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Trinh S, Keller L, Herpertz-Dahlmann B, Seitz J. [Fecal Microbiota Transplants in the Context of (Child and Adolescent) Psychiatric Disorders]. ZEITSCHRIFT FUR KINDER- UND JUGENDPSYCHIATRIE UND PSYCHOTHERAPIE 2023; 51:431-440. [PMID: 36892328 DOI: 10.1024/1422-4917/a000928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Fecal Microbiota Transplants in the Context of (Child and Adolescent) Psychiatric Disorders Abstract: There has recently been a significant increase in interest in gut microbiota and its interaction with the brain (gut-brain axis). Not only are the findings of microbiome research interesting for basic scientists, they also offer relevant insights for clinical practice. A causal relationship between gut microbiome and various somatic diseases such as diabetes mellitus, inflammatory bowel diseases, and obesity as well as psychiatric diseases such as major depression, anxiety disorders, and eating disorders seems plausible. To study the causal relationship of intestinal bacteria with individual phenotypes, researchers apply so-called stool transplantations (fecal microbiota transplantations) in the preclinical context. For this purpose, they transfer microbiota samples from patients into laboratory animals to observe possible changes in phenotype. In the clinical context, fecal microbiota transplantation is already being used with therapeutic intentions for selected diseases, for example, recurrent infections with Clostridioides difficile or inflammatory bowel diseases; they have already become part of the official clinical guidelines for C. difficile. For many other diseases, however, including mental illnesses, the potential of using fecal transplantations for therapeutic purposes is still being explored. Previous findings suggest that the intestinal microbiome, particularly fecal microbiota transplantations, represent a promising starting point for new therapeutic approaches.
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Affiliation(s)
- Stefanie Trinh
- Institut für Neuroanatomie, Uniklinik RWTH Aachen, Deutschland
| | - Lara Keller
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Uniklinik RWTH Aachen, Deutschland
| | - Beate Herpertz-Dahlmann
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Uniklinik RWTH Aachen, Deutschland
| | - Jochen Seitz
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Uniklinik RWTH Aachen, Deutschland
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2
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Ecker M, Haller D. Bedeutung des Mikrobioms für Adipositas und Glukosestoffwechsel. GYNAKOLOGISCHE ENDOKRINOLOGIE 2022. [DOI: 10.1007/s10304-022-00467-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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3
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Afrizal A, Hitch TCA, Viehof A, Treichel N, Riedel T, Abt B, Buhl EM, Kohlheyer D, Overmann J, Clavel T. Anaerobic single-cell dispensing facilitates the cultivation of human gut bacteria. Environ Microbiol 2022; 24:3861-3881. [PMID: 35233904 DOI: 10.1111/1462-2920.15935] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 12/22/2022]
Abstract
Cultivation via classical agar plate (CAP) approaches is widely used to study microbial communities, but they are time-consuming. An alternative approach is the application of single-cell dispensing (SCD), which allows high-throughput, label-free sorting of microscopic particles. We aimed to develop a new anaerobic SCD workflow to cultivate human gut bacteria and compared it with CAP using faecal communities on three rich culture media. We found that the SCD approach significantly decreased the experimental time to obtain pure cultures from 17 ± 4 to 5 ± 0 days, while the isolate diversity and relative abundance coverage were comparable for both approaches. We further tested the total captured fraction by sequencing the sorted bacteria directly after growth as bulk biomass from 2400 dispensed single cells without downstream identification of individual strains. In this approach, the cultured fraction increased from 35.2% to 52.2% for SCD, highlighting the potential for deeper cultivation projects from single samples. SCD-based cultivation also captured species not detected by sequencing (16 ± 5 per sample, including seven novel taxa). From this work, 82 human gut bacterial species across five phyla (Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes and Proteobacteria) and 24 families were obtained, including the first cultured member of 11 novel genera and 10 novel species that were fully characterized taxonomically.
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Affiliation(s)
- Afrizal Afrizal
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Alina Viehof
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Nicole Treichel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Birte Abt
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Eva M Buhl
- Electron Microscopy Facility, Institute of Pathology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.,Aachener Verfahrenstechnik (AVT-MSB), RWTH Aachen University, Aachen, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
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4
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Reitmeier S, Hitch TCA, Treichel N, Fikas N, Hausmann B, Ramer-Tait AE, Neuhaus K, Berry D, Haller D, Lagkouvardos I, Clavel T. Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling. ISME COMMUNICATIONS 2021; 1:31. [PMID: 37938227 PMCID: PMC9723555 DOI: 10.1038/s43705-021-00033-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 04/23/2023]
Abstract
16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.
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Affiliation(s)
- Sandra Reitmeier
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany
| | - Nicole Treichel
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany
| | - Nikolaos Fikas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Klaus Neuhaus
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - David Berry
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dirk Haller
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Ilias Lagkouvardos
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany.
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece.
| | - Thomas Clavel
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany.
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany.
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5
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Heidebrecht HJ, Lagkouvardos I, Reitmeier S, Hengst C, Kulozik U, Pfaffl MW. Alteration of Intestinal Microbiome of Clostridioides difficile-Infected Hamsters during the Treatment with Specific Cow Antibodies. Antibiotics (Basel) 2021; 10:antibiotics10060724. [PMID: 34208527 PMCID: PMC8235726 DOI: 10.3390/antibiotics10060724] [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: 05/06/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 01/04/2023] Open
Abstract
Clostridioides difficile infection (CDI) often develops after pretreatment with antibiotics, which can lead to damage of the intestinal microbiome. The approach of this study was to use specific polyclonal antibodies isolated from the milk of immunized cows to treat CDI, in contrast to the standard application of nonspecific antibiotics. To gain a deeper understanding of the role of the microbiome in the treatment of CDI with bovine antibodies, stool and intestinal fluid samples of hamsters were collected in large quantities from various treatments (>400 samples). The results show that the regeneration of the microbiome instantly begins with the start of the antibody treatment, in contrast to the Vancomycin-treated group where the diversity decreased significantly during the treatment duration. All antibody-treated hamsters that survived the initial phase also survived the entire study period. The results also show that the regeneration of the microbiome was not an antibody-induced regeneration, but a natural regeneration that occurred because no microbiota-inactivating substances were administered. In conclusion, the treatment with bovine antibodies is a functional therapy for both the acute treatment and the prevention of recurrence in hamsters and could meet the urgent need for CDI treatment alternatives in humans.
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Affiliation(s)
- Hans-Jürgen Heidebrecht
- Food- and Bioprocess Engineering, TUM School of Life Science, Technical University of Munich, Weihenstephaner Berg 1, 85354 Freising, Germany; (C.H.); (U.K.)
- Correspondence: ; Tel.: +49-8161713481
| | - Ilias Lagkouvardos
- ZIEL—Institute for Food & HealthCore Facility Microbiome, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (I.L.); (S.R.)
| | - Sandra Reitmeier
- ZIEL—Institute for Food & HealthCore Facility Microbiome, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (I.L.); (S.R.)
| | - Claudia Hengst
- Food- and Bioprocess Engineering, TUM School of Life Science, Technical University of Munich, Weihenstephaner Berg 1, 85354 Freising, Germany; (C.H.); (U.K.)
| | - Ulrich Kulozik
- Food- and Bioprocess Engineering, TUM School of Life Science, Technical University of Munich, Weihenstephaner Berg 1, 85354 Freising, Germany; (C.H.); (U.K.)
| | - Michael W. Pfaffl
- Animal Physiology and Immunology, TUM School of Life Science, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany;
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6
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Seitz J, Dahmen B, Keller L, Herpertz-Dahlmann B. Gut Feelings: How Microbiota Might Impact the Development and Course of Anorexia Nervosa. Nutrients 2020; 12:E3295. [PMID: 33126427 PMCID: PMC7693512 DOI: 10.3390/nu12113295] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022] Open
Abstract
Anorexia nervosa (AN) can probably be regarded as a "model" for studying the interaction of nutrition with the gut-brain axis, which has drawn increased attention from researchers and clinicians alike. The gut microbiota influences somatic effects, such as energy extraction from food and body weight gain, as well as appetite, gut permeability, inflammation and complex psychological behaviors, such as depression or anxiety, all of which play important roles in AN. As nutrition is one of the main factors that influence the gut microbiota, nutritional restriction and selective eating in AN are likely influencing factors; however, nutritional rehabilitation therapy is surprisingly understudied. Here, we review the general mechanisms of the interactions between nutrition, the gut microbiota and the host that may be relevant to AN, paying special attention to the gut-brain axis, and we present the first specific findings in patients with AN and corresponding animal models. In particular, nutritional interventions, including food selection, supplements, and pre-, pro- and synbiotics that have the potential to influence the gut microbiota, are important research targets to potentially support future AN therapy.
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Affiliation(s)
- Jochen Seitz
- Department of Child and Adolescent Psychiatry, Psychotherapy and Psychosomatics, RWTH University Hospital, Neuenhofer Weg 21, 52074 Aachen, Germany; (B.D.); (L.K.); (B.H.-D.)
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7
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Amadei SS, Notario V. A Significant Question in Cancer Risk and Therapy: Are Antibiotics Positive or Negative Effectors? Current Answers and Possible Alternatives. Antibiotics (Basel) 2020; 9:E580. [PMID: 32899961 PMCID: PMC7558931 DOI: 10.3390/antibiotics9090580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer is predominantly considered as an environmental disease caused by genetic or epigenetic alterations induced by exposure to extrinsic (e.g., carcinogens, pollutants, radiation) or intrinsic (e.g., metabolic, immune or genetic deficiencies). Over-exposure to antibiotics, which is favored by unregulated access as well as inappropriate prescriptions by physicians, is known to have led to serious health problems such as the rise of antibiotic resistance, in particular in poorly developed countries. In this review, the attention is focused on evaluating the effects of antibiotic exposure on cancer risk and on the outcome of cancer therapeutic protocols, either directly acting as extrinsic promoters, or indirectly, through interactions with the human gut microbiota. The preponderant evidence derived from information reported over the last 10 years confirms that antibiotic exposure tends to increase cancer risk and, unfortunately, that it reduces the efficacy of various forms of cancer therapy (e.g., chemo-, radio-, and immunotherapy alone or in combination). Alternatives to the current patterns of antibiotic use, such as introducing new antibiotics, bacteriophages or enzybiotics, and implementing dysbiosis-reducing microbiota modulatory strategies in oncology, are discussed. The information is in the end considered from the perspective of the most recent findings on the tumor-specific and intracellular location of the tumor microbiota, and of the most recent theories proposed to explain cancer etiology on the notion of regression of the eukaryotic cells and systems to stages characterized for a lack of coordination among their components of prokaryotic origin, which is promoted by injuries caused by environmental insults.
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Affiliation(s)
| | - Vicente Notario
- Department of Radiation Medicine, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA;
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8
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Breitenwieser F, Doll EV, Clavel T, Scherer S, Wenning M. Complementary Use of Cultivation and High-Throughput Amplicon Sequencing Reveals High Biodiversity Within Raw Milk Microbiota. Front Microbiol 2020; 11:1557. [PMID: 32742267 PMCID: PMC7365021 DOI: 10.3389/fmicb.2020.01557] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/16/2020] [Indexed: 12/16/2022] Open
Abstract
Raw milk microbiota are complex communities with a significant impact on the hygienic, sensory and technological quality of milk products. However, there is a lack of knowledge on factors determining their composition. In the present study, four bulk tank milk samples of two farms at two different time points were analyzed in detail for their microbiota using cultivation and 16S rRNA amplicon sequencing. Diversity in samples from the first time point was assessed via cultivation of 500 aerobic mesophilic bacterial isolates in each sample. A high biodiversity of 70 and 110 species per sample was determined, of which 25–28% corresponded to yet unknown taxa. The isolates were dominated by Gram-positive members of the genera Staphylococcus, Corynebacterium, Streptococcus, or Janibacter, whilst Chryseobacterium and Acinetobacter were most abundant among the Gram-negative taxa. At the second time point, samples of the same farms were analyzed via both cultivation (1,500 individual colonies each) and high-throughput 16S rRNA gene amplicon sequencing. The latter revealed a threefold higher biodiversity at the genus level, as anaerobic or fastidious species were also detected. However, cultivation identified genera not captured by sequencing, indicating that both approaches are complementary. Using amplicon sequencing, the relative abundance of a few genera was distorted, which seems to be an artifact of sample preparation. Therefore, attention needs to be paid to the library preparation procedure with special emphasis on cell lysis and PCR.
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Affiliation(s)
| | - Etienne V Doll
- Chair for Microbial Ecology, Weihenstephan School of Life Sciences, Technische Universität München, Freising, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany.,ZIEL - Institute for Food and Health, Technische Universität München, Freising, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, Weihenstephan School of Life Sciences, Technische Universität München, Freising, Germany.,ZIEL - Institute for Food and Health, Technische Universität München, Freising, Germany
| | - Mareike Wenning
- Chair for Microbial Ecology, Weihenstephan School of Life Sciences, Technische Universität München, Freising, Germany.,Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
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9
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Ul-Hasan S, Rodríguez-Román E, Reitzel AM, Adams RMM, Herzig V, Nobile CJ, Saviola AJ, Trim SA, Stiers EE, Moschos SA, Keiser CN, Petras D, Moran Y, Colston TJ. The emerging field of venom-microbiomics for exploring venom as a microenvironment, and the corresponding Initiative for Venom Associated Microbes and Parasites (iVAMP). Toxicon X 2019; 4:100016. [PMID: 32550573 PMCID: PMC7286055 DOI: 10.1016/j.toxcx.2019.100016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Venom is a known source of novel antimicrobial natural products. The substantial, increasing number of these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent and -independent studies on the microbial communities in venom microenvironments reveal the presence of archaea, algae, bacteria, fungi, protozoa, and viruses. Venom-centric microbiome studies are relatively sparse to date with the adaptive advantages that venom-associated microbes might offer to their hosts, or that hosts might provide to venom-associated microbes, remaining largely unknown. We highlight the potential for the discovery of venom microbiomes within the adaptive landscape of venom systems. The considerable number of convergently evolved venomous animals, juxtaposed with the comparatively few known studies to identify microbial communities in venom, provides new possibilities for both biodiversity and therapeutic discoveries. We present an evidence-based argument for integrating microbiology as part of venomics (i.e., venom-microbiomics) and introduce iVAMP, the Initiative for Venom Associated Microbes and Parasites (https://ivamp-consortium.github.io/), as a growing collaborative consortium. We express commitment to the diversity, inclusion and scientific collaboration among researchers interested in this emerging subdiscipline through expansion of the iVAMP consortium. Venom-microbiome studies as an integrative field of venomics and microbiology. Argument for multi-omics-based discovery through a microenvironment framework. Introduction of a venom-microbiome research consortium (iVAMP).
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Affiliation(s)
- Sabah Ul-Hasan
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, 95343, USA.,Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Eduardo Rodríguez-Román
- Center for Microbiology and Cell Biology, Venezuelan Institute for Scientific Research. Caracas, 1020A, Venezuela
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Rachelle M M Adams
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, 43212, USA
| | - Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Anthony J Saviola
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Steven A Trim
- Venomtech Ltd, Discovery Park, Sandwich, Kent, CT13 9ND, UK
| | - Erin E Stiers
- Department of Biological Science, Clemson University, Clemson, SC, 29634, USA
| | - Sterghios A Moschos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, NE1 8ST, UK
| | - Carl N Keiser
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, USA.,Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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10
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Insoluble dietary fiber from soy hulls regulates the gut microbiota in vitro and increases the abundance of bifidobacteriales and lactobacillales. Journal of Food Science and Technology 2019; 57:152-162. [PMID: 31975718 DOI: 10.1007/s13197-019-04041-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022]
Abstract
We evaluated soy hull dietary fibers (SHDF) extracted from different raw materials, in terms of their chemical composition, physicochemical properties, structure, and ability to regulate fecal microflora, in order to investigate the properties and functions of SHDF. The structures of insoluble dietary fiber from soy hull with oxalic acid extraction (IDFO) and insoluble dietary fiber from soy hull with citric acid extraction (IDFC) were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray diffraction. Compared with IDFO, IDFC had larger crystalline regions, and a higher water retention capacity (4.92 g/g), water swelling capacity (4.77 mL/g), oil adsorption capacity (1.60%), α-amylase activity inhibition ratio (12.72%), glucose adsorption capacity (1.59-13.42%), and bile acid retardation index (5.18-26.61%). Given that the gut microbiota plays a pivotal role in health homeostasis, we performed a detailed investigation of the effects of dietary fiber on fecal microbiota through 16S rDNA high-throughput sequencing. As revealed by Venn, principal component analysis, and 3D-principal co-ordinates analysis analysis, the structure of the fecal microbiota community was markedly altered by intake of IDFO and IDFC. In particular, the abundance of Bifidobacteriales and Lactobacillales significantly increased to varying degrees as a result of IDFO and IDFC intake. Altogether, this study demonstrates a prebiotic effect of SHDF on the fecal microbiota in vitro and provides a basis for the development of SHDF as a novel gut microbiota modulator for health promotion.
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11
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Abdellatif AM, Sarvetnick NE. Current understanding of the role of gut dysbiosis in type 1 diabetes. J Diabetes 2019; 11:632-644. [PMID: 30864231 DOI: 10.1111/1753-0407.12915] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 02/13/2019] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
Type 1 diabetes (T1D) is a chronic autoimmune disorder that results from destruction of the insulin-producing pancreatic β-cells. The disease mainly affects juveniles. Changes in the composition of the gut microbiota (dysbiosis) and changes in the properties of the gut barrier have been documented in T1D subjects. Because these factors affect immune system functions, they are likely to play a role in disease pathogenesis. However, their exact role is currently not fully understood and is under intensive investigation. In this article we discuss recent advancements depicting the role of intestinal dysbiosis on immunity and autoimmunity in T1D. We also discuss therapies aimed at maintaining a healthy gut barrier as prevention strategies for T1D.
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Affiliation(s)
- Ahmed M Abdellatif
- Department of Surgery-Transplant, University of Nebraska Medical Center, Omaha, Nebraska
- Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, Nebraska
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Nora E Sarvetnick
- Department of Surgery-Transplant, University of Nebraska Medical Center, Omaha, Nebraska
- Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, Nebraska
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12
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Robledo‐Sierra J, Ben‐Amy DP, Varoni E, Bavarian R, Simonsen JL, Paster BJ, Wade WG, Kerr AR, Peterson DE, Frandsen Lau E. World Workshop on Oral Medicine VII: Targeting the oral microbiome Part 2: Current knowledge on malignant and potentially malignant oral disorders. Oral Dis 2019; 25 Suppl 1:28-48. [DOI: 10.1111/odi.13107] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/19/2019] [Accepted: 04/11/2019] [Indexed: 02/06/2023]
Affiliation(s)
| | - Dalit Porat Ben‐Amy
- Oral Medicine Unit Department of Oral & Maxillofacial Surgery The Baruch Padeh Medical Center Poriya Israel
| | - Elena Varoni
- Department of Biomedical, Surgical and Dental Sciences University of Milan Milan Italy
| | - Roxanne Bavarian
- Division of Oral Medicine and Dentistry Brigham and Women's Hospital Boston Massachusetts
- Department of Oral Medicine, Infection, and Immunity Harvard School of Dental Medicine, Harvard University Cambridge Massachusetts
| | - Janne L. Simonsen
- Aarhus University Library – Health Sciences Aarhus University Aarhus Denmark
| | | | - William G. Wade
- Centre for Host‐Microbiome Interactions Faculty of Dentistry, Oral & Craniofacial Sciences King's College London London UK
| | - Alexander R. Kerr
- Department of Oral and Maxillofacial Pathology, Radiology and Medicine New York University College of Medicine New York City New York
| | - Douglas E. Peterson
- Oral Medicine Section School of Dental Medicine UConn Health University of Connecticut Mansfield Connecticut
| | - Ellen Frandsen Lau
- Section for Periodontology Department of Dentistry and Oral Health Faculty of Health Aarhus University Aarhus Denmark
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Microbial and Functional Profile of the Ceca from Laying Hens Affected by Feeding Prebiotics, Probiotics, and Synbiotics. Microorganisms 2019; 7:microorganisms7050123. [PMID: 31064055 PMCID: PMC6560406 DOI: 10.3390/microorganisms7050123] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/01/2019] [Accepted: 05/04/2019] [Indexed: 01/01/2023] Open
Abstract
Diet has an essential influence in the establishment of the cecum microbial communities in poultry, so its supplementation with safe additives, such as probiotics, prebiotics, and synbiotics might improve animal health and performance. This study showed the ceca microbiome modulations of laying hens, after feeding with dry whey powder as prebiotics, Pediococcus acidilactici as probiotics, and the combination of both as synbiotics. A clear grouping of the samples induced per diet was observed (p < 0.05). Operational taxonomic units (OTUs) identified as Olsenella spp., and Lactobacilluscrispatus increased their abundance in prebiotic and synbiotic treatments. A core of the main functions was shared between all metagenomes (45.5%), although the genes encoding for the metabolism of butanoate, propanoate, inositol phosphate, and galactose were more abundant in the prebiotic diet. The results indicated that dietary induced-changes in microbial composition did not imply a disturbance in the principal biological roles, while the specific functions were affected.
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Abstract
Growing interest exists in the association of gut bacteria with diseases, such as diabetes, obesity, inflammatory bowel disease, and psychiatric disorders. Gut microbiota influence the fermentation of nutrients, body-weight regulation, gut permeability, hormones, inflammation, immunology, and behavior (gut-brain axis). Regarding anorexia nervosa (AN), altered microbial diversity and taxa abundance were found and associated with depressive, anxious, and eating disorder symptoms. Potential mechanisms involve increased gut permeability, low-grade inflammation, autoantibodies, and reduced brain cell neogenesis and learning. Gut microbiome is strongly influenced by refeeding practices. Microbiota-modulating strategies like nutritional interventions or psychobiotics application could become relevant additions to AN treatment.
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15
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Seitz J, Belheouane M, Schulz N, Dempfle A, Baines JF, Herpertz-Dahlmann B. The Impact of Starvation on the Microbiome and Gut-Brain Interaction in Anorexia Nervosa. Front Endocrinol (Lausanne) 2019; 10:41. [PMID: 30809191 PMCID: PMC6379250 DOI: 10.3389/fendo.2019.00041] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/17/2019] [Indexed: 12/20/2022] Open
Abstract
Interactions between the gut microbiome and the brain are of increasing interest to both researchers and clinicians. Evidence is mounting on the causal role of an altered gut microbiome in inflammatory diseases such as arthritis, inflammatory bowel disease, obesity and diabetes, and psychiatric diseases like anxiety and depression. Mechanisms include altered energy harvest from food, hormonal changes, increased gut permeability, inflammation, immune response, and a direct influence on the brain and behavior. Anorexia nervosa (AN) is the third most common disease in adolescence and exacts a high burden on patients and caregivers. It often becomes chronic and has the highest mortality of all psychiatric diseases. As AN is characterized by nutritional restrictions, weight loss, and severe behavioral symptoms including weight phobia, comorbid anxiety and depression, accompanied by endocrine alterations, increased inflammation, and immune response, exploring the role of the gut microbiome is crucial. Here, we present an overview of the potential mechanisms of interaction between the gut microbiome, the host and particularly the brain in AN and summarize the initial findings of microbiome research on AN. We conclude by identifying future research directions and potential therapeutic approaches, including nutritional interventions, probiotics, prebiotics and food supplements, that could become important additions to current AN therapy.
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Affiliation(s)
- Jochen Seitz
- Department of Child and Adolescent Psychiatry, Psychotherapy and Psychosomatics, University Hospital, RWTH University Aachen, Aachen, Germany
- *Correspondence: Jochen Seitz
| | - Meriem Belheouane
- Institute for Experimental Medicine, Kiel University and Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Nina Schulz
- Department of Child and Adolescent Psychiatry, Psychotherapy and Psychosomatics, University Hospital, RWTH University Aachen, Aachen, Germany
| | - Astrid Dempfle
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - John F. Baines
- Institute for Experimental Medicine, Kiel University and Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Beate Herpertz-Dahlmann
- Department of Child and Adolescent Psychiatry, Psychotherapy and Psychosomatics, University Hospital, RWTH University Aachen, Aachen, Germany
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16
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Effects of a Superabsorbent Resin with Boron on Bacterial Diversity of Peat Substrate and Maize Straw. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6071085. [PMID: 30320136 PMCID: PMC6167581 DOI: 10.1155/2018/6071085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/26/2018] [Indexed: 12/30/2022]
Abstract
As a chemical water-saving material, superabsorbent resin is often applied to improve soil physicochemical properties for the purpose of promoting crop growth. In this study, a new type of superabsorbent resin with boron (SARB) was used as a functional material mixed with peat substrate and maize straw in percentages (mass ratio) of 0.05%, 0.1%, 0.15%, and 0.2%, respectively, and high-throughput sequencing technology was used to test bacterial diversity, analyzing and exploring ecological safety of the superabsorbent resin with boron (SARB) in order to provide theoretical support for field applications. The research results show that the superabsorbent resin with boron (SARB) can promote bacterial community diversity in the maize straw. In ten treatments, Proteobacteria accounted for the absolute advantage of the bacterial population in the CT group and in the JG group. However, the superabsorbent resin with boron (SARB) synthesized in the laboratory cannot change the original structure of the bacterial community and has scarcely any toxic effect on the bacterial community in both peat substrate and maize straw, and, indeed, it has a strengthening effect on Proteobacteria and Actinobacteria and a weakening effect on Acidobacteria and Firmicutes to some extent.
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17
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de Souza EL, de Albuquerque TMR, Dos Santos AS, Massa NML, de Brito Alves JL. Potential interactions among phenolic compounds and probiotics for mutual boosting of their health-promoting properties and food functionalities - A review. Crit Rev Food Sci Nutr 2018; 59:1645-1659. [PMID: 29377718 DOI: 10.1080/10408398.2018.1425285] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Several foods are rich sources of phenolic compounds (PC) and their beneficial effects on human health may be increased through the action of probiotics. Additionally, probiotics may use PC as substrates, increasing their survival and functionality. This review presents available studies on the effects of PC on probiotics, including their physiological functionalities, interactions and capability of surviving during exposure to gastrointestinal conditions and when incorporated into food matrices. Studies have shown that PC can improve the adhesion capacity and survival of probiotics during exposure to conditions that mimic the gastrointestinal tract. There is strong evidence that PC can modulate the composition of the gut microbiota in hosts, improving a variety of biochemical markers and risk factors for chronic diseases. Available literature also indicates that metabolites of PC formed by intestinal microorganisms, including probiotics, exert a variety of benefits on host health. These metabolites are typically more active than parental dietary PC. The presence of PC commonly enhances probiotic survival in different foods. Finally, further clinical studies need to be developed to confirm in vitro and experimental findings concerning the beneficial interactions among different PC and probiotics.
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Affiliation(s)
- Evandro Leite de Souza
- a Department of Nutrition , Health Sciences Center, Federal University of Paraíba , João Pessoa , Paraíba , Brazil
| | | | - Aldeir Sabino Dos Santos
- a Department of Nutrition , Health Sciences Center, Federal University of Paraíba , João Pessoa , Paraíba , Brazil
| | - Nayara Moreira Lacerda Massa
- a Department of Nutrition , Health Sciences Center, Federal University of Paraíba , João Pessoa , Paraíba , Brazil
| | - José Luiz de Brito Alves
- a Department of Nutrition , Health Sciences Center, Federal University of Paraíba , João Pessoa , Paraíba , Brazil
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18
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Lagkouvardos I, Overmann J, Clavel T. Cultured microbes represent a substantial fraction of the human and mouse gut microbiota. Gut Microbes 2017; 8:493-503. [PMID: 28418756 PMCID: PMC5628658 DOI: 10.1080/19490976.2017.1320468] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 02/03/2023] Open
Abstract
During the last 15 years, molecular techniques have been preferred over culture-based approaches for the study of mammalian gut microbiota, i.e. the communities of microorganisms dwelling in the intestine of mammals. The main reason is the belief that the majority of gut bacteria, especially strict anaerobes, escape cultivation. Despite numerous such statements in publications, the literature does not provide a clear overview on the subject. In the present manuscript, we highlight recent work on the cultivation of bacteria from the intestine of mammals, review the literature and provide novel data pertaining to cultured fractions of mammalian gut microbiota. These data show that, despite marked inter-sample variations, 35 to 65% of molecular species detected by sequencing have representative strains in culture.
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Affiliation(s)
- Ilias Lagkouvardos
- ZIEL Institute for Food and Health, Core Facility Microbiome/NGS, Technical University of Munich, Munich, Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Thomas Clavel
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
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19
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Clavel T, Lagkouvardos I, Stecher B. From complex gut communities to minimal microbiomes via cultivation. Curr Opin Microbiol 2017. [DOI: 10.1016/j.mib.2017.05.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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The gut microbiota: A key factor in the therapeutic effects of (poly)phenols. Biochem Pharmacol 2017; 139:82-93. [PMID: 28483461 DOI: 10.1016/j.bcp.2017.04.033] [Citation(s) in RCA: 368] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/21/2017] [Indexed: 12/13/2022]
Abstract
(Poly)phenols (PPs) constitute a large family of phytochemicals with high chemical diversity that are known to be active principles of plant-derived nutraceuticals and herbal medicinal products. Their pharmacological activity, however, is difficult to demonstrate due to their mild physiological effects, and to the large inter-individual variability observed. Many PPs have little bioavailability and reach the colon almost unaltered. There they encounter the gut microbes resulting in a two-way interaction in which PPs modulate the gut microbiota composition, and the intestinal microbes catabolize the ingested PPs to release metabolites that are often more active and better absorbed than the native phenolic compounds. The type and quantity of the PP metabolites produced in humans depend on the gut microbiota composition and function, and different metabotypes have been identified. However, not all the metabolites have the same biological activity, and therefore the final health effects of dietary PPs depend on the gut microbiota composition. Stratification in clinical trials according to individuals' metabotypes is necessary to fully understand the health effects of PPs. In this review, we present and discuss the most significant and updated knowledge regarding the reciprocal interrelation of the gut microbiota with dietary PPs as a key factor that modulates the health effects of these compounds. The review will focus in those PPs that are known to be metabolized by gut microbiota resulting in bioactive metabolites.
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21
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Kong HH, Andersson B, Clavel T, Common JE, Jackson SA, Olson ND, Segre JA, Traidl-Hoffmann C. Performing Skin Microbiome Research: A Method to the Madness. J Invest Dermatol 2017; 137:561-568. [PMID: 28063650 PMCID: PMC5468751 DOI: 10.1016/j.jid.2016.10.033] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 02/07/2023]
Abstract
Growing interest in microbial contributions to human health and disease has increasingly led investigators to examine the microbiome in both healthy skin and cutaneous disorders, including acne, psoriasis, and atopic dermatitis. The need for common language, effective study design, and validated methods is critical for high-quality standardized research. Features, unique to skin, pose particular challenges when conducting microbiome research. This review discusses microbiome research standards and highlights important factors to consider, including clinical study design, skin sampling, sample processing, DNA sequencing, control inclusion, and data analysis.
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Affiliation(s)
- Heidi H Kong
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Clavel
- Core Facility NGS/Microbiome, ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
| | | | - Scott A Jackson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Nathan D Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Julia A Segre
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Claudia Traidl-Hoffmann
- Institute of Environmental Medicine, UNIKA-T, Technical University of Munich and Helmholtz Zentrum München-German Research Center for Environmental Health, Augsburg, Germany; Christine Kühne Center for Allergy Research and Education, Davos, Switzerland
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22
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Lagkouvardos I, Fischer S, Kumar N, Clavel T. Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons. PeerJ 2017; 5:e2836. [PMID: 28097056 PMCID: PMC5234437 DOI: 10.7717/peerj.2836] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023] Open
Abstract
The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.
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Affiliation(s)
- Ilias Lagkouvardos
- ZIEL-Core Facility Microbiome/NGS, Technical University of Munich , Freising , Germany
| | - Sandra Fischer
- ZIEL-Core Facility Microbiome/NGS, Technical University of Munich , Freising , Germany
| | - Neeraj Kumar
- ZIEL-Core Facility Microbiome/NGS, Technical University of Munich , Freising , Germany
| | - Thomas Clavel
- ZIEL-Core Facility Microbiome/NGS, Technical University of Munich , Freising , Germany
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23
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Manook A, Hiergeist A, Rupprecht R, Baghai TC. Dickdarmmikrobiom und Depression. DER NERVENARZT 2016; 87:1227-1240. [DOI: 10.1007/s00115-016-0230-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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24
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Stubbendieck RM, Vargas-Bautista C, Straight PD. Bacterial Communities: Interactions to Scale. Front Microbiol 2016; 7:1234. [PMID: 27551280 PMCID: PMC4976088 DOI: 10.3389/fmicb.2016.01234] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/25/2016] [Indexed: 12/11/2022] Open
Abstract
In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.
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Affiliation(s)
- Reed M. Stubbendieck
- Interdisciplinary Program in Genetics, Texas A&M University, College StationTX, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College StationTX, USA
| | - Carol Vargas-Bautista
- Department of Plant Pathology and Microbiology, Texas A&M Agrilife Research, WeslacoTX, USA
| | - Paul D. Straight
- Interdisciplinary Program in Genetics, Texas A&M University, College StationTX, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College StationTX, USA
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