupled with computational models and the metadata obtained from interventional and epidemiological studies may decipher the complex interactome of diet- microbiota-disease pathophysiology. In addition, it will also open new avenues for the development of therapeutics derived from the microbiome or implementation of personalized nutrition. In addition, the identification of biomarkers can also help towards the development of new diagnostic tools and eventually will lead to strategic management of disease.
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Affiliation(s)
| | - Sangeeta Negi
- NMC Biolab, New Mexico Consortium, Los Alamos, NM, USA; Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Supratim Basu
- NMC Biolab, New Mexico Consortium, Los Alamos, NM, USA
| | - Joel Faintuch
- Department of Gastroenterology, Sao Paulo University Medical School, São Paulo, SP 01246-903, Brazil
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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11
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The human "contaminome": bacterial, viral, and computational contamination in whole genome sequences from 1000 families. Sci Rep 2022; 12:9863. [PMID: 35701436 PMCID: PMC9198055 DOI: 10.1038/s41598-022-13269-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/18/2022] [Indexed: 01/11/2023] Open
Abstract
The unmapped readspace of whole genome sequencing data tends to be large but is often ignored. We posit that it contains valuable signals of both human infection and contamination. Using unmapped and poorly aligned reads from whole genome sequences (WGS) of over 1000 families and nearly 5000 individuals, we present insights into common viral, bacterial, and computational contamination that plague whole genome sequencing studies. We present several notable results: (1) In addition to known contaminants such as Epstein-Barr virus and phiX, sequences from whole blood and lymphocyte cell lines contain many other contaminants, likely originating from storage, prep, and sequencing pipelines. (2) Sequencing plate and biological sample source of a sample strongly influence contamination profile. And, (3) Y-chromosome fragments not on the human reference genome commonly mismap to bacterial reference genomes. Both experiment-derived and computational contamination is prominent in next-generation sequencing data. Such contamination can compromise results from WGS as well as metagenomics studies, and standard protocols for identifying and removing contamination should be developed to ensure the fidelity of sequencing-based studies.
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12
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Georgescu D, Ionita I, Lascu A, Hut EF, Dragan S, Ancusa OE, Ionita M, Calamar-Popovici D, Georgescu LA, Lighezan DF. Gallstone Disease and Bacterial Metabolic Performance of Gut Microbiota in Middle-Aged and Older Patients. Int J Gen Med 2022; 15:5513-5531. [PMID: 35702368 PMCID: PMC9188808 DOI: 10.2147/ijgm.s350104] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/16/2022] [Indexed: 12/12/2022] Open
Abstract
Background Gallstone disease (GSD) is more commonly presented in aged people. Purpose The purpose of the study was to explore the insights of metabolic performance of bacterial species from gut microbiota as well as the clinical background in middle-aged and elderly patients with GSD. Patients and Methods This is an observational study concerning 120 research participants. Of those, 90 patients with symptomatic GSD addressed for cholecystectomy, average age 59.83 ± 15.32 years: 45 with cholesterol rich gallstones (CGSs), 45 with pigment gallstones (PGSs) and 30 healthy controls joined this observational study. Clinical examination, lab work-ups, upper and lower digestive video-endoscopies, abdominal ultrasound/CT and gallbladder motility assessment by Dodd’s method were performed. Overall stool dysbiosis (DB) was assessed as 1 = minor, 2 = mild, 3 = severe, species being identified by matrix-assisted laser desorption ionization method. Stool samples from dysbiotic patients were analyzed by a next generation sequencing method with operational taxonomic unit identification. Results Patients with GSD presented with a significant high range of overall gut DB (p < 0.0001) when compared with controls. Those with CGSs compared with those having PGSs displayed significant clinical differences related to elderly age, lifestyle and diet particularities, obesity, dyslipidemia, nonalcoholic fatty liver disease, hypertension, type 2 diabetes mellitus or impaired glucose tolerance, as well as motility disturbances of gallbladder with a decrease of the ejection fraction. Significant increase of overall DB range and alterations of several functional bacterial species with a decrease of butyrate, lactate, acetate/propionate and methane producers, mucin degrading bacteria, biodiversity index of microbiota, as well as an increase of lipopolysaccharide positive bacteria were significantly present in patients with CGSs. Conclusion Middle-aged and elderly patients with GSD and a clinical background characterized by particular lifestyle, metabolic and gallbladder motility issues displayed significant modifications of biodiversity, overall gut DB and alterations of several functional bacterial species, with a decrease of their metabolic performance.
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Affiliation(s)
- Doina Georgescu
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology/Department of Internal Medicine I, University of Medicine and Pharmacy “V Babes”, Timisoara, Romania
| | - Ioana Ionita
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology/Department of Internal Medicine I, University of Medicine and Pharmacy “V Babes”, Timisoara, Romania
- Correspondence: Ioana Ionita, Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology/Department of Internal Medicine I, University of Medicine and Pharmacy “V Babes”, 5 Gh Dima, Timisoara, 300079, Romania, Tel +40 723 539 800, Fax +40 256 490 626, Email
| | - Ana Lascu
- Department of Functional Sciences, University of Medicine and Pharmacy “V Babes”, Timisoara, Romania
- Ana Lascu, Department of Functional Sciences, University of Medicine and Pharmacy “V Babes”, 2 Eftimie Murgu Plaza, Timisoara, 300041, Romania, Tel +40 745 803 821, Fax +40 256 490 626, Email
| | - Emil-Florin Hut
- Department IX of Surgery I/Compartment of Hepatic-Biliary-Pancreatic Surgery, University of Medicine and Pharmacy “V Babes”, Timisoara, Romania
| | - Simona Dragan
- Department of Cardiology, University of Medicine and Pharmacy “V Babes”, Timisoara, Romania
| | - Oana-Elena Ancusa
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology/Department of Internal Medicine I, University of Medicine and Pharmacy “V Babes”, Timisoara, Romania
| | - Mihai Ionita
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology/Department of Internal Medicine I, University of Medicine and Pharmacy “V Babes”, Timisoara, Romania
| | - Despina Calamar-Popovici
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology/Department of Internal Medicine I, University of Medicine and Pharmacy “V Babes”, Timisoara, Romania
| | - Liviu-Andrei Georgescu
- Clinic of Obstetrics and Gynecology, “Pius Brinzeu” Academic Emergency County Hospital, Timisoara, Romania
| | - Daniel-Florin Lighezan
- Center of Advanced Researches in Cardiovascular Diseases and Hemostaseology/Department of Internal Medicine I, University of Medicine and Pharmacy “V Babes”, Timisoara, Romania
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Zhang S, Zhu J. Untargeted Metabolomics Sensitively Differentiates Gut Bacterial Species in Single Culture and Co-Culture Systems. ACS OMEGA 2022; 7:14643-14652. [PMID: 35557670 PMCID: PMC9088763 DOI: 10.1021/acsomega.1c07114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/15/2022] [Indexed: 05/28/2023]
Abstract
Gut microbiome plays a vital role in human health, and its characteristic has been widely identified through next-generation sequencing techniques. Although with great genomic insights into gut microbiome, its functional information is not clearly elaborated through metagenomic techniques. On the other hand, it is suggested that fecal metabolome can be used as a functional readout of the microbiome composition; therefore, we designed a proof-of-concept study to first characterize the metabolome of different gut microbes and then investigate the relationship between bacterial metabolomes and their compositions in co-culture systems. We selected eight representative bacteria species from Bifidobacterium (2), Bacteroides (1), Lactobacillus (4), and Akkermansia (1) genera as our model microbes. Liquid chromatography coupled mass spectrometry-based untargeted metabolomics was utilized to explore the microbial metabolome of bacteria single cultures and co-culture systems. Through spectral comparisons, our results showed that untargeted metabolomics could capture the similarity and differences in metabolic profiles from eight representative gut bacteria. Also, untargeted metabolomics could sensitively differentiate gut bacterial species based on our statistical analyses. For example, citrulline and histamine levels were significantly different among four Lactobacillus species. In addition, in the co-culture systems with different bacteria population ratios, gut bacterial metabolomes can be used to quantitatively reflect bacterial population in a mixed culture. For instance, the relative abundance of 2-hydroxybutyric acid changed proportionately with the changed population ratio of Lactobacillus reuteri in the co-culture system. In summary, we proposed a workflow that could demonstrate the capability of untargeted metabolomics in differentiating gut bacterial species and detecting their characteristic metabolites proportionally to the microbial population in co-culture systems.
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Affiliation(s)
- Shiqi Zhang
- Human
Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jiangjiang Zhu
- Human
Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, Ohio 43210, United States
- James
Comprehensive Cancer Center, The Ohio State
University, Columbus, Ohio 43210, United States
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14
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Mohsin Bukhari S, Ahmed Alghamdi H, Ur Rehman K, Andleeb S, Ahmad S, Khalid N. Metagenomics analysis of the fecal microbiota in Ring-necked pheasants ( Phasianus colchicus) and Green pheasants ( Phasianus versicolor) using next generation sequencing. Saudi J Biol Sci 2022; 29:1781-1788. [PMID: 35280539 PMCID: PMC8913415 DOI: 10.1016/j.sjbs.2021.10.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/06/2021] [Accepted: 10/18/2021] [Indexed: 11/26/2022] Open
Abstract
Pheasant reintroduction and conservation efforts have been in place in Pakistan since the 1980 s, yet there is still a scarcity of data on pheasant microbiome and zoonosis. Instead of growing vast numbers of bacteria in the laboratory, to investigate the fecal microbiome, pheasants (green and ring neck pheasant) were analyzed using 16S rRNA metagenomics and using IonS5TMXL sequencing from two flocks more than 10 birds. Operational taxonomic unit (OTU) cluster analysis and phylogenetic tree analysis was performed using Mothur software against the SSUrRNA database of SILVA and the MUSCLE (Version 3.8.31) software. Results of the analysis showed that firmicutes were the most abundant phylum among the top ten phyla, in both pheasant species, followed by other phyla such as actinobacteria and proteobacteria in ring necked pheasant and bacteroidetes in green necked pheasant. Bacillus was the most relatively abundant genus in both pheasants followed by Oceanobacillus and Teribacillus for ring necked pheasant and Lactobacillus for green necked pheasant. Because of their well-known beneficial characteristics, these genus warrants special attention. Bird droppings comprise germs from the urinary system, gut, and reproductive sites, making it difficult to research each anatomical site at the same time. We conclude that metagenomic analysis and classification provides baseline information of the pheasant fecal microbiome that plays a role in disease and health.
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Affiliation(s)
- Syed Mohsin Bukhari
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha, Saudi Arabia
| | - Khalil Ur Rehman
- Department of Environmental Sciences, GCW University, Sailkot 51310, Pakistan
| | - Shahla Andleeb
- Department of Environmental Sciences, GCW University, Sailkot 51310, Pakistan
| | - Shahbaz Ahmad
- Department of Entomology, University of the Punjab, 54590 Lahore, Pakistan
| | - Nimra Khalid
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
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15
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Georgescu D, Caraba A, Ionita I, Lascu A, Hut EF, Dragan S, Ancusa OE, Suceava I, Lighezan D. Dyspepsia and Gut Microbiota in Female Patients with Postcholecystectomy Syndrome. Int J Womens Health 2022; 14:41-56. [PMID: 35136356 PMCID: PMC8816732 DOI: 10.2147/ijwh.s342882] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/06/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Gallstone disease (GSD) represents one of the most frequent digestive disorders, highly reported in female gender. The purpose of the study was to explore the clinical and gut microbiota particularities of female patients with postcholecystectomy syndrome (PCS) and the possible relationship between gut dysbiosis (DB) and abdominal complaints. PATIENTS AND METHODS In total, 129 female participants: 104 outpatients divided into two equal groups, 52 PCS (+), 52 PCS (-) and 25 healthy controls were consecutively enrolled in this observational study. Patients underwent clinical examination with assessment of pain, bloating, transit disturbances, abdominal ultrasound/computer tomography/magnetic resonance imaging/endoscopic retrograde cholangiopancreatography, upper and lower digestive endoscopies. Laboratory work-ups and stool microbiology assessments were performed for all study participants (patients and controls). Stool microorganisms were identified by matrix-assisted laser desorption ionization - time-of-flight- mass spectrometry and in patients with DB also by next-generation sequencing. RESULTS Older age, complicated gallstones disease, associated conditions like diabetes mellitus/impaired glucose tolerance and irritable bowel syndrome were significantly present in PCS (+) group, as well as sedentary lifestyle and diets characterized by a low fiber intake (p<0.0001). PCS (+) patients displayed significant differences related to the incidence and severity of overall gut microbiota DB, decreased H index of biodiversity and the unbalanced Firmicutes/Bacteroidetes (F/B) ratios by comparison to the PCS (-) group (p<0.0001). Strong positive correlations of the severity of overall DB with bloating and the intestinal habit disorders, as well as of F/B ratios to all abdominal symptoms were noted. CONCLUSION PCS in female patients was associated with older age, sedentary lifestyle, specific dietary habits, history of complicated gallstone disease, diabetes mellitus/impaired glucose tolerance and irritable bowel syndrome, as well as gut microbiota particularities. Overall DB and unbalanced F/B ratios were strongly correlated to abdominal complaints.
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Affiliation(s)
- Doina Georgescu
- Department of Internal Medicine I, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
| | - Alexandru Caraba
- Department of Internal Medicine I, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
| | - Ioana Ionita
- Department of Internal Medicine I, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
| | - Ana Lascu
- Department of Functional Sciences, Discipline of Pathophysiology, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
| | - Emil Florin Hut
- Department IX of Surgery I/Compartment of Hepato-Bilio-Pancreatic Surgery, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
| | - Simona Dragan
- Department of Cardiology, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
| | - Oana Elena Ancusa
- Department of Internal Medicine I, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
| | - Ioana Suceava
- Department of Internal Medicine I, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
| | - Daniel Lighezan
- Department of Internal Medicine I, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
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Mahapatra S, Mohanty S, Mishra R, Prasad P. An overview of cancer and the human microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 191:83-139. [DOI: 10.1016/bs.pmbts.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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17
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Toni T, Alverdy J, Gershuni V. Re-examining chemically defined liquid diets through the lens of the microbiome. Nat Rev Gastroenterol Hepatol 2021; 18:903-911. [PMID: 34594028 PMCID: PMC8815794 DOI: 10.1038/s41575-021-00519-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Trends in nutritional science are rapidly shifting as information regarding the value of eating unprocessed foods and its salutary effect on the human microbiome emerge. Unravelling the evolution and ecology by which humans have harboured a microbiome that participates in every facet of health and disease is daunting. Most strikingly, the host habitat has sought out naturally occurring foodstuff that can fulfil its own metabolic needs and also the needs of its microbiota, each of which remain inexorably connected to one another. With the introduction of modern medicine and complexities of critical care, came the assumption that the best way to feed a critically ill patient is by delivering fibre-free chemically defined sterile liquid foods (that is, total enteral nutrition). In this Perspective, we uncover the potential flaws in this assumption and discuss how emerging technology in microbiome sciences might inform the best method of feeding malnourished and critically ill patients.
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Affiliation(s)
- Tiffany Toni
- University of Chicago, Pritzker School of Medicine, Chicago, IL, USA
| | - John Alverdy
- University of Chicago, Pritzker School of Medicine, Chicago, IL, USA
| | - Victoria Gershuni
- University of Pennsylvania, Department of Surgery, Philadelphia, PA, USA and Washington University in St Louis, Department of Surgery, St Louis, MO, USA,Corresponding author
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18
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Goolam Mahomed T, Peters RPH, Allam M, Ismail A, Mtshali S, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Sci Rep 2021; 11:19758. [PMID: 34611216 PMCID: PMC8492659 DOI: 10.1038/s41598-021-99127-w] [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: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.
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Affiliation(s)
- T. Goolam Mahomed
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - R. P. H. Peters
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.442327.40000 0004 7860 2538Foundation for Professional Development, Research Unit, East London, South Africa
| | - M. Allam
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - A. Ismail
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - S. Mtshali
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - V. Ueckermann
- grid.49697.350000 0001 2107 2298Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M. M. Kock
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
| | - M. M. Ehlers
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
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Ezzamouri B, Shoaie S, Ledesma-Amaro R. Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies. Front Microbiol 2021; 12:681982. [PMID: 34531833 PMCID: PMC8438329 DOI: 10.3389/fmicb.2021.681982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/31/2021] [Indexed: 12/26/2022] Open
Abstract
A number of studies have shown that the microbial communities of the human body are integral for the maintenance of human health. Advances in next-generation sequencing have enabled rapid and large-scale quantification of the composition of microbial communities in health and disease. Microorganisms mediate diverse host responses including metabolic pathways and immune responses. Using a system biology approach to further understand the underlying alterations of the microbiota in physiological and pathological states can help reveal potential novel therapeutic and diagnostic interventions within the field of synthetic biology. Tools such as biosensors, memory arrays, and engineered bacteria can rewire the microbiome environment. In this article, we review the computational tools used to study microbiome communities and the current limitations of these methods. We evaluate how genome-scale metabolic models (GEMs) can advance our understanding of the microbe-microbe and microbe-host interactions. Moreover, we present how synergies between these system biology approaches and synthetic biology can be harnessed in human microbiome studies to improve future therapeutics and diagnostics and highlight important knowledge gaps for future research in these rapidly evolving fields.
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Affiliation(s)
- Bouchra Ezzamouri
- Unit for Population-Based Dermatology Research, St John’s Institute of Dermatology, Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kindom
- Faculty of Dentistry, Centre for Host-Microbiome Interactions, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Saeed Shoaie
- Faculty of Dentistry, Centre for Host-Microbiome Interactions, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
- Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, Sweden
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
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White KA, McEntire KD, Buan NR, Robinson L, Barbar E. Charting a New Frontier Integrating Mathematical Modeling in Complex Biological Systems from Molecules to Ecosystems. Integr Comp Biol 2021; 61:2255-2266. [PMID: 34283225 DOI: 10.1093/icb/icab165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Nicole R Buan
- University of Nebraska-Lincoln, Department of Biochemistry
| | | | - Elisar Barbar
- Oregon State University, Department of Biochemistry and Biophysics
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21
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Peterson D, Bonham KS, Rowland S, Pattanayak CW, Klepac-Ceraj V. Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes. Front Microbiol 2021; 12:670336. [PMID: 34335499 PMCID: PMC8320171 DOI: 10.3389/fmicb.2021.670336] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/28/2021] [Indexed: 01/04/2023] Open
Abstract
The colonization of the human gut microbiome begins at birth, and over time, these microbial communities become increasingly complex. Most of what we currently know about the human microbiome, especially in early stages of development, was described using culture-independent sequencing methods that allow us to identify the taxonomic composition of microbial communities using genomic techniques, such as amplicon or shotgun metagenomic sequencing. Each method has distinct tradeoffs, but there has not been a direct comparison of the utility of these methods in stool samples from very young children, which have different features than those of adults. We compared the effects of profiling the human infant gut microbiome with 16S rRNA amplicon vs. shotgun metagenomic sequencing techniques in 338 fecal samples; younger than 15, 15-30, and older than 30 months of age. We demonstrate that observed changes in alpha-diversity and beta-diversity with age occur to similar extents using both profiling methods. We also show that 16S rRNA profiling identified a larger number of genera and we find several genera that are missed or underrepresented by each profiling method. We present the link between alpha diversity and shotgun metagenomic sequencing depth for children of different ages. These findings provide a guide for selecting an appropriate method and sequencing depth for the three studied age groups.
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Affiliation(s)
- Danielle Peterson
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Kevin S Bonham
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Sophie Rowland
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Cassandra W Pattanayak
- Department of Mathematics, Quantitative Reasoning Program, and the Quantitative Analysis Institute at Wellesley College, Wellesley, MA, United States
| | | | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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Kim J, Lee HK. The Role of Gut Microbiota in Modulating Tumor Growth and Anticancer Agent Efficacy. Mol Cells 2021; 44:356-362. [PMID: 33972463 PMCID: PMC8175145 DOI: 10.14348/molcells.2021.0032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 02/08/2023] Open
Abstract
An increasing number of studies have revealed an interaction between gut microbiota and tumors. The enrichment of specific bacteria strains in the intestines has been found to modulate tumor growth and influence the mechanisms of tumor treatment. Various bacteria are involved in modulating the effects of chemotherapeutic drugs currently used to treat patients with cancer, and they affect not only gastrointestinal tract tumors but also distant organ tumors. In addition, changes in the gut microbiota are known to be involved in the antitumor immune response as well as the modulation of the intestinal immune system. As a result, the gut microbiota plays an important role in modulating the efficacy of immune checkpoint inhibitors. Therefore, gut microbiota could be considered as an adjuvant treatment option with other cancer treatment or as another marker for predicting treatment response. In this review, we examine how gut microbiota affects cancer treatments.
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Affiliation(s)
- Jaeho Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Heung Kyu Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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23
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Park I, Goo D, Nam H, Wickramasuriya SS, Lee K, Zimmerman NP, Smith AH, Rehberger TG, Lillehoj HS. Effects of Dietary Maltol on Innate Immunity, Gut Health, and Growth Performance of Broiler Chickens Challenged With Eimeria maxima. Front Vet Sci 2021; 8:667425. [PMID: 34095279 PMCID: PMC8173067 DOI: 10.3389/fvets.2021.667425] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/22/2021] [Indexed: 12/18/2022] Open
Abstract
Two studies were conducted to evaluate the effects of maltol as a postbiotic on innate immunity, gut health, and enteric infection. In the first study, an in vitro culture system was used to evaluate the effects of maltol on the innate immune response of chicken macrophage cells (CMC), gut integrity of chicken intestinal epithelial cells (IEC), anti-parasitic activity against Eimeria maxima, and differentiation of quail muscle cells (QMC) and primary chicken embryonic muscle cells (PMC). All cells seeded in the 24-well plates were treated with maltol at concentrations of 0.1, 1.0, and 10.0 μg. CMC and IEC were stimulated by lipopolysaccharide to induce an innate immune response, and QMC and PMC were treated with 0.5 and 2% fetal bovine serum, respectively. After 18 h of incubation, pro-inflammatory cytokines, tight junction proteins (TJPs), and muscle cell growth markers were measured. In the second study, the dietary effect of maltol was evaluated on disease parameters in broiler chickens infected with E. maxima. Eighty male 1-day-old broiler chickens were allocated into the following four treatment groups: (1) Control group without infection, (2) Basal diet with E. maxima, (3) High maltol (HI; 10.0 mg /kg feed) with E. maxima, and (4) Low maltol (LO; 1.0 mg/kg feed) with E. maxima. Body weights (BW) were measured on days 0, 7, 14, 20, and 22. All chickens except the CON group were orally infected with 104E. maxima per chicken on day 14. Jejunum samples were collected for gut lesion scoring, and the gene expression of cytokines and TJPs. Data was analyzed using PROC MIXED in SAS. In vitro, maltol not only increased TJPs in IEC and cytokines in the LPS-stimulated CMC but also showed direct cytotoxicity against sporozoites of E. maxima. In vivo, the HI group improved the BW, reduced the gut lesion scores and fecal oocyst shedding, and decreased jejunal TNFSF15 and IL-1β expression in E. maxima-infected chickens. In conclusion, these results demonstrate the beneficial effects of dietary maltol in the enhancement of growth performance, gut health, and coccidiosis resistance and the applicability of maltol as a postbiotic for the replacement of antibiotic growth promoters in commercial poultry production.
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Affiliation(s)
- Inkyung Park
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Doyun Goo
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Hyoyoun Nam
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Samiru S Wickramasuriya
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
| | - Noah P Zimmerman
- Arm & Hammer Animal and Food Production, Waukesha, WI, United States
| | - Alexandra H Smith
- Arm & Hammer Animal and Food Production, Waukesha, WI, United States
| | | | - Hyun S Lillehoj
- Animal Bioscience and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
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Andremont A, Cervesi J, Bandinelli PA, Vitry F, de Gunzburg J. Spare and repair the gut microbiota from antibiotic-induced dysbiosis: state-of-the-art. Drug Discov Today 2021; 26:2159-2163. [PMID: 33639249 DOI: 10.1016/j.drudis.2021.02.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/02/2021] [Accepted: 02/16/2021] [Indexed: 02/08/2023]
Abstract
Homeostasis of the intestinal microbiota is currently recognized as a major contributor to human health. Furthermore, intestinal dysbiosis is associated with a multitude of consequences, including intestinal colonization by antibiotic-resistant or pathogenic bacteria, such as Clostridioides difficile, and reduced efficacy of promising anticancer immunotherapies. By far, the most immediate and drastic exposure leading to dysbiosis is antibiotic treatment. Many attempts have been made to prevent or repair antibiotic-associated dysbiosis. Here, we review these innovations and the difficulties associated with their development.
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Affiliation(s)
- Antoine Andremont
- Da Volterra, Paris, France; Université de Paris, IAME, INSERM, Paris, France.
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25
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Jean-Pierre F, Henson MA, O'Toole GA. Metabolic Modeling to Interrogate Microbial Disease: A Tale for Experimentalists. Front Mol Biosci 2021; 8:634479. [PMID: 33681294 PMCID: PMC7930556 DOI: 10.3389/fmolb.2021.634479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
The explosion of microbiome analyses has helped identify individual microorganisms and microbial communities driving human health and disease, but how these communities function is still an open question. For example, the role for the incredibly complex metabolic interactions among microbial species cannot easily be resolved by current experimental approaches such as 16S rRNA gene sequencing, metagenomics and/or metabolomics. Resolving such metabolic interactions is particularly challenging in the context of polymicrobial communities where metabolite exchange has been reported to impact key bacterial traits such as virulence and antibiotic treatment efficacy. As novel approaches are needed to pinpoint microbial determinants responsible for impacting community function in the context of human health and to facilitate the development of novel anti-infective and antimicrobial drugs, here we review, from the viewpoint of experimentalists, the latest advances in metabolic modeling, a computational method capable of predicting metabolic capabilities and interactions from individual microorganisms to complex ecological systems. We use selected examples from the literature to illustrate how metabolic modeling has been utilized, in combination with experiments, to better understand microbial community function. Finally, we propose how such combined, cross-disciplinary efforts can be utilized to drive laboratory work and drug discovery moving forward.
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Affiliation(s)
- Fabrice Jean-Pierre
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Michael A Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, United States
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
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26
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Badran M, Mashaqi S, Gozal D. The gut microbiome as a target for adjuvant therapy in obstructive sleep apnea. Expert Opin Ther Targets 2020; 24:1263-1282. [PMID: 33180654 PMCID: PMC9394230 DOI: 10.1080/14728222.2020.1841749] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Gut dysbiosis is assumed to play a role in obstructive sleep apnea (OSA)-associated morbidities. Pre- and probiotics, short chain fatty acids (SCFA) and fecal matter transplantation (FMT) may offer potential as novel therapeutic strategies that target this gut dysbiosis. As more mechanisms of OSA-induced dysbiosis are being elucidated, these novel approaches are being tested in preclinical and clinical development. Areas covered: We examined the evidence linking OSA to gut dysbiosis and discuss the effects of pre- and probiotics on associated cardiometabolic, neurobehavioral and gastrointestinal disorders. The therapeutic potential of SCFA and FMT are also discussed. We reviewed the National Center for Biotechnology Information database, including PubMed and PubMed Central between 2000 - 2020. Expert opinion: To date, there are no clinical trials and only limited evidence from animal studies describing the beneficial effects of pre- and probiotic supplementation on OSA-mediated dysbiosis. Thus, more work is necessary to assess whether prebiotics, probiotics and SCFA are promising future novel strategies for targeting OSA-mediated dysbiosis.
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Affiliation(s)
- Mohammad Badran
- Department of Child Health and the Child Health Research Institute, University of Missouri School of Medicine , Columbia, MO, USA
| | - Saif Mashaqi
- Department of Pulmonary, Critical Care and Sleep Medicine, University of Arizona School of Medicine , Tucson, AZ, USA
| | - David Gozal
- Department of Child Health and the Child Health Research Institute, University of Missouri School of Medicine , Columbia, MO, USA
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Behera BK, Patra B, Chakraborty HJ, Sahu P, Rout AK, Sarkar DJ, Parida PK, Raman RK, Rao AR, Rai A, Das BK, Jena J, Mohapatra T. Metagenome analysis from the sediment of river Ganga and Yamuna: In search of beneficial microbiome. PLoS One 2020; 15:e0239594. [PMID: 33021988 PMCID: PMC7537857 DOI: 10.1371/journal.pone.0239594] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/10/2020] [Indexed: 12/13/2022] Open
Abstract
Beneficial microbes are all around us and it remains to be seen, whether all diseases and disorders can be prevented or treated with beneficial microbes. In this study, the presence of various beneficial bacteria were identified from the sediments of Indian major Rivers Ganga and Yamuna from nine different sites using a metagenomic approach. The metagenome sequence analysis using the Kaiju Web server revealed the presence of 69 beneficial bacteria. Phylogenetic analysis among these bacterial species revealed that they were highly diverse. Relative abundance analysis of these bacterial species is highly correlated with different pollution levels among the sampling sites. The PCA analysis revealed that Lactobacillus spp. group of beneficial bacteria are more associated with sediment sampling sites, KAN-2 and ND-3; whereas Bacillus spp. are more associated with sites, FAR-2 and ND-2. This is the first report revealing the richness of beneficial bacteria in the Indian rivers, Ganga and Yamuna. The study might be useful in isolating different important beneficial microorganisms from these river sediments, for possible industrial applications.
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Affiliation(s)
- Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
- * E-mail: (BKB); (BKD)
| | - Biswanath Patra
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Hirak Jyoti Chakraborty
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Parameswar Sahu
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Dhruba Jyoti Sarkar
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Pranaya Kumar Parida
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Rohan Kumar Raman
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | | | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
- * E-mail: (BKB); (BKD)
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28
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Alawneh JI, Barreto MO, Moore RJ, Soust M, Al-Harbi H, James AS, Krishnan D, Olchowy TWJ. Systematic review of an intervention: the use of probiotics to improve health and productivity of calves. Prev Vet Med 2020; 183:105147. [PMID: 32977172 DOI: 10.1016/j.prevetmed.2020.105147] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 12/24/2022]
Abstract
The aims of this study were to undertake a systematic review and meta-analysis of the types of probiotic formulations that are commercially available and to critically appraise the available evidence for the effectiveness of probiotics in improving the health and productivity of calves. Relevant papers were identified to answer the question: 'In calves aged between birth to one year, is the use of probiotics associated with changes in haematological or biochemical parameters, faecal bacteria counts, average daily live weight gain, dry matter intake, or feed conversion ratio?' The search of the literature yielded 67 studies that fit the primary screening criteria. Included studies were assessed for bias and confounding using a predefined risk assessment tool adapted from the Cochrane Collaboration's tool for assessing risk of bias in randomised trials and GRADE guidelines. Meta-analysis was performed using Review Manager and R. Random sequence generation was low in more than 59 % of studies. Risk of allocation concealment and performance bias were largely unclear in over 68 % of studies. Calves fed probiotics had increased average daily live weight gains (ADG) from birth to weaning (mean difference [MD] = 83.14 g/d 95 % CI = 58.36-107.91, P < 0.001) compared with calves on a control diet. Calf age reduced the level of heterogeneity of the effect of probiotics on ADG for calves between one to three weeks of age (τ2 = 73.15; I2 = 4%; P = 0.40) but not for calves older than three weeks of age (τ2 = 2892.91; I2 = 73 %; P < 0.001). Feed conversion ratio (FCR) was lower for calves on probiotics (MD = -0.13 kg of dry matter intake (DMI) to kg of live weight (LW) gain, 95 % CI = -0.17 to -0.09, P < 0.001), and the heterogeneity of effect was large in younger aged calves (τ2 = 0.05; I2 = 78 %; P = 0.03). The risk of bias regarding the methodology in the included studies was high. The quality of evidence for each outcome was categorised as moderate. There is sufficient data to support the effectiveness of probiotic use in some applications such as for the improvement of performance and productivity parameters of calves. However, the evidence is weak for other potential probiotic uses in calves such as improved health and reduced risk of disease. Therefore, the existing data are inconclusive and do not support the use of probiotics as an alternative to antimicrobials to improve calf health and productivity.
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Affiliation(s)
- John I Alawneh
- Good Clinical Practice Research Group, The University of Queensland, School of Veterinary Science, Gatton, Queensland, 4343, Australia; The University of Queensland, School of Veterinary Science, Gatton, Queensland, 4343, Australia.
| | - Michelle O Barreto
- Good Clinical Practice Research Group, The University of Queensland, School of Veterinary Science, Gatton, Queensland, 4343, Australia; The University of Queensland, School of Veterinary Science, Gatton, Queensland, 4343, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora, Melbourne, Victoria, 3083, Australia
| | - Martin Soust
- Terragen Biotech Pty Ltd., Coolum Beach, Queensland, 4573, Australia
| | - Hulayyil Al-Harbi
- Good Clinical Practice Research Group, The University of Queensland, School of Veterinary Science, Gatton, Queensland, 4343, Australia; The University of Queensland, School of Veterinary Science, Gatton, Queensland, 4343, Australia
| | - Ameh S James
- Good Clinical Practice Research Group, The University of Queensland, School of Veterinary Science, Gatton, Queensland, 4343, Australia; The University of Queensland, School of Veterinary Science, Gatton, Queensland, 4343, Australia
| | - Divya Krishnan
- The University of Queensland, School of Veterinary Science, Gatton, Queensland, 4343, Australia
| | - Timothy W J Olchowy
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T3R 1J3, Canada
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29
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Rosario D, Boren J, Uhlen M, Proctor G, Aarsland D, Mardinoglu A, Shoaie S. Systems Biology Approaches to Understand the Host-Microbiome Interactions in Neurodegenerative Diseases. Front Neurosci 2020; 14:716. [PMID: 32733199 PMCID: PMC7360858 DOI: 10.3389/fnins.2020.00716] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative diseases (NDDs) comprise a broad range of progressive neurological disorders with multifactorial etiology contributing to disease pathophysiology. Evidence of the microbiome involvement in the gut-brain axis urges the interest in understanding metabolic interactions between the microbiota and host physiology in NDDs. Systems Biology offers a holistic integrative approach to study the interplay between the different biologic systems as part of a whole, and may elucidate the host–microbiome interactions in NDDs. We reviewed direct and indirect pathways through which the microbiota can modulate the bidirectional communication of the gut-brain axis, and explored the evidence of microbial dysbiosis in Alzheimer’s and Parkinson’s diseases. As the gut microbiota being strongly affected by diet, the potential approaches to targeting the human microbiota through diet for the stimulation of neuroprotective microbial-metabolites secretion were described. We explored the potential of Genome-scale metabolic models (GEMs) to infer microbe-microbe and host-microbe interactions and to identify the microbiome contribution to disease development or prevention. Finally, a systemic approach based on GEMs and ‘omics integration, that would allow the design of sustainable personalized anti-inflammatory diets in NDDs prevention, through the modulation of gut microbiota was described.
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Affiliation(s)
- Dorines Rosario
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Jan Boren
- Department of Molecular and Clinical Medicine, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Gordon Proctor
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Dag Aarsland
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom.,Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom.,Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
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30
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Ye L, Das P, Li P, Ji B, Nielsen J. Carbohydrate active enzymes are affected by diet transition from milk to solid food in infant gut microbiota. FEMS Microbiol Ecol 2020; 95:5582603. [PMID: 31589310 DOI: 10.1093/femsec/fiz159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/04/2019] [Indexed: 01/09/2023] Open
Abstract
Infants experience a dramatic change in their food in the first year after birth when they shift from breast milk to solid food. This results in a large change in presence of indigestible polysaccharides, a primary energy resource of gut microbes. How the gut microbiota adapts to this dietary shift has not been well examined. Here, by using metagenomics data, we studied carbohydrate-active enzymes (CAZymes) of gut microbiota, which are essential enzymes catalyzing the breakdown of polysaccharides, during this dietary shift. We developed a new approach to categorize CAZyme families by food intake and found CAZyme families associated with milk or solid food. We also found CAZymes with most abundance in 12 months infants that are not associated with solid food or milk but may be related to modulating carbohydrates in the mucus. Additionally, the abundance of gut CAZymes were found to be affected by many other factors, including delivery modes and life style in adults. Taken together, our findings provide novel insights into the dynamic change of gut CAZymes in early human life and provide potential markers for food interference or gut microbiota restoration.
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Affiliation(s)
- Lingqun Ye
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, SE-412 96 Gothenburg, Sweden
| | - Promi Das
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, SE-412 96 Gothenburg, Sweden
| | - Peishun Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, SE-412 96 Gothenburg, Sweden
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, SE-412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, SE-412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kgs. Lyngby DK2800, Denmark.,BioInnovation Institute, Ole Maaløes Vej, DK2200 Copenhagen N, Denmark
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31
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Wijdeveld M, Nieuwdorp M, IJzerman R. The interaction between microbiome and host central nervous system: the gut-brain axis as a potential new therapeutic target in the treatment of obesity and cardiometabolic disease. Expert Opin Ther Targets 2020; 24:639-653. [PMID: 32441559 DOI: 10.1080/14728222.2020.1761958] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The role of the intestinal microbiota in host cardiometabolic health and disease has gained significant attention over recent decades. Previous studies have shown effects on metabolic health through gut microbiota modulation; this suggests diverse interaction pathways that constitute the communication between gut microbiota and host central nervous system, the so-called gut-brain axis. AREAS COVERED This article provides an overview of the various mechanisms that may mediate the gut-brain axis. It places an emphasis on cardiometabolic health, including effects of short-chain fatty acids (SCFA), alterations in neurotransmitters and gut peptides and microbial effects on chronic inflammation and immune function. Moreover, this paper sheds light on whether these mechanisms afford therapeutic targets to promote metabolic health. To this end, a PubMed search with the terms 'gut microbiota,' 'obesity' and 'insulin sensitivity' was performed. EXPERT OPINION Many properties of the human gut microbiome are associated with the central regulation of appetite and metabolic status. Some of these relationships are causal and there are positive effects from certain intervention methods. Microbial manipulation may offer a means to prevent or treat obesity and associated co-morbidities. However, to establish direct causal relations between altered gut microbiota and metabolic disease, clinical intervention studies are necessary.
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Affiliation(s)
- Madelief Wijdeveld
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers , Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers , Amsterdam, The Netherlands
| | - Richard IJzerman
- Department of Endocrinology, Amsterdam University Medical Centers , Amsterdam, The Netherlands
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32
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Applying Differential Neural Networks to Characterize Microbial Interactions in an Ex Vivo Gastrointestinal Gut Simulator. Processes (Basel) 2020. [DOI: 10.3390/pr8050593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The structure of mixed microbial cultures—such as the human gut microbiota—is influenced by a complex interplay of interactions among its community members. The objective of this study was to propose a strategy to characterize microbial interactions between particular members of the community occurring in a simulator of the human gastrointestinal tract used as the experimental system. Four runs were carried out separately in the simulator: two of them were fed with a normal diet (control system), and two more had the same diet supplemented with agave fructans (fructan-supplemented system). The growth kinetics of Lactobacillus spp., Bifidobacterium spp., Salmonella spp., and Clostridium spp. were assessed in the different colon sections of the simulator for a nine-day period. The time series of microbial concentrations were used to estimate specific growth rates and pair-wise interaction coefficients as considered by the generalized Lotka-Volterra (gLV) model. A differential neural network (DNN) composed of a time-adaptive set of differential equations was applied for the nonparametric identification of the mixed microbial culture, and an optimization technique was used to determine the interaction parameters, considering the DNN identification results and the structure of the gLV model. The assessment of the fructan-supplemented system showed that microbial interactions changed significantly after prebiotics administration, demonstrating their modulating effect on microbial interactions. The strategy proposed here was applied satisfactorily to gain quantitative and qualitative knowledge of a broad spectrum of microbial interactions in the gut community, as described by the gLV model. In the future, it may be utilized to study microbial interactions within mixed cultures using other experimental approaches and other mathematical models (e.g., metabolic models), which will yield crucial information for optimizing mixed microbial cultures to perform certain processes—such as environmental bioremediation or modulation of gut microbiota—and to predict their dynamics.
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Kuang E, Marney M, Cuevas D, Edwards RA, Forsberg EM. Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics. Metabolites 2020; 10:metabo10040156. [PMID: 32316423 PMCID: PMC7240944 DOI: 10.3390/metabo10040156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 11/21/2022] Open
Abstract
Genomics-based metabolic models of microorganisms currently have no easy way of corroborating predicted biomass with the actual metabolites being produced. This study uses untargeted mass spectrometry-based metabolomics data to generate a list of accurate metabolite masses produced from the human commensal bacteria Citrobacter sedlakii grown in the presence of a simple glucose carbon source. A genomics-based flux balance metabolic model of this bacterium was previously generated using the bioinformatics tool PyFBA and phenotypic growth curve data. The high-resolution mass spectrometry data obtained through timed metabolic extractions were integrated with the predicted metabolic model through a program called MS_FBA. This program correlated untargeted metabolomics features from C. sedlakii with 218 of the 699 metabolites in the model using an exact mass match, with 51 metabolites further confirmed using predicted isotope ratios. Over 1400 metabolites were matched with additional metabolites in the ModelSEED database, indicating the need to incorporate more specific gene annotations into the predictive model through metabolomics-guided gap filling.
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Affiliation(s)
- Ellen Kuang
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA
| | - Matthew Marney
- Department of Biomedical Informatics, San Diego State University, San Diego, CA 92182, USA
| | - Daniel Cuevas
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Robert A. Edwards
- Department of Biomedical Informatics, San Diego State University, San Diego, CA 92182, USA
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Erica M. Forsberg
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA
- Department of Biomedical Informatics, San Diego State University, San Diego, CA 92182, USA
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
- Correspondence: ; Tel.: +1-619-594-5806
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Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. Resources and tools for the high-throughput, multi-omic study of intestinal microbiota. Brief Bioinform 2020; 20:1032-1056. [PMID: 29186315 DOI: 10.1093/bib/bbx156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022] Open
Abstract
The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions.
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Affiliation(s)
| | | | | | - Anália Lourenço
- Dpto. de Informática - Universidade de Vigo, ESEI - Escuela Superior de Ingeniería Informática, Edificio politécnico, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain
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35
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Glowska E, Filutowska ZK, Dabert M, Gerth M. Microbial composition of enigmatic bird parasites: Wolbachia and Spiroplasma are the most important bacterial associates of quill mites (Acariformes: Syringophilidae). Microbiologyopen 2020; 9:e964. [PMID: 32141700 PMCID: PMC7221428 DOI: 10.1002/mbo3.964] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Background The microbiome is an integral component of many animal species, potentially affecting behavior, physiology, and other biological properties. Despite this importance, bacterial communities remain vastly understudied in many groups of invertebrates, including mites. Quill mites (Acariformes: Syringophilidae) are a poorly known group of permanent bird ectoparasites that occupy quills of feathers and feed on bird subcutaneous tissue and fluids. Most of the known species have strongly female‐biased sex ratio, and it was hypothesized that this is caused by endosymbiotic bacteria. Previously, Anaplasma phagocytophilum (Foggie) and a high diversity of Wolbachia strains were detected in quill mites via targeted PCR screens. Here, we use an unbiased 16S rRNA gene amplicon sequencing approach to determine other bacteria that potentially impact quill mite biology. Results We performed 16S rRNA gene amplicon sequencing of 126 quill mite individuals from eleven species parasitizing twelve species (four families) of passeriform birds. In addition to Wolbachia, we found Spiroplasma as potential symbiont of quill mites. Consistently, high Spiroplasma titers were only found in individuals of two mite species associated with finches of the genus Carduelis, suggesting a history of horizontal transfers of Spiroplasma via the bird host. Furthermore, there was evidence for Spiroplasma negatively affecting Wolbachia titers. We found no evidence for the previously reported Anaplasma in quill mites, but detected sequences of high similarity to the potential pathogens Brucella and Bartonella at low abundances. Other amplicon sequence variants (ASVs) could be assigned to a diverse number of bacterial taxa, including several that were previously isolated from bird skin. Further, many frequently found ASVs were assigned to taxa that show a very broad distribution with no strong prior evidence for symbiotic association with animals. We interpret these findings as evidence for a scarcity of resident microbial associates (other than inherited symbionts) in quill mites.
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Affiliation(s)
- Eliza Glowska
- Faculty of Biology, Department of Animal Morphology, Adam Mickiewicz University in Poznań, Poznan, Poland
| | - Zuzanna Karolina Filutowska
- Faculty of Biology, Molecular Biology Techniques Laboratory, Adam Mickiewicz University in Poznań, Poznan, Poland.,Faculty of Biology, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznan, Poland
| | - Miroslawa Dabert
- Faculty of Biology, Molecular Biology Techniques Laboratory, Adam Mickiewicz University in Poznań, Poznan, Poland
| | - Michael Gerth
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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Li J, Chen Z, Wang Y. Contents, Construction Methods, Data Resources, and Functions Comparative Analysis of Bacteria Databases. Int J Biol Sci 2020; 16:838-848. [PMID: 32071553 PMCID: PMC7019132 DOI: 10.7150/ijbs.39289] [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] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/11/2019] [Indexed: 11/20/2022] Open
Abstract
Many bacterial-related databases are developed to meet the researchers' needs of analysis and search for a number of bacterial information. However, these databases have different data resources, construction methods, data formats, and analysis tools. It's difficult for researchers to select appropriate databases and analysis tools to promote their researches. In the paper, we compared the contents, construction methods, data sources, update frequency, scope and scale of data, analysis tools, and features of nine famous bacterial databases: CARD, EffectiveDB, MBGD, MPD, PATRCI, PHI-base, VFDB, gcMeta and SILVA, and help researchers to better make better use of these databases. In addition, we also hope this review can help researchers develop a more comprehensive database and better tools to meet the needs of researchers.
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Affiliation(s)
- Jie Li
- School of Computer Science and Technology, Harbin Institute of Technology, China
| | - Zhuo Chen
- School of Computer Science and Technology, Harbin Institute of Technology, China
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, China
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37
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Chowdhury S, Fong SS. Computational Modeling of the Human Microbiome. Microorganisms 2020; 8:microorganisms8020197. [PMID: 32023941 PMCID: PMC7074762 DOI: 10.3390/microorganisms8020197] [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: 12/16/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/20/2022] Open
Abstract
The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.
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Affiliation(s)
- Shomeek Chowdhury
- Integrative Life Sciences, Virginia Commonwealth University, 1000 West Cary Street, Richmond, VA 23284 USA;
| | - Stephen S. Fong
- Chemical and Life Science Engineering, Virginia Commonwealth University, 601 West Main Street, Richmond, VA 23284, USA
- Correspondence:
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Rezasoltani S, Ahmadi Bashirzadeh D, Nazemalhosseini Mojarad E, Asadzadeh Aghdaei H, Norouzinia M, Shahrokh S. Signature of Gut Microbiome by Conventional and Advanced Analysis Techniques: Advantages and Disadvantages. Middle East J Dig Dis 2019; 12:5-11. [PMID: 32082515 PMCID: PMC7023644 DOI: 10.15171/mejdd.2020.157] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Gut microbiota is considered as a human organ with its own specific functions and complexity. Development of novel techniques such as shut gun sequencing, metagenomics, and next-generation sequencing (NGS) has enabled bypassing the traditional culturedependent bias and has significantly expanded our understanding of the composition, diversity, and roles of the gut microbiota in human health and diseases. Although amplicon sequencing characterizes the taxonomic composition of the gut microbiome, it is impossible to cover the direct evidence of the microbial biological functions related to the gut microbial community. Hence, the critical next step for gut microbiome studies is shifting from gene/ genome-centric analysis to mechanism-centric techniques by integrating omics data with experimental results. Realizing gut microbial diversity and their bioactive metabolites function will provide insight into the clinical application of gut microbiota in diagnoses and treatments of several diseases. In this review, we focused on explaining the conventional and advanced microbiome analysis techniques regarding gut microbiota investigation with considering the advantages and disadvantages of the platforms.
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Affiliation(s)
- Sama Rezasoltani
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Dorrieh Ahmadi Bashirzadeh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Norouzinia
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Gabaldón T. Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 2019; 43:517-547. [PMID: 31158289 PMCID: PMC8038933 DOI: 10.1093/femsre/fuz015] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/31/2019] [Indexed: 12/29/2022] Open
Abstract
The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
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40
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The Role of Adipose Tissue in the Pathogenesis and Therapeutic Outcomes of Inflammatory Bowel Disease. Cells 2019; 8:cells8060628. [PMID: 31234447 PMCID: PMC6627060 DOI: 10.3390/cells8060628] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/16/2019] [Accepted: 06/18/2019] [Indexed: 02/06/2023] Open
Abstract
Though historically regarded as an inert energy store, adipose tissue is a complex endocrine organ, which is increasingly implicated in the pathogenesis of inflammatory bowel disease (IBD). Accumulating evidence points to visceral adipose tissue and specifically to its mesenteric component, or “creeping fat” as impacting on the disease course through its immunomodulatory properties. On the one hand, mesenteric fat acts as a physical barrier to inflammation and is involved in controlling host immune response to translocation of gut bacteria. On the other hand, however, there exists a strong link between visceral fat and complicated course of the disease with unfavorable therapeutic outcomes. Furthermore, “creeping fat” appears to play different roles in different IBD phenotypes, with the greatest pathogenetic contribution probably to an ileal form of Crohn’s disease. In this review, we summarize and discuss the existing literature on the subject and identify high-priority areas for future research. It may be that a better understanding of the role of mesenteric fat in IBD will determine new therapeutic targets and translate into improved clinical outcomes.
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Celi P, Verlhac V, Pérez Calvo E, Schmeisser J, Kluenter AM. Biomarkers of gastrointestinal functionality in animal nutrition and health. Anim Feed Sci Technol 2019. [DOI: 10.1016/j.anifeedsci.2018.07.012] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Abstract
The liver is the central organ involved in lipid metabolism and the gastrointestinal (GI) tract is responsible for nutrient absorption and partitioning. Obesity, dyslipidemia and metabolic disorders are of increasing public health concern worldwide, and novel therapeutics that target both the liver and the GI tract (gut-liver axis) are much needed. In addition to aiding fat digestion, bile acids act as important signaling molecules that regulate lipid, glucose and energy metabolism via activating nuclear receptor, G protein-coupled receptors (GPCRs), Takeda G protein receptor 5 (TGR5) and sphingosine-1-phosphate receptor 2 (S1PR2). Sphingosine-1-phosphate (S1P) is synthesized by two sphingosine kinase isoforms and is a potent signaling molecule that plays a critical role in various diseases such as fatty liver, inflammatory bowel disease (IBD) and colorectal cancer. In this review, we will focus on recent findings related to the role of S1P-mediated signaling pathways in the gut-liver axis.
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Affiliation(s)
- Eric K. Kwong
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA,McGuire VA Medical Center, Richmond, VA, USA
| | - Huiping Zhou
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA,McGuire VA Medical Center, Richmond, VA, USA,Corresponding author. Department of Microbiology and Immunology, Virginia Commonwealth University, McGuire Veterans Affairs Medical Center, Richmond, VA, USA. (H. Zhou)
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43
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Megat Mohd Azlan PIH, Chin SF, Low TY, Neoh HM, Jamal R. Analyzing the Secretome of Gut Microbiota as the Next Strategy For Early Detection of Colorectal Cancer. Proteomics 2019; 19:e1800176. [PMID: 30557447 DOI: 10.1002/pmic.201800176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 12/02/2018] [Indexed: 12/20/2022]
Abstract
Dysbiosis of gut microbiome can contribute to inflammation, and subsequently initiation and progression of colorectal cancer (CRC). Throughout these stages, various proteins and metabolites are secreted to the external environment by microorganisms or the hosts themselves. Studying these proteins may help enhance our understanding of the host-microorganism relationship or they may even serve as useful biomarkers for CRC. However, secretomic studies of gut microbiome of CRC patients, until now, are scarcely performed. In this review article, the focus is on the roles of gut microbiome in CRC, the current findings on CRC secretome are highlighted, and the emerging challenges and strategies to drive forward this area of research are addressed.
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Affiliation(s)
| | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia
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44
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Kiernan MG, Coffey JC, McDermott K, Cotter PD, Cabrera-Rubio R, Kiely PA, Dunne CP. The Human Mesenteric Lymph Node Microbiome Differentiates Between Crohn's Disease and Ulcerative Colitis. J Crohns Colitis 2019; 13:58-66. [PMID: 30239655 PMCID: PMC6302955 DOI: 10.1093/ecco-jcc/jjy136] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND AND AIMS Mesenteric lymph nodes are sites in which translocated bacteria incite and progress immunological responses. For this reason, understanding the microbiome of mesenteric lymph nodes in inflammatory bowel disease is important. The bacterial profile of Crohn's disease mesenteric lymph nodes has been analysed using culture-independent methods in only one previous study. This study aimed to investigate the mesenteric lymph node microbiota from both Crohn's disease and ulcerative colitis patients. METHODS Mesenteric lymph nodes were collected from Crohn's disease and ulcerative colitis patients undergoing resection. Total DNA was extracted from mesenteric lymph nodes and assessed for the presence of bacterial DNA [16S]. All work was completed in a sterile environment using aseptic techniques. Samples positive for 16S DNA underwent next-generation sequencing, and the identity of bacterial phyla and species were determined. RESULTS Crohn's disease mesenteric lymph nodes had a distinctly different microbial profile to that observed in ulcerative colitis. The relative abundance of Firmicutes was greater in nodes from ulcerative colitis patients, whereas Proteobacteria were more abundant in Crohn's disease. Although species diversity was reduced in the mesenteric lymph nodes of patients with Crohn's disease, these lymph nodes contained greater numbers of less dominant phyla, mainly Fusobacteria. CONCLUSION This study confirms that there are distinct differences between the Crohn's disease and ulcerative colitis mesenteric lymph node microbiomes. Such microbial differences could aid in the diagnosis of Crohn's disease or ulcerative colitis, particularly in cases of indeterminate colitis at time of resection, or help explain their mechanisms of development and progression.
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Affiliation(s)
- Miranda G Kiernan
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity [4i], University of Limerick, Limerick, Ireland
| | - J Calvin Coffey
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity [4i], University of Limerick, Limerick, Ireland,Department of Surgery, University Hospital Limerick, Limerick, Ireland
| | - Kieran McDermott
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity [4i], University of Limerick, Limerick, Ireland
| | - Paul D Cotter
- APC Microbiome Institute, University College Cork, Cork, Ireland,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Raul Cabrera-Rubio
- APC Microbiome Institute, University College Cork, Cork, Ireland,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Patrick A Kiely
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity [4i], University of Limerick, Limerick, Ireland
| | - Colum P Dunne
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity [4i], University of Limerick, Limerick, Ireland,Corresponding author: Professor Colum Dunne, Director of Research, Graduate Entry Medical School, University of Limerick, Limerick V94 T9PX, Ireland. Tel: +353-[0]61-234703;
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Esteban-Torres M, Santamaría L, Cabrera-Rubio R, Plaza-Vinuesa L, Crispie F, de Las Rivas B, Cotter P, Muñoz R. A Diverse Range of Human Gut Bacteria Have the Potential To Metabolize the Dietary Component Gallic Acid. Appl Environ Microbiol 2018; 84:e01558-18. [PMID: 30054365 PMCID: PMC6146992 DOI: 10.1128/aem.01558-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022] Open
Abstract
The human gut microbiota contains a broad variety of bacteria that possess functional genes, with resultant metabolites that affect human physiology and therefore health. Dietary gallates are phenolic components that are present in many foods and beverages and are regarded as having health-promoting attributes. However, the potential for metabolism of these phenolic compounds by the human microbiota remains largely unknown. The emergence of high-throughput sequencing (HTS) technologies allows this issue to be addressed. In this study, HTS was used to assess the incidence of gallate-decarboxylating bacteria within the gut microbiota of healthy individuals for whom bacterial diversity was previously determined to be high. This process was facilitated by the design and application of degenerate PCR primers to amplify a region encoding the catalytic C subunit of gallate decarboxylase (LpdC) from total metagenomic DNA extracted from human fecal samples. HTS resulted in the generation of a total of 3,261,967 sequence reads and revealed that the primary gallate-decarboxylating microbial phyla in the intestinal microbiota were Firmicutes (74.6%), Proteobacteria (17.6%), and Actinobacteria (7.8%). These reads corresponded to 53 genera, i.e., 47% of the bacterial genera detected previously in these samples. Among these genera, Anaerostipes and Klebsiella accounted for the majority of reads (40%). The usefulness of the HTS-lpdC method was demonstrated by the production of pyrogallol from gallic acid, as expected for functional gallate decarboxylases, among representative strains belonging to species identified in the human gut microbiota by this method.IMPORTANCE Despite the increasing wealth of sequencing data, the health contributions of many bacteria found in the human gut microbiota have yet to be elucidated. This study applies a novel experimental approach to predict the ability of gut microbes to carry out a specific metabolic activity, i.e., gallate metabolism. The study showed that, while gallate-decarboxylating bacteria represented 47% of the bacterial genera detected previously in the same human fecal samples, no gallate decarboxylase homologs were identified from representatives of Bacteroidetes The presence of functional gallate decarboxylases was demonstrated in representative Proteobacteria and Firmicutes strains from the human microbiota, an observation that could be of considerable relevance to the in vivo production of pyrogallol, a physiologically important bioactive compound.
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Affiliation(s)
- María Esteban-Torres
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Laura Santamaría
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
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Chellapandi P, Bharathi M, Sangavai C, Prathiviraj R. Methanobacterium formicicum as a target rumen methanogen for the development of new methane mitigation interventions: A review. Vet Anim Sci 2018; 6:86-94. [PMID: 32734058 PMCID: PMC7386643 DOI: 10.1016/j.vas.2018.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 08/29/2018] [Accepted: 09/12/2018] [Indexed: 12/18/2022] Open
Abstract
Methanobacterium formicicum (Methanobacteriaceae family) is an endosymbiotic methanogenic Archaean found in the digestive tracts of ruminants and elsewhere. It has been significantly implicated in global CH4 emission during enteric fermentation processes. In this review, we discuss current genomic and metabolic aspects of this microorganism for the purpose of the discovery of novel veterinary therapeutics. This microorganism encompasses a typical H2 scavenging system, which facilitates a metabolic symbiosis across the H2 producing cellulolytic bacteria and fumarate reducing bacteria. To date, five genome-scale metabolic models (iAF692, iMG746, iMB745, iVS941 and iMM518) have been developed. These metabolic reconstructions revealed the cellular and metabolic behaviors of methanogenic archaea. The characteristics of its symbiotic behavior and metabolic crosstalk with competitive rumen anaerobes support understanding of the physiological function and metabolic fate of shared metabolites in the rumen ecosystem. Thus, systems biological characterization of this microorganism may provide a new insight to realize its metabolic significance for the development of a healthy microbiota in ruminants. An in-depth knowledge of this microorganism may allow us to ensure a long term sustainability of ruminant-based agriculture.
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Affiliation(s)
- P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024, India
| | - M Bharathi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024, India
| | - C Sangavai
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024, India
| | - R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024, India
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Bauer E, Thiele I. From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease. NPJ Syst Biol Appl 2018; 4:27. [PMID: 30083388 PMCID: PMC6068170 DOI: 10.1038/s41540-018-0063-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 05/17/2018] [Accepted: 05/30/2018] [Indexed: 12/13/2022] Open
Abstract
Crohn's disease (CD) is associated with an ecological imbalance of the intestinal microbiota, consisting of hundreds of species. The underlying complexity as well as individual differences between patients contributes to the difficulty to define a standardized treatment. Computational modeling can systematically investigate metabolic interactions between gut microbes to unravel mechanistic insights. In this study, we integrated metagenomic data of CD patients and healthy controls with genome-scale metabolic models into personalized in silico microbiotas. We predicted short chain fatty acid (SFCA) levels for patients and controls, which were overall congruent with experimental findings. As an emergent property, low concentrations of SCFA were predicted for CD patients and the SCFA signatures were unique to each patient. Consequently, we suggest personalized dietary treatments that could improve each patient's SCFA levels. The underlying modeling approach could aid clinical practice to find dietary treatment and guide recovery by rationally proposing food aliments.
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Affiliation(s)
- Eugen Bauer
- Luxembourg Centre for Systems Biomedicine, Universite du Luxembourg, Esch-sur-Alzette, Luxembourg, L-4362 Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, Universite du Luxembourg, Esch-sur-Alzette, Luxembourg, L-4362 Luxembourg
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Rosario D, Benfeitas R, Bidkhori G, Zhang C, Uhlen M, Shoaie S, Mardinoglu A. Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling. Front Physiol 2018; 9:775. [PMID: 29988585 PMCID: PMC6026676 DOI: 10.3389/fphys.2018.00775] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/04/2018] [Indexed: 01/21/2023] Open
Abstract
Dysbiosis in the gut microbiome composition may be promoted by therapeutic drugs such as metformin, the world’s most prescribed antidiabetic drug. Under metformin treatment, disturbances of the intestinal microbes lead to increased abundance of Escherichia spp., Akkermansia muciniphila, Subdoligranulum variabile and decreased abundance of Intestinibacter bartlettii. This alteration may potentially lead to adverse effects on the host metabolism, with the depletion of butyrate producer genus. However, an increased production of butyrate and propionate was verified in metformin-treated Type 2 diabetes (T2D) patients. The mechanisms underlying these nutritional alterations and their relation with gut microbiota dysbiosis remain unclear. Here, we used Genome-scale Metabolic Models of the representative gut bacteria Escherichia spp., I. bartlettii, A. muciniphila, and S. variabile to elucidate their bacterial metabolism and its effect on intestinal nutrient pool, including macronutrients (e.g., amino acids and short chain fatty acids), minerals and chemical elements (e.g., iron and oxygen). We applied flux balance analysis (FBA) coupled with synthetic lethality analysis interactions to identify combinations of reactions and extracellular nutrients whose absence prevents growth. Our analyses suggest that Escherichia sp. is the bacteria least vulnerable to nutrient availability. We have also examined bacterial contribution to extracellular nutrients including short chain fatty acids, amino acids, and gasses. For instance, Escherichia sp. and S. variabile may contribute to the production of important short chain fatty acids (e.g., acetate and butyrate, respectively) involved in the host physiology under aerobic and anaerobic conditions. We have also identified pathway susceptibility to nutrient availability and reaction changes among the four bacteria using both FBA and flux variability analysis. For instance, lipopolysaccharide synthesis, nucleotide sugar metabolism, and amino acid metabolism are pathways susceptible to changes in Escherichia sp. and A. muciniphila. Our observations highlight important commensal and competing behavior, and their association with cellular metabolism for prevalent gut microbes. The results of our analysis have potential important implications for development of new therapeutic approaches in T2D patients through the development of prebiotics, probiotics, or postbiotics.
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Affiliation(s)
- Dorines Rosario
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Rui Benfeitas
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Gholamreza Bidkhori
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, United Kingdom.,Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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49
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Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe. Methods 2018; 149:3-12. [PMID: 29715508 DOI: 10.1016/j.ymeth.2018.04.029] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/06/2018] [Accepted: 04/22/2018] [Indexed: 02/06/2023] Open
Abstract
It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted.
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50
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Henson MA, Phalak P. Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis. BMC SYSTEMS BIOLOGY 2017; 11:145. [PMID: 29282051 PMCID: PMC5745886 DOI: 10.1186/s12918-017-0522-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Inflammatory bowel diseases (IBD), which include ulcerative colitis and Crohn's disease, cause chronic inflammation of the digestive tract in approximately 1.6 million Americans. A signature of IBD is dysbiosis of the gut microbiota marked by a significant reduction of obligate anaerobes and a sharp increase in facultative anaerobes. Numerous experimental studies have shown that IBD is strongly correlated with a decrease of Faecalibacterium prausnitzii and an increase of Escherichia coli. One hypothesis is that chronic inflammation induces increased oxygen levels in the gut, which in turn causes an imbalance between obligate and facultative anaerobes. RESULTS To computationally investigate the oxygen hypothesis, we developed a multispecies biofilm model based on genome-scale metabolic reconstructions of F. prausnitzii, E. coli and the common gut anaerobe Bacteroides thetaiotaomicron. Application of low bulk oxygen concentrations at the biofilm boundary reproduced experimentally observed behavior characterized by a sharp decrease of F. prausnitzii and a large increase of E. coli, demonstrating that dysbiosis consistent with IBD disease progression could be qualitatively predicted solely based on metabolic differences between the species. A diet with balanced carbohydrate and protein content was predicted to represent a metabolic "sweet spot" that increased the oxygen range over which F. prausnitzii could remain competitive and IBD could be sublimated. Host-microbiota feedback incorporated via a simple linear feedback between the average F. prausnitzii concentration and the bulk oxygen concentration did not substantially change the range of oxygen concentrations where dysbiosis was predicted, but the transition from normal species abundances to severe dysbiosis was much more dramatic and occurred over a much longer timescale. Similar predictions were obtained with sustained antibiotic treatment replacing a sustained oxygen perturbation, demonstrating how IBD might progress over several years with few noticeable effects and then suddenly produce severe disease symptoms. CONCLUSIONS The multispecies biofilm metabolic model predicted that oxygen concentrations of ∼1 micromolar within the gut could cause microbiota dysbiosis consistent with those observed experimentally for inflammatory bowel diseases. Our model predictions could be tested directly through the development of an appropriate in vitro system of the three species community and testing of microbiota-host interactions in gnotobiotic mice.
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Affiliation(s)
- Michael A. Henson
- Department of Chemical Engineering and the Institute for Applied Life Sciences, University of Massachusetts, 140 Thatcher Way, Amherst, 01003 MA USA
| | - Poonam Phalak
- Department of Chemical Engineering and the Institute for Applied Life Sciences, University of Massachusetts, 140 Thatcher Way, Amherst, 01003 MA USA
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