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Santiago-Rodriguez TM, Le François B, Macklaim JM, Doukhanine E, Hollister EB. The Skin Microbiome: Current Techniques, Challenges, and Future Directions. Microorganisms 2023; 11:1222. [PMID: 37317196 DOI: 10.3390/microorganisms11051222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses whose membership and function may differ depending on the various specialized niches or micro-environments of the skin. The group of microorganisms inhabiting the skin, also known as the skin microbiome, offers protection against pathogens while actively interacting with the host's immune system. Some members of the skin microbiome can also act as opportunistic pathogens. The skin microbiome is influenced by factors such as skin site, birth mode, genetics, environment, skin products, and skin conditions. The association(s) of the skin microbiome with health and disease has (have) been identified and characterized via culture-dependent and culture-independent methods. Culture-independent methods (such as high-throughput sequencing), in particular, have expanded our understanding of the skin microbiome's role in maintaining health or promoting disease. However, the intrinsic challenges associated with the low microbial biomass and high host content of skin microbiome samples have hindered advancements in the field. In addition, the limitations of current collection and extraction methods and biases derived from sample preparation and analysis have significantly influenced the results and conclusions of many skin microbiome studies. Therefore, the present review discusses the technical challenges associated with the collection and processing of skin microbiome samples, the advantages and disadvantages of current sequencing approaches, and potential future areas of focus for the field.
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Santiago-Rodriguez TM, Hollister EB. Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach. Viruses 2023; 15:236. [PMID: 36680277 PMCID: PMC9863393 DOI: 10.3390/v15010236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The One Health framework recognizes that human, animal, and environmental health are linked and highly interdependent. Fecal contamination of water, soil, foodstuff, and air may impact many aspects of One Health, and culture, PCR-based, and sequencing methods are utilized in the detection of fecal contamination to determine source, load, and risk to inform targeted mitigation strategies. Viruses, particularly, have been considered as fecal contamination indicators given the narrow host range many exhibit and their association with other biological contaminants. Culture- and molecular-based methods are considered the gold-standards for virus detection and for determining specific sources of fecal contamination via viral indicators. However, viral metagenomics is also being considered as a tool for tracking sources of fecal contamination. In the present review, studies tracking potential sources of fecal contamination in freshwaters, marine waters, foodstuff, soil, and air using viral metagenomics are discussed to highlight the potential of viral metagenomics for optimizing fecal source tracking. Limitations of the use of viral metagenomics to track fecal contamination sources, including sample processing, nucleic acid recovery, sequencing depth, and bioinformatics are also discussed. Finally, the present review discusses the potential of viral metagenomics as part of the toolbox of methods in a One Health approach.
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Abstract
Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.
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Kellermayer R, Wu Q, Nagy-Szakal D, Queliza K, Ihekweazu FD, Bocchini CE, Magee AR, Oezguen N, Spinler JK, Hollister EB, Shulman RJ, Versalovic J, Luna RA, Savidge TC. Fecal Microbiota Transplantation Commonly Failed in Children With Co-Morbidities. J Pediatr Gastroenterol Nutr 2022; 74:227-235. [PMID: 34724447 PMCID: PMC8799498 DOI: 10.1097/mpg.0000000000003336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Fecal microbiota transplantation (FMT) is arguably the most effective treatment for recurrent Clostridioides difficile infection (rCDI). Clinical reports on pediatric FMT have not systematically evaluated microbiome restoration in patients with co-morbidities. Here, we determined whether FMT recipient age and underlying co-morbidity influenced clinical outcomes and microbiome restoration when treated from shared fecal donor sources. METHODS Eighteen rCDI patients participating in a single-center, open-label prospective cohort study received fecal preparation from a self-designated (single case) or two universal donors. Twelve age-matched healthy children and four pediatric ulcerative colitis (UC) cases from an independent serial FMT trial, but with a shared fecal donor were examined as controls for microbiome restoration using 16S rRNA gene sequencing of longitudinal fecal specimens. RESULTS FMT was significantly more effective in rCDI recipients without underlying chronic co-morbidities where fecal microbiome composition in post-transplant responders was restored to levels of healthy children. Microbiome reconstitution was not associated with symptomatic resolution in some rCDI patients who had co-morbidities. Significant elevation in Bacteroidaceae, Bifidobacteriaceae, Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceae was consistently observed in pediatric rCDI responders, while Enterobacteriaceae decreased, correlating with augmented complex carbohydrate degradation capacity. CONCLUSION Recipient background disease was a significant risk factor influencing FMT outcomes. Special attention should be taken when considering FMT for pediatric rCDI patients with underlying co-morbidities.
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Affiliation(s)
- Richard Kellermayer
- Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
- USDA/ARS Children’s Nutrition Research Center, Houston, Texas, USA
| | - Qinglong Wu
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Dorottya Nagy-Szakal
- Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
| | - Karen Queliza
- Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
| | - Faith D. Ihekweazu
- Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
| | - Claire E. Bocchini
- Pediatric Infectious Diseases, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
| | - Abria R. Magee
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Numan Oezguen
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Jennifer K. Spinler
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Emily B. Hollister
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Robert J. Shulman
- Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Ruth Ann Luna
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Tor C. Savidge
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
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Ansley RJ, Boutton TW, Hollister EB. Can prescribed fires restore C
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grasslands invaded by a C
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woody species and a co‐dominant C
3
grass species? Ecosphere 2021. [DOI: 10.1002/ecs2.3885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- R. James Ansley
- Natural Resource Ecology and Management Department Oklahoma State University Stillwater Oklahoma 74078 USA
| | - Thomas W. Boutton
- Department of Ecology and Conservation Biology Texas A&M University College Station Texas 77843‐2258 USA
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Abstract
The application of 'omic techniques including, but not limited to genomics/metagenomics, transcriptomics/meta-transcriptomics, proteomics/meta-proteomics, and metabolomics to generate multiple datasets from a single sample have facilitated hypothesis generation leading to the identification of biological, molecular and ecological functions and mechanisms, as well as associations and correlations. Despite their power and promise, a variety of challenges must be considered in the successful design and execution of a multi-omics study. In this review, various 'omic technologies applicable to single- and meta-organisms (i.e., host + microbiome) are described, and considerations for sample collection, storage and processing prior to data generation and analysis, as well as approaches to data storage, dissemination and analysis are discussed. Finally, case studies are included as examples of multi-omic applications providing novel insights and a more holistic understanding of biological processes.
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Affiliation(s)
| | - Emily B Hollister
- Diversigen, Inc, 3 Greenway Plaza, Suite 1575, Houston, TX 77046, USA.
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Boonma P, Shapiro JM, Hollister EB, Badu S, Wu Q, Weidler EM, Abraham BP, Devaraj S, Luna RA, Versalovic J, Heitkemper MM, Savidge TC, Shulman RJ. Probiotic VSL#3 Treatment Reduces Colonic Permeability and Abdominal Pain Symptoms in Patients With Irritable Bowel Syndrome. Front Pain Res 2021; 2:691689. [PMID: 35295488 PMCID: PMC8915646 DOI: 10.3389/fpain.2021.691689] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/25/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Little is known regarding the clinical impact of treatment and treatment duration of probiotic VSL#3 on gut and microbiome function in irritable bowel syndrome (IBS). As part of a safety trial, we assessed the effect of VSL#3 treatment duration on abdominal pain, stooling, gut permeability, microbiome composition and function. Methods: Adults with IBS were randomized into an open label trial to receive the probiotic VSL#3 for 4 or 8 weeks. Adverse events, abdominal pain, and stooling patterns were recorded daily. Gut permeability, fecal bile acid levels, and microbiome composition were profiled at baseline and after treatment. Results: Fifteen subjects completed the trial (4-week: n = 8; 8-week: n = 7). Number of pain episodes decreased in both groups (P = 0.049 and P = 0.034; 4- vs. 8-week, respectively). Probiotic organisms contained in VSL#3 were detected in feces by whole shotgun metagenomic sequencing analysis and relative abundances of Streptococcus thermophilus, Bifidobacterium animalis, Lactobacillus plantarum, and Lactobacillus casei subsp. paraccasei correlated significantly with improved abdominal pain symptoms and colonic permeability at study completion. Although abdominal pain correlated significantly with the detection of probiotic species at study completion, a composite view of gut microbiome structure showed no changes in community diversity or composition after VSL#3 treatment. Conclusions: Probiotic organisms identified in stool correlated significantly with improvement in colonic permeability and clinical symptoms, prompting future studies to investigate the mechanistic role of VSL#3 and colonic permeability in IBS pathophysiology in a larger randomized controlled trial. Clinical Trial Registration:www.clinicaltrials.gov, Identifier: NCT00971711.
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Affiliation(s)
- Prapaporn Boonma
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Jordan M. Shapiro
- Department of Medicine, Baylor College of Medicine,Houston, TX, United States
| | - Emily B. Hollister
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Shyam Badu
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Qinglong Wu
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Erica M. Weidler
- Center for Pediatric Abdominal Pain Research, Texas Children's Hospital, Houston, TX, United States
- Children's Nutrition Research Center, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Bincy P. Abraham
- Division of Gastroenterology, Houston Methodist Hospital, Houston, TX, United States
| | - Sridevi Devaraj
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Ruth Ann Luna
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - James Versalovic
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Margaret M. Heitkemper
- Department of Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, WA, United States
| | - Tor C. Savidge
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Robert J. Shulman
- Center for Pediatric Abdominal Pain Research, Texas Children's Hospital, Houston, TX, United States
- Children's Nutrition Research Center, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- *Correspondence: Robert J. Shulman
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8
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Santiago-Rodriguez TM, Garoutte A, Adams E, Nasser W, Ross MC, La Reau A, Henseler Z, Ward T, Knights D, Petrosino JF, Hollister EB. Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method. Genes (Basel) 2020; 11:E1380. [PMID: 33233349 PMCID: PMC7700633 DOI: 10.3390/genes11111380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022] Open
Abstract
Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcomings of SSMS, as well as annotation tools for metagenomic analyses in human stool samples. Results may also translate to other sample types and may open the opportunity to explore the effect of sequencing depth and annotation method.
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Affiliation(s)
| | - Aaron Garoutte
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Emmase Adams
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Waleed Nasser
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Matthew C. Ross
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alex La Reau
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Zachariah Henseler
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Tonya Ward
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Dan Knights
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joseph F. Petrosino
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily B. Hollister
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
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9
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Santiago-Rodriguez TM, Hollister EB. Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses. Appl Environ Microbiol 2020; 86:e01794-20. [PMID: 32917759 PMCID: PMC7642086 DOI: 10.1128/aem.01794-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Viruses are ubiquitous particles comprising genetic material that can infect bacteria, archaea, and fungi, as well as human and other animal cells. Given that determining virus composition and function in association with states of human health and disease is of increasing interest, we anticipate that the field of viral metagenomics will continue to expand and be applied in a variety of areas ranging from surveillance to discovery and will rely heavily upon the continued development of reference materials and databases. Information regarding viral composition and function readily translates into biological and clinical applications, including the rapid sequence identification of pathogenic viruses in various sample types. However, viral metagenomic approaches often lack appropriate standards and reference materials to enable cross-study comparisons and assess potential biases which can be introduced at the various stages of collection, storage, processing, and sequence analysis. In addition, implementation of appropriate viral reference materials can aid in the benchmarking of current and development of novel assays for virus identification, discovery, and surveillance. As the field of viral metagenomics expands and standardizes, results will continue to translate into diverse applications.
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10
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Oezguen N, Yalcinkaya N, Kücükali CI, Dahdouli M, Hollister EB, Luna RA, Türkoglu R, Kürtüncü M, Eraksoy M, Savidge TC, Tüzün E. Microbiota stratification identifies disease-specific alterations in neuro-Behçet's disease and multiple sclerosis. Clin Exp Rheumatol 2019; 37 Suppl 121:58-66. [PMID: 31172918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVES Altered gut microbiota community dynamics are implicated in diverse human diseases including inflammatory disorders such as neuro-Behçet's disease (NBD) and multiple sclerosis (MS). Traditionally, microbiota communities are analysed uniformly across control and disease groups, but recent reports of subsample clustering indicate a potential need for analytical stratification. The objectives of this study are to analyse and compare faecal microbiota community signatures of ethno-geographical, age and gender matched adult healthy controls (HC), MS and NBD individuals. METHODS Faecal microbiota community compositions in adult HC (n=14), NBD patients (n=13) and MS (n=13) were analysed by 16S rRNA gene sequencing and standard bioinformatics pipelines. Bipartite networks were then used to identify and re-analyse dominant compositional clusters in respective groups. RESULTS We identified Prevotella and Bacteroides dominated subsample clusters in HC, MS, and NBD cohorts. Our study confirmed previous reports that Prevotella is a major dysbiotic target in these diseases. We demonstrate that subsample stratification is required to identify significant disease-associated microbiota community shifts with increased Clostridiales evident in Prevotella-stratified NBD and Bacteroides-stratified MS patients. CONCLUSIONS Patient cohort stratification may be needed to facilitate identification of common microbiota community shifts for causation testing in disease.
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Affiliation(s)
- Numan Oezguen
- Baylor College of Medicine, Department of Pathology & Immunology, and Texas Children's Microbiome Center, Houston TX, USA.
| | - Nazli Yalcinkaya
- Baylor College of Medicine, Department of Pathology & Immunology, and Texas Children's Microbiome Center, Houston TX, USA
| | - Cem I Kücükali
- Istanbul University, Department of Neuroscience, Institute for Experimental Medical Research, Istanbul, Turkey
| | - Mahmoud Dahdouli
- Baylor College of Medicine, Department of Pathology & Immunology, and Texas Children's Microbiome Center, Houston TX, USA
| | | | - Ruth A Luna
- Baylor College of Medicine, Department of Pathology & Immunology, and Texas Children's Microbiome Center, Houston TX, USA
| | - Recai Türkoglu
- Haydarpasa Numune Training and Research Hospital, Department of Neurology, Istanbul, Turkey
| | - Murat Kürtüncü
- Istanbul University, Department of Neuroscience, Institute for Experimental Medical Research, Istanbul, Turkey
| | - Mefküre Eraksoy
- Istanbul University, Istanbul School of Medicine, Department of Neurology, Istanbul, Turkey
| | - Tor C Savidge
- Baylor College of Medicine, Department of Pathology & Immunology, and Texas Children's Microbiome Center, Houston TX, USA
| | - Erdem Tüzün
- Istanbul University, Department of Neuroscience, Institute for Experimental Medical Research, Istanbul, Turkey
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11
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Santiago-Rodriguez TM, Hollister EB. Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut. Viruses 2019; 11:v11070656. [PMID: 31323792 PMCID: PMC6669467 DOI: 10.3390/v11070656] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/14/2019] [Accepted: 07/15/2019] [Indexed: 02/06/2023] Open
Abstract
The virome is comprised of endogenous retroviruses, eukaryotic viruses, and bacteriophages and is increasingly being recognized as an essential part of the human microbiome. The human virome is associated with Type-1 diabetes (T1D), Type-2 diabetes (T2D), Inflammatory Bowel Disease (IBD), Human Immunodeficiency Virus (HIV) infection, and cancer. Increasing evidence also supports trans-kingdom interactions of viruses with bacteria, small eukaryotes and host in disease progression. The present review focuses on virus ecology and biology and how this translates mostly to human gut virome research. Current challenges in the field and how the development of bioinformatic tools and controls are aiding to overcome some of these challenges are also discussed. Finally, the present review also focuses on how human gut virome research could result in translational and clinical studies that may facilitate the development of therapeutic approaches.
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Affiliation(s)
| | - Emily B Hollister
- Diversigen Inc., 2450 Holcombe Blvd, Suite BCMA, 77021 Houston, TX, USA.
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12
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Daniels SR, Pratt CA, Hollister EB, Labarthe D, Cohen DA, Walker JR, Beech BM, Balagopal PB, Beebe DW, Gillman MW, Goodrich JM, Jaquish C, Kit B, Miller AL, Olds D, Oken E, Rajakumar K, Sherwood NE, Spruijt-Metz D, Steinberger J, Suglia SF, Teitelbaum SL, Urbina EM, Van Horn L, Ward D, Young ME. Promoting Cardiovascular Health in Early Childhood and Transitions in Childhood through Adolescence: A Workshop Report. J Pediatr 2019; 209:240-251.e1. [PMID: 30904171 DOI: 10.1016/j.jpeds.2019.01.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/08/2019] [Accepted: 01/23/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Stephen R Daniels
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO
| | - Charlotte A Pratt
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD.
| | - Emily B Hollister
- Department of Information Technology & Analytics, Diversigen, Inc, Houston, TX
| | - Darwin Labarthe
- Department of Preventive Medicine, Northwestern Feinberg School of Medicine, Chicago, IL
| | | | - Jenelle R Walker
- Center for Translation Research and Implementation Science, NHLBI, Bethesda, MD
| | - Bettina M Beech
- Department of Pediatrics and Family Medicine, University of Mississippi Medical Centre, Jackson, MS
| | - P Babu Balagopal
- Nemours Children's Clinic, Mayo Clinic College of Medicine, Rochester, MN
| | - Dean W Beebe
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Matthew W Gillman
- Office of the Director, National Institutes of Health (NIH), Bethesda, MD
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI
| | - Cashell Jaquish
- Division of Cardiovascular Sciences, NHLBI, NIH, Bethesda, MD
| | - Brian Kit
- Division of Cardiovascular Sciences, NHLBI, NIH, Bethesda, MD
| | - Alison L Miller
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, Ann Arbor, MI
| | - David Olds
- Prevention Research Center for Family and Child Health, University of Colorado, Denver, CO
| | - Emily Oken
- Department of Population Medicine, Harvard Pilgrim Health Care Inc, Wellesley, MA
| | - Kumaravel Rajakumar
- Division of General Academic Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Nancy E Sherwood
- School of Public Health, University of Minnesota, Minneapolis, MN
| | - Donna Spruijt-Metz
- Dornsife Center for Economic and Social Research, University of Southern California, Los Angeles, CA
| | | | - Shakira F Suglia
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA
| | - Susan L Teitelbaum
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Elaine M Urbina
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Linda Van Horn
- Department of Preventive Medicine, Northwestern Feinberg School of Medicine, University, Chicago, IL
| | - Dianne Ward
- Department of Nutrition, University of North Carolina, Chapel Hill, NC
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13
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Hollister EB, Oezguen N, Chumpitazi BP, Luna RA, Weidler EM, Rubio-Gonzales M, Dahdouli M, Cope JL, Mistretta TA, Raza S, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Heitkemper M, Savidge TC, Shulman RJ, Versalovic J. Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. J Mol Diagn 2019; 21:449-461. [PMID: 31005411 PMCID: PMC6504675 DOI: 10.1016/j.jmoldx.2019.01.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/30/2018] [Accepted: 01/06/2019] [Indexed: 02/06/2023] Open
Abstract
Accurate diagnosis and stratification of children with irritable bowel syndrome (IBS) remain challenging. Given the central role of recurrent abdominal pain in IBS, we evaluated the relationships of pediatric IBS and abdominal pain with intestinal microbes and fecal metabolites using a comprehensive clinical characterization and multiomics strategy. Using rigorous clinical phenotyping, we identified preadolescent children (aged 7 to 12 years) with Rome III IBS (n = 23) and healthy controls (n = 22) and characterized their fecal microbial communities using whole-genome shotgun metagenomics and global unbiased fecal metabolomic profiling. Correlation-based approaches and machine learning algorithms identified associations between microbes, metabolites, and abdominal pain. IBS cases differed from controls with respect to key bacterial taxa (eg, Flavonifractor plautii and Lachnospiraceae bacterium 7_1_58FAA), metagenomic functions (eg, carbohydrate metabolism and amino acid metabolism), and higher-order metabolites (eg, secondary bile acids, sterols, and steroid-like compounds). Significant associations between abdominal pain frequency and severity and intestinal microbial features were identified. A random forest classifier built on metagenomic and metabolic markers successfully distinguished IBS cases from controls (area under the curve, 0.93). Leveraging multiple lines of evidence, intestinal microbes, genes/pathways, and metabolites were associated with IBS, and these features were capable of distinguishing children with IBS from healthy children. These multi-omics features, and their links to childhood IBS coupled with nutritional interventions, may lead to new microbiome-guided diagnostic and therapeutic strategies.
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Affiliation(s)
- Emily B Hollister
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Diversigen, Inc., Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Bruno P Chumpitazi
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Texas Children's Hospital, Houston, Texas
| | - Ruth Ann Luna
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Erica M Weidler
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Texas Children's Hospital, Houston, Texas; Children's Nutrition Research Center, Houston, Texas
| | - Michelle Rubio-Gonzales
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Mahmoud Dahdouli
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Julia L Cope
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Toni-Ann Mistretta
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Sabeen Raza
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas; Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas
| | - Margaret Heitkemper
- Department of Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, Washington
| | - Tor C Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Robert J Shulman
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Texas Children's Hospital, Houston, Texas; Children's Nutrition Research Center, Houston, Texas
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas.
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14
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Hu P, Wu L, Hollister EB, Wang AS, Somenahally AC, Hons FM, Gentry TJ. Fungal Community Structural and Microbial Functional Pattern Changes After Soil Amendments by Oilseed Meals of Jatropha curcas and Camelina sativa: A Microcosm Study. Front Microbiol 2019; 10:537. [PMID: 30984123 PMCID: PMC6450180 DOI: 10.3389/fmicb.2019.00537] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/01/2019] [Indexed: 11/13/2022] Open
Abstract
The meals after oil extraction from many oilseed crops have nutrition and biofumigation potential for land application. Oilseed meal (SM) from the dedicated bioenergy crop Jatropha curcas were implicated to contain compounds that have antibacterial properties on some soil pathogens. However, little is known about its effect on non-targeted soil microbial community, especially on fungi. SM from Camelina sativa contains moderate level of glucosinolates (GLS) and was under studied. To investigate soil fungal community responses to jatropha and camelina SMs, we conducted a lab based microcosm study, amending soil with 1% SMs of jatropha, camelina, flax, and biomass of wheat straw. Fungal community abundance and structure were analyzed based on the ITS region using qPCR and tag-pyrosequencing. Microbial functional changes were examined by community level physiological profile (CLPP) using Biolog assay. Both SMs from jatropha and camelina showed biofumigant properties and inhibited fungal proliferation. Jatropha SM significantly altered soil fungal community structures with lower fungal biodiversity and higher Chaetomium composition. Camelina SM amended soil promoted Fusarium proliferation. CLPP indicated sequential hierarchy for C metabolism in the oilseed-amended microcosms was generally complex C > phosphate-associated C > carboxylic acids > carbohydrates > amines > amino acids. No significant difference in CLPP was detected due to the type of SM treatment. Our data indicate that both SMs of jatropha and camelina have biofumigant properties and can differentially impact soil microbial communities, and the changes were relatively persistent over time. Microbial functional patterns on the other side were not impacted by SM type. Our study revealed biofumigant and nutritional influence of SMs from dedicated biofuel plants on soil microbial community. This information will help properly using jatropha and camelina SMs for pathogen control while minimizing their negative impacts on non-target microorganisms. However, further studies in the field are demanded to investigate their influences in real practice.
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Affiliation(s)
- Ping Hu
- Key Laboratory of Environment and Health (HUST), Ministry of Education and Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liangjun Wu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Emily B. Hollister
- Baylor College of Medicine, Houston, TX, United States
- Texas Children’s Hospital, Houston, TX, United States
| | - Autumn S. Wang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | | | - Frank M. Hons
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Terry J. Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
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15
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Brumlow CE, Luna RA, Hollister EB, Gomez JA, Burcham LA, Cowdrey MB, Primm TP. Biochemical but not compositional recovery of skin mucosal microbiome communities after disruption. Infect Drug Resist 2019; 12:399-416. [PMID: 30863123 PMCID: PMC6388737 DOI: 10.2147/idr.s185992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background The microbiomes of animals are complex communities that strongly affect the health of the hosts. Microbiomes on mucosal surfaces have the highest densities and most extensive biochemical exchanges with the hosts. Although antibiotics are potent tools to manage infections, they can disrupt the normal microbiota, causing numerous side effects. Materials and methods Taking a community ecology approach, mucosal microbiome community responses to five disruptive conditions (two broad-spectrum antibiotics, a biocide, elevated temperature, and rinsing) were analyzed. Skin of the fish Gambusia affinis was the mucosal model. Microbiome recovery was measured by culturable counts, community biochemical profiles, genetic fingerprinting, and community 16S gene sequencing (rinsing condition only). Results Following all disruptions, the total counts rose and then returned to the pre-treatment (PT) level. This overgrowth was confirmed via direct staining and community metabolic activity measurements. After rinsing, diversity decreased and one taxon dominated (family Aeromonadaceae) temporarily, the findings similar to numerous other studies with antibiotics. While the community did not return to the PT taxonomic composition, the biochemical profile did. Conclusion This suggests that the biochemical pathways in a community are important during recovery, and a return to the original composition is not required to restore original function.
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Affiliation(s)
- Chelcy E Brumlow
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA,
| | - Ruth A Luna
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Emily B Hollister
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Javier A Gomez
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA,
| | - Lindsey A Burcham
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA,
| | - Madison B Cowdrey
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA,
| | - Todd P Primm
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA,
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16
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Pammi M, Lal CV, Wagner BD, Mourani PM, Lohmann P, Luna RA, Sisson A, Shivanna B, Hollister EB, Abman SH, Versalovic J, Connett GJ, Bhandari V, Ambalavanan N. Airway Microbiome and Development of Bronchopulmonary Dysplasia in Preterm Infants: A Systematic Review. J Pediatr 2019; 204:126-133.e2. [PMID: 30297287 DOI: 10.1016/j.jpeds.2018.08.042] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/03/2018] [Accepted: 08/17/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVES To summarize evidence regarding microbial dysbiosis of the airway associated with bronchopulmonary dysplasia (BPD) and to explore heterogeneity among studies. STUDY DESIGN We included studies that evaluated the airway microbiome in preterm infants who developed BPD using culture-independent molecular techniques and reported alpha- and beta-diversity metrics and microbial profiles. RESULTS The 6 included studies had substantial clinical and methodological heterogeneity. Most studies reported the presence of an airway microbiome early after birth and an evolution in the first weeks of life with increasing bacterial loads. The early airway microbiome was dominated by Staphylococcus and Ureaplasma spp. Two studies reported differences in alpha- and beta- diversity indices in preterm infants with BPD compared with those who did not develop BPD. Increased microbial community turnover, changes in the relative abundance of Proteobacteria and Firmicutes, and decreased Lactobacilli were reported with BPD progression. Most included infants were born by cesarean delivery, and a majority were exposed to postnatal antibiotics. No data regarding feeding human milk or correlations with the development of gut microbiota (gut-lung axis) were available. CONCLUSIONS Microbial dysbiosis may be associated with BPD progression and severity, and further study of microbiome optimization in preterm infants at risk for BPD is warranted.
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Affiliation(s)
- Mohan Pammi
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX.
| | - Charitharth Vivek Lal
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Brandie D Wagner
- Section of Pulmonary Medicine, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, CO
| | - Peter M Mourani
- Pediatric Heart Lung Center, Section of Critical Care Medicine, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, CO
| | - Pablo Lohmann
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Ruth Ann Luna
- Texas Children's Microbiome Center, Texas Children's Hospital and Department of Pathology, Baylor College of Medicine, Houston, TX
| | - Amy Sisson
- Texas Medical Center Library, Houston, TX
| | - Binoy Shivanna
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Emily B Hollister
- Texas Children's Microbiome Center, Texas Children's Hospital and Department of Pathology, Baylor College of Medicine, Houston, TX
| | - Steven H Abman
- Section of Pulmonary Medicine, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, CO; Pediatric Heart Lung Center, Section of Critical Care Medicine, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, CO
| | - James Versalovic
- Texas Children's Microbiome Center, Texas Children's Hospital and Department of Pathology, Baylor College of Medicine, Houston, TX
| | - Gary J Connett
- Department of Pediatrics, Southampton University Hospitals NHS Trust, Southampton, United Kingdom
| | - Vineet Bhandari
- Department of Pediatrics, Drexel University College of Medicine, Philadelphia, PA
| | - Namasivayam Ambalavanan
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
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17
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Shah MS, DeSantis TZ, Weinmaier T, McMurdie PJ, Cope JL, Altrichter A, Yamal JM, Hollister EB. Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer. Gut 2018; 67:882-891. [PMID: 28341746 DOI: 10.1136/gutjnl-2016-313189] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Colorectal cancer (CRC) is the second leading cause of cancer-associated mortality in the USA. The faecal microbiome may provide non-invasive biomarkers of CRC and indicate transition in the adenoma-carcinoma sequence. Re-analysing raw sequence and metadata from several studies uniformly, we sought to identify a composite and generalisable microbial marker for CRC. DESIGN Raw 16S rRNA gene sequence data sets from nine studies were processed with two pipelines, (1) QIIME closed reference (QIIME-CR) or (2) a strain-specific method herein termed SS-UP (Strain Select, UPARSE bioinformatics pipeline). A total of 509 samples (79 colorectal adenoma, 195 CRC and 235 controls) were analysed. Differential abundance, meta-analysis random effects regression and machine learning analyses were carried out to determine the consistency and diagnostic capabilities of potential microbial biomarkers. RESULTS Definitive taxa, including Parvimonas micra ATCC 33270, Streptococcus anginosus and yet-to-be-cultured members of Proteobacteria, were frequently and significantly increased in stools from patients with CRC compared with controls across studies and had high discriminatory capacity in diagnostic classification. Microbiome-based CRC versus control classification produced an area under receiver operator characteristic (AUROC) curve of 76.6% in QIIME-CR and 80.3% in SS-UP. Combining clinical and microbiome markers gave a diagnostic AUROC of 83.3% for QIIME-CR and 91.3% for SS-UP. CONCLUSIONS Despite technological differences across studies and methods, key microbial markers emerged as important in classifying CRC cases and such could be used in a universal diagnostic for the disease. The choice of bioinformatics pipeline influenced accuracy of classification. Strain-resolved microbial markers might prove crucial in providing a microbial diagnostic for CRC.
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Affiliation(s)
- Manasi S Shah
- Department of Epidemiology, University of Texas School of Public Health, Houston, Texas, USA.,Bioinformatics, Second Genome Inc, South San Francisco, California, USA.,Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, HoustonTexas, USA
| | - Todd Z DeSantis
- Bioinformatics, Second Genome Inc, South San Francisco, California, USA
| | - Thomas Weinmaier
- Bioinformatics, Second Genome Inc, South San Francisco, California, USA
| | - Paul J McMurdie
- Bioinformatics, Second Genome Inc, South San Francisco, California, USA.,Bioinformatics, Whole Biome Inc, San Francisco, California, USA
| | - Julia L Cope
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, HoustonTexas, USA.,Diversigen, Inc, Houston, Texas, USA
| | - Adam Altrichter
- Bioinformatics, Second Genome Inc, South San Francisco, California, USA
| | - Jose-Miguel Yamal
- Department of Epidemiology, University of Texas School of Public Health, Houston, Texas, USA
| | - Emily B Hollister
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, HoustonTexas, USA
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18
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Heitkemper MM, Cain KC, Shulman RJ, Burr RL, Ko C, Hollister EB, Callen N, Zia J, Han CJ, Jarrett ME. Stool and urine trefoil factor 3 levels: associations with symptoms, intestinal permeability, and microbial diversity in irritable bowel syndrome. Benef Microbes 2018; 9:345-355. [PMID: 29633639 DOI: 10.3920/bm2017.0059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Previously we showed that urine trefoil factor 3 (TFF3) levels were higher in females with irritable bowel syndrome (IBS) compared to non-IBS females. To assess if TFF3 is associated with symptoms and/or reflect alterations in gastrointestinal permeability and gut microbiota in an IBS population, we correlated stool and urine TFF3 levels with IBS symptoms, intestinal permeability, stool microbial diversity and relative abundance of predominant bacterial families and genera. We also tested the relationship of stool TFF3 to urine TFF3, and compared results based on hormone contraception use. Samples were obtained from 93 females meeting Rome III IBS criteria and completing 4-week symptom diaries. TFF3 levels were measured by ELISA. Permeability was assessed with the urine lactulose/mannitol (L/M) ratio. Stool microbiota was assessed using 16S rRNA. Stool TFF3, but not urine TFF3, was associated positively with diarrhoea and loose stool consistency. Higher stool TFF3 was also associated with lower L/M ratio and microbial diversity. Of the 20 most abundant bacterial families Mogibacteriaceae and Christensenellaceae were inversely related to stool TFF3, with only Christensenellaceae remaining significant after multiple comparison adjustment. There were no significant relationships between stool or urine TFF3 levels and other symptoms, nor between stool and urine levels. In premenopausal females, urine TFF3 levels were higher in those reporting hormone contraception. Collectively these results suggest that higher stool TFF3 levels are associated with IBS symptoms (loose/diarrhoeal stools), lower gut permeability, and altered stool bacteria composition (decreased diversity and decreased Christensenellaceae), which further suggests that TFF3 may be an important marker of host-bacteria interaction.
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Affiliation(s)
- M M Heitkemper
- 1 Department of Biobehavioral Nursing and Health Informatics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-7266, USA
| | - K C Cain
- 2 Department of Biostatistics and Office of Nursing Research, University of Washington, 1959 NE Pacific Street, Seattle, WA, USA
| | - R J Shulman
- 3 Children's Nutrition Research Center, Baylor College of Medicine, Texas Children's Hospital, 6621 Fannin Street, Houston, TX 77030, USA
| | - R L Burr
- 1 Department of Biobehavioral Nursing and Health Informatics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-7266, USA
| | - C Ko
- 4 University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - E B Hollister
- 5 Department of Pathology and Immunology, Baylor College of Medicine, Texas Children's Microbiome Center, Texas Children's Hospital, 6621 Fannin Street, Houston, TX 77030, USA
| | - N Callen
- 6 Department of Family and Child Nursing, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - J Zia
- 4 University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - C J Han
- 1 Department of Biobehavioral Nursing and Health Informatics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-7266, USA
| | - M E Jarrett
- 1 Department of Biobehavioral Nursing and Health Informatics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-7266, USA
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19
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Abstract
BACKGROUND Variations in gut microbiota composition and diversity have been associated with childhood adiposity, although most studies describing this have been cross-sectional in nature. Our objective was to evaluate associations between body weight and the gut microbiota over time in obese preschool-age children. METHODS Obese, preschool-age, Hispanic children provided stool samples at baseline and following a 6-month behavioral intervention. Normal-weight (NW) children also provided stool samples. Stool microbial community composition was characterized using 16S rRNA gene sequencing. Estimates of within-sample diversity were calculated on operational taxonomic unit (OTU) count data, and the Firmicutes:Bacteroidetes (F:B) ratio was determined on per-sample basis. Estimates of between-sample diversity were generated using the weighted Unifrac metric, differential abundances were evaluated using Wilcoxon rank-sum tests, and associations of microbiome features with clinical data were quantified using Spearman rank correlations. RESULTS For the 30 obese children sampled preintervention and postintervention, a decrease in body mass index (BMI) z-score from 2.55 to 2.34 (p = 0.004, paired t-test) was observed. Bacteroides massiliensis was significantly enriched in obese children, while B. plebius was significantly enriched in NW controls. We identified significant correlations between multiple Bacteroides-like OTUs and BMI z-score, but neither F:B ratios nor OTU-level abundances were altered in conjunction with weight change in the obese children. Rather, highly individualized OTU-level responses were observed. CONCLUSIONS Although differences exist between the gut microbiota of obese and NW children, we detected highly individualized responses of the gut microbiota of obese children over time and following weight loss.
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Affiliation(s)
- Emily B. Hollister
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Byron A. Foster
- Departments of Dermatology and Pediatrics, Oregon Health & Science University, Portland, OR
| | - Mahmoud Dahdouli
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Jesica Ramirez
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX
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20
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DeSantis TZ, Shah MS, Cope JL, Hollister EB. Microbial markers in the diagnosis of colorectal cancer: the promise, reality and challenge. Future Microbiol 2017; 12:1341-1344. [PMID: 28972391 DOI: 10.2217/fmb-2017-0185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Todd Z DeSantis
- Informatics Department, Second Genome Inc., South San Francisco, CA 94080, USA
| | - Manasi S Shah
- Algorithms & Data Analysis, Microarray Business Unit, Thermo Fisher Scientific, Santa Clara, CA 95051, USA
| | - Julia L Cope
- Department of Scientific Operations, Diversigen, Inc., Houston, TX 77046, USA
| | - Emily B Hollister
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
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21
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Labus JS, Hollister EB, Jacobs J, Kirbach K, Oezguen N, Gupta A, Acosta J, Luna RA, Aagaard K, Versalovic J, Savidge T, Hsiao E, Tillisch K, Mayer EA. Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome. Microbiome 2017; 5:49. [PMID: 28457228 PMCID: PMC5410709 DOI: 10.1186/s40168-017-0260-z] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/27/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND Preclinical and clinical evidence supports the concept of bidirectional brain-gut microbiome interactions. We aimed to determine if subgroups of irritable bowel syndrome (IBS) subjects can be identified based on differences in gut microbial composition, and if there are correlations between gut microbial measures and structural brain signatures in IBS. METHODS Behavioral measures, stool samples, and structural brain images were collected from 29 adult IBS and 23 healthy control subjects (HCs). 16S ribosomal RNA (rRNA) gene sequencing was used to profile stool microbial communities, and various multivariate analysis approaches were used to quantitate microbial composition, abundance, and diversity. The metagenomic content of samples was inferred from 16S rRNA gene sequence data using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). T1-weighted brain images were acquired on a Siemens Allegra 3T scanner, and morphological measures were computed for 165 brain regions. RESULTS Using unweighted Unifrac distances with hierarchical clustering on microbial data, samples were clustered into two IBS subgroups within the IBS population (IBS1 (n = 13) and HC-like IBS (n = 16)) and HCs (n = 23) (AUROC = 0.96, sensitivity 0.95, specificity 0.67). A Random Forest classifier provided further support for the differentiation of IBS1 and HC groups. Microbes belonging to the genera Faecalibacterium, Blautia, and Bacteroides contributed to this subclassification. Clinical features distinguishing the groups included a history of early life trauma and duration of symptoms (greater in IBS1), but not self-reported bowel habits, anxiety, depression, or medication use. Gut microbial composition correlated with structural measures of brain regions including sensory- and salience-related regions, and with a history of early life trauma. CONCLUSIONS The results confirm previous reports of gut microbiome-based IBS subgroups and identify for the first time brain structural alterations associated with these subgroups. They provide preliminary evidence for the involvement of specific microbes and their predicted metabolites in these correlations.
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Affiliation(s)
- Jennifer S. Labus
- Division of Digestive Diseases, David Geffen School at UCLA, Los Angeles, CA 90095 USA
- Oppenheimer Center for Neurobiology of Stress and Resilience, CHS 42-210 MC737818 10833 Le Conte Avenue, Los Angeles, CA 90095-7378 USA
| | - Emily B. Hollister
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, 1102 Bates Ave., Houston, TX USA
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX USA
| | - Jonathan Jacobs
- Division of Digestive Diseases, David Geffen School at UCLA, Los Angeles, CA 90095 USA
| | - Kyleigh Kirbach
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Numan Oezguen
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, 1102 Bates Ave., Houston, TX USA
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX USA
| | - Arpana Gupta
- Division of Digestive Diseases, David Geffen School at UCLA, Los Angeles, CA 90095 USA
- Oppenheimer Center for Neurobiology of Stress and Resilience, CHS 42-210 MC737818 10833 Le Conte Avenue, Los Angeles, CA 90095-7378 USA
| | - Jonathan Acosta
- Division of Digestive Diseases, David Geffen School at UCLA, Los Angeles, CA 90095 USA
| | - Ruth Ann Luna
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, 1102 Bates Ave., Houston, TX USA
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX USA
| | - Kjersti Aagaard
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, 1102 Bates Ave., Houston, TX USA
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX USA
| | - James Versalovic
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, 1102 Bates Ave., Houston, TX USA
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX USA
| | - Tor Savidge
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, 1102 Bates Ave., Houston, TX USA
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX USA
| | - Elaine Hsiao
- Division of Digestive Diseases, David Geffen School at UCLA, Los Angeles, CA 90095 USA
| | - Kirsten Tillisch
- Division of Digestive Diseases, David Geffen School at UCLA, Los Angeles, CA 90095 USA
- Oppenheimer Center for Neurobiology of Stress and Resilience, CHS 42-210 MC737818 10833 Le Conte Avenue, Los Angeles, CA 90095-7378 USA
| | - Emeran A. Mayer
- Division of Digestive Diseases, David Geffen School at UCLA, Los Angeles, CA 90095 USA
- Oppenheimer Center for Neurobiology of Stress and Resilience, CHS 42-210 MC737818 10833 Le Conte Avenue, Los Angeles, CA 90095-7378 USA
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Shulman RJ, Hollister EB, Cain K, Czyzewski DI, Self MM, Weidler EM, Devaraj S, Luna RA, Versalovic J, Heitkemper M. Psyllium Fiber Reduces Abdominal Pain in Children With Irritable Bowel Syndrome in a Randomized, Double-Blind Trial. Clin Gastroenterol Hepatol 2017; 15:712-719.e4. [PMID: 27080737 PMCID: PMC5064811 DOI: 10.1016/j.cgh.2016.03.045] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS We sought to determine the efficacy of psyllium fiber treatment on abdominal pain and stool patterns in children with irritable bowel syndrome (IBS). We evaluated effects on breath hydrogen and methane production, gut permeability, and microbiome composition. We also investigated whether psychological characteristics of children or parents affected the response to treatment. METHODS We performed a randomized, double-blind trial of 103 children (mean age, 13 ± 3 y) with IBS seen at primary or tertiary care settings. After 2 weeks on their habitual diet, children began an 8-day diet excluding carbohydrates thought to cause symptoms of IBS. Children with ≥75% improvement in abdominal pain were excluded (n = 17). Children were assigned randomly to groups given psyllium (n = 37) or placebo (maltodextrin, n = 47) for 6 weeks. Two-week pain and stool diaries were compared at baseline and during the final 2 weeks of treatment. We assessed breath hydrogen and methane production, intestinal permeability, and the composition of the microbiome before and after administration of psyllium or placebo. Psychological characteristics of children were measured at baseline. RESULTS Children in the psyllium group had a greater reduction in the mean number of pain episodes than children in the placebo group (mean reduction of 8.2 ± 1.2 after receiving psyllium vs mean reduction of 4.1 ± 1.3 after receiving placebo; P = .03); the level of pain intensity did not differ between the groups. Psychological characteristics were not associated with response. At the end of the study period, the percentage of stools that were normal (Bristol scale scores, 3-5), breath hydrogen or methane production, intestinal permeability, and microbiome composition were similar between groups. CONCLUSIONS Psyllium fiber reduced the number of abdominal pain episodes in children with IBS, independent of psychological factors. Psyllium did not alter breath hydrogen or methane production, gut permeability, or microbiome composition. ClinicalTrials.gov no: NCT00526903.
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Affiliation(s)
- Robert J Shulman
- Department of Pediatrics, Baylor College of Medicine; Children's Nutrition Research Center; Texas Children's Hospital.
| | - Emily B Hollister
- Texas Children's Hospital; Texas Children's Microbiome Center; Department of Pathology and Immunology, Baylor College of Medicine; Department of Pathology, Texas Children's Hospital
| | - Kevin Cain
- Department of Biostatistics and Office of Nursing Research, University of Washington, Seattle, Washington
| | - Danita I Czyzewski
- Texas Children's Hospital; Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine
| | - Mariella M Self
- Texas Children's Hospital; Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine
| | - Erica M Weidler
- Department of Pediatrics, Baylor College of Medicine; Children's Nutrition Research Center; Texas Children's Hospital
| | - Sridevi Devaraj
- Texas Children's Hospital; Texas Children's Microbiome Center; Department of Pathology and Immunology, Baylor College of Medicine; Department of Pathology, Texas Children's Hospital
| | - Ruth Ann Luna
- Texas Children's Hospital; Texas Children's Microbiome Center; Department of Pathology and Immunology, Baylor College of Medicine; Department of Pathology, Texas Children's Hospital
| | - James Versalovic
- Texas Children's Hospital; Texas Children's Microbiome Center; Department of Pathology and Immunology, Baylor College of Medicine; Department of Pathology, Texas Children's Hospital
| | - Margaret Heitkemper
- Department of Biobehavioral Nursing and Health Systems, University of Washington, Seattle, Washington
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Pammi M, Cope J, Tarr PI, Warner BB, Morrow AL, Mai V, Gregory KE, Kroll JS, McMurtry V, Ferris MJ, Engstrand L, Lilja HE, Hollister EB, Versalovic J, Neu J. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. Microbiome 2017; 5:31. [PMID: 28274256 PMCID: PMC5343300 DOI: 10.1186/s40168-017-0248-8] [Citation(s) in RCA: 402] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 02/27/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results. METHODS AND RESULTS Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies. We searched MEDLINE, PubMed, CINAHL, and conference abstracts from the proceedings of Pediatric Academic Societies and reference lists of relevant identified articles in April 2016. Studies comparing the intestinal microbiome in preterm infants who developed NEC to those of controls, using culture-independent molecular techniques and reported α and β-diversity metrics, and microbial profiles were included. In addition, 16S ribosomal ribonucleic acid (rRNA) sequence data with clinical meta-data were requested from the authors of included studies or searched in public data repositories. We reprocessed the 16S rRNA sequence data through a uniform analysis pipeline, which were then synthesized by meta-analysis. We included 14 studies in this review, and data from eight studies were available for quantitative synthesis (106 NEC cases, 278 controls, 2944 samples). The age of NEC onset was at a mean ± SD of 30.1 ± 2.4 weeks post-conception (n = 61). Fecal microbiome from preterm infants with NEC had increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes prior to NEC onset. Alpha- or beta-diversity indices in preterm infants with NEC were not consistently different from controls, but we found differences in taxonomic profiles related to antibiotic exposure, formula feeding, and mode of delivery. Exploring heterogeneity revealed differences in microbial profiles by study and the target region of the 16S rRNA gene (V1-V3 or V3-V5). CONCLUSIONS Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes. Microbiome optimization may provide a novel strategy for preventing NEC.
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Affiliation(s)
- Mohan Pammi
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, 77030 Houston, TX USA
| | - Julia Cope
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX USA
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO USA
| | - Barbara B. Warner
- Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO USA
| | - Ardythe L. Morrow
- Department of Pediatrics, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Ohio, USA
| | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, FL USA
| | | | - J. Simon Kroll
- Department of Medicine, Section of Paediatrics, Imperial College London, London, UK
| | - Valerie McMurtry
- Department of Microbiology, Immunology and Parasitology, Children’s Hospital, New Orleans, LA USA
| | - Michael J Ferris
- Department of Microbiology, Immunology and Parasitology, Children’s Hospital, New Orleans, LA USA
| | - Lars Engstrand
- Director of Clinical Genomics and Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | | | - Emily B. Hollister
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX USA
| | - James Versalovic
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX USA
| | - Josef Neu
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, 77030 Houston, TX USA
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Shulman RJ, Hollister EB, Cain K, Heitkemper M. Reply. Clin Gastroenterol Hepatol 2016; 14:1667-1668. [PMID: 27377875 DOI: 10.1016/j.cgh.2016.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | | | - Kevin Cain
- University of Washington, Seattle, Washington
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Preidis GA, Luna RA, Hollister EB, Schady D, Gao C, Finegold MJ, Versalovic J, Shulman RJ. The mucosal microbiota in a young child with severe non-Helicobacter gastritis. Therap Adv Gastroenterol 2016; 9:749-51. [PMID: 27582889 PMCID: PMC4984332 DOI: 10.1177/1756283x16653582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
| | | | | | | | - Chunxu Gao
- Baylor College of Medicine, Houston, TX, USA
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Shah R, Cope JL, Nagy-Szakal D, Dowd S, Versalovic J, Hollister EB, Kellermayer R. Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis. Gut Microbes 2016; 7:384-96. [PMID: 27217061 PMCID: PMC5046168 DOI: 10.1080/19490976.2016.1190073] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic intestinal inflammatory disorders characterized by a complex disruption of the physiologic interaction between the host immune system and intestinal microbes precipitated by environmental factors. Numerous observations indicate the altered composition and function of the intestinal microbiome of patients with ulcerative colitis (UC), a subtype of IBD. The accuracy of these results may be limited by confounding factors, such as concurrent medication use. To address these limitations, we examined the colonic mucosal microbiome of pediatric patients with UC prior to initiating treatment. Based on bacterial 16S rRNA gene sequencing, we identified a significant decrease in the phylum Verrucomicrobia in patients with UC. At the genus level, we observed a significant decrease in the short chain fatty acid producer Roseburia. Despite these compositional changes, we did not identify inferred gene content differences between the UC and control groups. To determine if microbial taxa may be associated with clinical outcomes, we retrospectively assessed the clinical course of the UC patients. Despite similar metrics of OTU richness and diversity, multiple OTU differences were observed between patients who responded to therapy and those who did not. Our observations regarding the mucosal microbiome and the associations with differential clinical outcomes support the contributions of gut microbes to disease onset and modulation.
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Affiliation(s)
- Rajesh Shah
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Julia L. Cope
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA
| | - Dorottya Nagy-Szakal
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,USDA/ARS Children's Nutrition Research Center, Texas Children's Hospital, Houston, TX, USA
| | - Scot Dowd
- Molecular Research (MR DNA), Shallowater, TX, USA
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA
| | - Emily B. Hollister
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA
| | - Richard Kellermayer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,USDA/ARS Children's Nutrition Research Center, Texas Children's Hospital, Houston, TX, USA
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Durgan DJ, Ganesh BP, Cope JL, Ajami NJ, Phillips SC, Petrosino JF, Hollister EB, Bryan RM. Role of the Gut Microbiome in Obstructive Sleep Apnea-Induced Hypertension. Hypertension 2015; 67:469-74. [PMID: 26711739 DOI: 10.1161/hypertensionaha.115.06672] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/02/2015] [Indexed: 12/13/2022]
Abstract
Individuals suffering from obstructive sleep apnea (OSA) are at increased risk for systemic hypertension. The importance of a healthy gut microbiota, and detriment of a dysbiotic microbiota, on host physiology is becoming increasingly evident. We tested the hypothesis that gut dysbiosis contributes to hypertension observed with OSA. OSA was modeled in rats by inflating a tracheal balloon during the sleep cycle (10-s inflations, 60 per hour). On normal chow diet, OSA had no effect on blood pressure; however, in rats fed a high-fat diet, blood pressure increased 24 and 29 mm Hg after 7 and 14 days of OSA, respectively (P<0.05 each). Bacterial community characterization was performed on fecal pellets isolated before and after 14 days of OSA in chow and high-fat fed rats. High-fat diet and OSA led to significant alterations of the gut microbiota, including decreases in bacterial taxa known to produce the short chain fatty acid butyrate (P<0.05). Finally, transplant of dysbiotic cecal contents from hypertensive OSA rats on high-fat diet into OSA recipient rats on normal chow diet (shown to be normotensive) resulted in hypertension similar to that of the donor (increased 14 and 32 mm Hg after 7 and 14 days of OSA, respectively; P<0.05). These studies demonstrate a causal relationship between gut dysbiosis and hypertension, and suggest that manipulation of the microbiota may be a viable treatment for OSA-induced, and possibly other forms of, hypertension.
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Affiliation(s)
- David J Durgan
- From the Departments of Anesthesiology (D.J.D., S.C.P., R.M.B.), Pathology and Immunology (B.P.G., J.L.C., E.B.H.), Molecular Physiology and Biophysics (R.M.B.), The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology (N.J.A., J.F.P.), and Texas Children's Microbiome Center, Department of Pathology, Baylor College of Medicine, Houston (J.L.C., E.B.H.); and Department of Medicine, Texas Children's Hospital, Houston (J.L.C., E.B.H.).
| | - Bhanu P Ganesh
- From the Departments of Anesthesiology (D.J.D., S.C.P., R.M.B.), Pathology and Immunology (B.P.G., J.L.C., E.B.H.), Molecular Physiology and Biophysics (R.M.B.), The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology (N.J.A., J.F.P.), and Texas Children's Microbiome Center, Department of Pathology, Baylor College of Medicine, Houston (J.L.C., E.B.H.); and Department of Medicine, Texas Children's Hospital, Houston (J.L.C., E.B.H.)
| | - Julia L Cope
- From the Departments of Anesthesiology (D.J.D., S.C.P., R.M.B.), Pathology and Immunology (B.P.G., J.L.C., E.B.H.), Molecular Physiology and Biophysics (R.M.B.), The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology (N.J.A., J.F.P.), and Texas Children's Microbiome Center, Department of Pathology, Baylor College of Medicine, Houston (J.L.C., E.B.H.); and Department of Medicine, Texas Children's Hospital, Houston (J.L.C., E.B.H.)
| | - Nadim J Ajami
- From the Departments of Anesthesiology (D.J.D., S.C.P., R.M.B.), Pathology and Immunology (B.P.G., J.L.C., E.B.H.), Molecular Physiology and Biophysics (R.M.B.), The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology (N.J.A., J.F.P.), and Texas Children's Microbiome Center, Department of Pathology, Baylor College of Medicine, Houston (J.L.C., E.B.H.); and Department of Medicine, Texas Children's Hospital, Houston (J.L.C., E.B.H.)
| | - Sharon C Phillips
- From the Departments of Anesthesiology (D.J.D., S.C.P., R.M.B.), Pathology and Immunology (B.P.G., J.L.C., E.B.H.), Molecular Physiology and Biophysics (R.M.B.), The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology (N.J.A., J.F.P.), and Texas Children's Microbiome Center, Department of Pathology, Baylor College of Medicine, Houston (J.L.C., E.B.H.); and Department of Medicine, Texas Children's Hospital, Houston (J.L.C., E.B.H.)
| | - Joseph F Petrosino
- From the Departments of Anesthesiology (D.J.D., S.C.P., R.M.B.), Pathology and Immunology (B.P.G., J.L.C., E.B.H.), Molecular Physiology and Biophysics (R.M.B.), The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology (N.J.A., J.F.P.), and Texas Children's Microbiome Center, Department of Pathology, Baylor College of Medicine, Houston (J.L.C., E.B.H.); and Department of Medicine, Texas Children's Hospital, Houston (J.L.C., E.B.H.)
| | - Emily B Hollister
- From the Departments of Anesthesiology (D.J.D., S.C.P., R.M.B.), Pathology and Immunology (B.P.G., J.L.C., E.B.H.), Molecular Physiology and Biophysics (R.M.B.), The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology (N.J.A., J.F.P.), and Texas Children's Microbiome Center, Department of Pathology, Baylor College of Medicine, Houston (J.L.C., E.B.H.); and Department of Medicine, Texas Children's Hospital, Houston (J.L.C., E.B.H.)
| | - Robert M Bryan
- From the Departments of Anesthesiology (D.J.D., S.C.P., R.M.B.), Pathology and Immunology (B.P.G., J.L.C., E.B.H.), Molecular Physiology and Biophysics (R.M.B.), The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology (N.J.A., J.F.P.), and Texas Children's Microbiome Center, Department of Pathology, Baylor College of Medicine, Houston (J.L.C., E.B.H.); and Department of Medicine, Texas Children's Hospital, Houston (J.L.C., E.B.H.)
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Hollister EB. Abstract PL01-01: Meet your microbiome: An introduction to the who, what, and how of mixed microbial communities. Cancer Prev Res (Phila) 2015. [DOI: 10.1158/1940-6215.prev-14-pl01-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The human microbiome is comprised of the bacteria, archaea, fungi, protists, and viruses that live in and on our bodies. It is estimated that the microbial cells that comprise your individual microbiome outnumber your own cells by a factor of 10 and that their collective gene content outnumbers your own by a factor of 100. Although scientists and physicians have appreciated the diversity of our “fellow travelers” for decades, our ability to count, study, and categorize our microbes was long limited by the challenges associated with their culture in the laboratory. The utilization of high-throughput sequencing platforms, development of new and improved bioinformatics resources, and the introduction of other ‘omics technologies have shed new light on the composition and function of the human microbiome. The NIH-sponsored Human Microbiome Project characterized the microbial communities of hundreds of healthy individuals in an attempt to define the “healthy” microbiome at various sites throughout the body, and other projects have examined the human microbiome under varying states of disease and health. Microbiome and metagenomic studies have revealed that microbes may contribute to metabolic disorders, inflammatory bowel disease, heart disease, and cancer; and emerging evidence from mouse models suggests a strong link between gut microbiome composition and brain development and behavior. Microbiome and metagenomic studies have also demonstrated that our microbiota may confer protective or beneficial effects, and the depletion or loss of these “good” microbes may leave us susceptible to disease or infection. This talk will introduce the concept of the human microbiome, discuss the techniques that are used to characterize the structure and function of mixed microbial communities, and highlight recent findings from the literature.
Citation Format: Emily B. Hollister. Meet your microbiome: An introduction to the who, what, and how of mixed microbial communities. [abstract]. In: Proceedings of the Thirteenth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2014 Sep 27-Oct 1; New Orleans, LA. Philadelphia (PA): AACR; Can Prev Res 2015;8(10 Suppl): Abstract nr PL01-01.
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Hollister EB, Riehle K, Luna RA, Weidler EM, Rubio-Gonzales M, Mistretta TA, Raza S, Doddapaneni HV, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Shulman RJ, Versalovic J. Structure and function of the healthy pre-adolescent pediatric gut microbiome. Microbiome 2015; 3:36. [PMID: 26306392 PMCID: PMC4550057 DOI: 10.1186/s40168-015-0101-x] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/12/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND The gut microbiome influences myriad host functions, including nutrient acquisition, immune modulation, brain development, and behavior. Although human gut microbiota are recognized to change as we age, information regarding the structure and function of the gut microbiome during childhood is limited. Using 16S rRNA gene and shotgun metagenomic sequencing, we characterized the structure, function, and variation of the healthy pediatric gut microbiome in a cohort of school-aged, pre-adolescent children (ages 7-12 years). We compared the healthy pediatric gut microbiome with that of healthy adults previously recruited from the same region (Houston, TX, USA). RESULTS Although healthy children and adults harbored similar numbers of taxa and functional genes, their composition and functional potential differed significantly. Children were enriched in Bifidobacterium spp., Faecalibacterium spp., and members of the Lachnospiraceae, while adults harbored greater abundances of Bacteroides spp. From a functional perspective, significant differences were detected with respect to the relative abundances of genes involved in vitamin synthesis, amino acid degradation, oxidative phosphorylation, and triggering mucosal inflammation. Children's gut communities were enriched in functions which may support ongoing development, while adult communities were enriched in functions associated with inflammation, obesity, and increased risk of adiposity. CONCLUSIONS Previous studies suggest that the human gut microbiome is relatively stable and adult-like after the first 1 to 3 years of life. Our results suggest that the healthy pediatric gut microbiome harbors compositional and functional qualities that differ from those of healthy adults and that the gut microbiome may undergo a more prolonged development than previously suspected.
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Affiliation(s)
- Emily B Hollister
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA.
| | - Kevin Riehle
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Bioinformatics Research Laboratory, Baylor College of Medicine, Houston, TX, USA
| | - Ruth Ann Luna
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Erica M Weidler
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Children's Nutrition Research Center, Houston, TX, USA
- Pediatric Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Houston, TX, USA
| | - Michelle Rubio-Gonzales
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Toni-Ann Mistretta
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Sabeen Raza
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | | | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Joseph F Petrosino
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Robert J Shulman
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Children's Nutrition Research Center, Houston, TX, USA
- Pediatric Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Houston, TX, USA
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA
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Chumpitazi BP, Cope JL, Hollister EB, Tsai CM, McMeans AR, Luna RA, Versalovic J, Shulman RJ. Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome. Aliment Pharmacol Ther 2015; 42:418-27. [PMID: 26104013 PMCID: PMC4514898 DOI: 10.1111/apt.13286] [Citation(s) in RCA: 262] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/13/2015] [Accepted: 05/30/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND A low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet can ameliorate symptoms in adult irritable bowel syndrome (IBS) within 48 h. AIM To determine the efficacy of a low FODMAP diet in childhood IBS and whether gut microbial composition and/or metabolic capacity are associated with its efficacy. METHODS In a double-blind, crossover trial, children with Rome III IBS completed a 1-week baseline period. They then were randomised to a low FODMAP diet or typical American childhood diet (TACD), followed by a 5-day washout period before crossing over to the other diet. GI symptoms were assessed with abdominal pain frequency being the primary outcome. Baseline gut microbial composition (16S rRNA sequencing) and metabolic capacity (PICRUSt) were determined. Metagenomic biomarker discovery (LEfSe) compared Responders (≥50% decrease in abdominal pain frequency on low FODMAP diet only) vs. Nonresponders (no improvement during either intervention). RESULTS Thirty-three children completed the study. Less abdominal pain occurred during the low FODMAP diet vs. TACD [1.1 ± 0.2 (SEM) episodes/day vs. 1.7 ± 0.4, P < 0.05]. Compared to baseline (1.4 ± 0.2), children had fewer daily abdominal pain episodes during the low FODMAP diet (P < 0.01) but more episodes during the TACD (P < 0.01). Responders were enriched at baseline in taxa with known greater saccharolytic metabolic capacity (e.g. Bacteroides, Ruminococcaceae, Faecalibacterium prausnitzii) and three Kyoto Encyclopedia of Genes and Genomes orthologues, of which two relate to carbohydrate metabolism. CONCLUSIONS In childhood IBS, a low FODMAP diet decreases abdominal pain frequency. Gut microbiome biomarkers may be associated with low FODMAP diet efficacy. ClinicalTrials.gov identifier: NCT01339117.
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Affiliation(s)
- B P Chumpitazi
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - J L Cope
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - E B Hollister
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - C M Tsai
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - A R McMeans
- Children's Nutrition Research Center, Houston, TX, USA
| | - R A Luna
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - J Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - R J Shulman
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Children's Nutrition Research Center, Houston, TX, USA
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Davidovics ZH, Carter BA, Luna RA, Hollister EB, Shulman RJ, Versalovic J. The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome. JPEN J Parenter Enteral Nutr 2015; 40:1106-1113. [PMID: 26059898 DOI: 10.1177/0148607115591216] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/18/2015] [Indexed: 01/01/2023]
Abstract
BACKGROUND Changes in the intestinal microbiome of patients with short bowel syndrome (SBS) are thought to significantly affect clinical outcome. These changes may not only delay enteral diet advancement but may also predispose patients to bacterial translocation, bacteremia, and liver disease. Patients with SBS are thought to be more susceptible to changes in gut microbial communities due to intestinal dysmotility and/or lack of anatomic safeguards such as the ileocecal valve. MATERIALS AND METHODS We analyzed the bacterial composition of 21 fecal specimens from 9 children with SBS and 8 healthy children ages 4 months to 8 years by 16S ribosomal RNA gene sequencing. The sequences were quality filtered and analyzed using QIIME, the Ribosomal Database Project Classifier, and the randomForest supervised learning algorithm. RESULTS The fecal microbiome of patients with SBS is different from that of healthy controls. Stool from patients with SBS had a significantly greater abundance of the bacterial classes Gammaproteobacteria and Bacilli. Stool from patients with SBS who experienced increased stool frequency tended to have increased abundance of Lactobacillus (P = .057) and decreased abundance of Ruminococcus. CONCLUSION This study shows that the fecal microbiome of patients with SBS is significantly different from that of healthy controls when analyzed by 16S metagenomics. Differences in the composition and function of gut microbiomes in children with SBS may affect bowel physiology, and these findings may provide new opportunities for intestinal rehabilitation and clinical management.
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Affiliation(s)
- Zev H Davidovics
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Division of Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Houston, Texas
| | - Beth A Carter
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Division of Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Houston, Texas
| | - Ruth Ann Luna
- Texas Children's Microbiome Center, Houston, Texas.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas.,Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Emily B Hollister
- Texas Children's Microbiome Center, Houston, Texas.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas.,Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Robert J Shulman
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Division of Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Houston, Texas.,Children's Nutrition Research Center, Houston, Texas
| | - James Versalovic
- Texas Children's Microbiome Center, Houston, Texas .,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas.,Department of Pathology, Texas Children's Hospital, Houston, Texas
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Kao CC, Cope JL, Hsu JW, Dwarkanath P, Karnes JM, Luna RA, Hollister EB, Thame MM, Kurpad AV, Jahoor F. The Microbiome, Intestinal Function, and Arginine Metabolism of Healthy Indian Women Are Different from Those of American and Jamaican Women. J Nutr 2015; 146:706-713. [PMID: 26962180 DOI: 10.3945/jn.115.227579] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/07/2016] [Accepted: 02/09/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Indian women have slower arginine flux during pregnancy compared with American and Jamaican women. Arginine is a semi-essential amino acid that becomes essential during periods of rapid lean tissue deposition. It is synthesized only from citrulline, a nondietary amino acid produced mainly in the gut. The gut is therefore a key site of arginine and citrulline metabolism, and gut microbiota may affect their metabolism. OBJECTIVE The objective of this study was to identify differences in the gut microbiota of nonpregnant American, Indian, and Jamaican women and characterize the relations between the gut microbiota, gut function, and citrulline and arginine metabolism. METHODS Thirty healthy American, Indian, and Jamaican women (n = 10/group), aged 28.3 ± 0.8 y, were infused intravenously with [guanidino-15N2]arginine, [5,5-2H2]citrulline, and [15N2]ornithine and given oral [U-13C6]arginine in the fasting and postprandial states. Fecal bacterial communities were characterized by 16S rRNA gene sequencing. RESULTS In the fasting state, Indian women had lower citrulline flux than did American and Jamaican women [7.0 ± 0.4 compared with 9.1 ± 0.4 and 8.9 ± 0.2 μmol ⋅ kg fat-free mass (FFM)-1 ⋅ h-1, P = 0.01] and greater enteral arginine conversion to ornithine than did American women (1.4 ± 0.11 compared with 1.0 ± 0.08 μmol ⋅ kg FFM-1 ⋅ h-1, P = 0.04). They also had lower mannitol excretion than American and Jamaican women (154 ± 37.1 compared with 372 ± 51.8 and 410 ± 39.6 mg/6 h, P < 0.01). Three dominant stool community types characterized by increased abundances of the genera Prevotella, Bacteroides, and Bacteroides with Clostridium were identified. Indian women had increased mean relative abundances of Prevotella (42%) compared to American and Jamaican women (7% and < 1%, P = 0.03) which were associated with diet, impaired intestinal absorptive capacity, and arginine flux. CONCLUSIONS These findings suggest that dysregulated intestinal function and a unique gut microbiome may contribute to altered arginine metabolism in Indian women.
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Affiliation(s)
- Christina C Kao
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX.,Section of Pulmonary, Critical Care, and Sleep, Department of Medicine, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Julia L Cope
- Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX.,Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Jean W Hsu
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Pratibha Dwarkanath
- St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Jeffrey M Karnes
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Ruth A Luna
- Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX.,Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Emily B Hollister
- Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX.,Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Minerva M Thame
- Department of Child and Adolescent Health, University of West Indies, Mona, Kingston, Jamaica
| | - Anura V Kurpad
- St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Farook Jahoor
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
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Kellermayer R, Nagy-Szakal D, Harris RA, Luna RA, Pitashny M, Schady D, Mir SA, Lopez ME, Gilger MA, Belmont J, Hollister EB, Versalovic J. Serial fecal microbiota transplantation alters mucosal gene expression in pediatric ulcerative colitis. Am J Gastroenterol 2015; 110:604-6. [PMID: 25853207 PMCID: PMC4883582 DOI: 10.1038/ajg.2015.19] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Richard Kellermayer
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, Texas, USA,USDA/ARS Children's Nutrition Research Center, Houston, Texas, USA
| | - Dorottya Nagy-Szakal
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, Texas, USA,USDA/ARS Children's Nutrition Research Center, Houston, Texas, USA
| | - R. Alan Harris
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ruth Ann Luna
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Milena Pitashny
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Deborah Schady
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Sabina A.V. Mir
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, Texas, USA,USDA/ARS Children's Nutrition Research Center, Houston, Texas, USA
| | - Monica E. Lopez
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Mark A. Gilger
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, Texas, USA
| | - John Belmont
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Emily B. Hollister
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - James Versalovic
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
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Hu P, Hollister EB, Somenahally AC, Hons FM, Gentry TJ. Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation. Front Microbiol 2015; 5:729. [PMID: 25709600 PMCID: PMC4288022 DOI: 10.3389/fmicb.2014.00729] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 12/03/2014] [Indexed: 11/13/2022] Open
Abstract
The meals from many oilseed crops have potential for biofumigation due to their release of biocidal compounds such as isothiocyanates (ITCs). Various ITCs are known to inhibit numerous pathogens; however, much less is known about how the soil microbial community responds to the different types of ITCs released from oilseed meals (SMs). To simulate applying ITC-releasing SMs to soil, we amended soil with 1% flax SM (contains no biocidal chemicals) along with four types of ITCs (allyl, butyl, phenyl, and benzyl ITC) in order to determine their effects on soil fungal and bacterial communities in a replicated microcosm study. Microbial communities were analyzed based on the ITS region for fungi and 16S rRNA gene for bacteria using qPCR and tag-pyrosequencing with 454 GS FLX titanium technology. A dramatic decrease in fungal populations (~85% reduction) was observed after allyl ITC addition. Fungal community compositions also shifted following ITC amendments (e.g., Humicola increased in allyl and Mortierella in butyl ITC amendments). Bacterial populations were less impacted by ITCs, although there was a transient increase in the proportion of Firmicutes, related to bacteria know to be antagonistic to plant pathogens, following amendment with allyl ITC. Our results indicate that the type of ITC released from SMs can result in differential impacts on soil microorganisms. This information will aid selection and breeding of plants for biofumigation-based control of soil-borne pathogens while minimizing the impacts on non-target microorganisms.
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Affiliation(s)
- Ping Hu
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, TX, USA
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of SciencesShenyang, China
| | - Emily B. Hollister
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, TX, USA
| | | | - Frank M. Hons
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, TX, USA
| | - Terry J. Gentry
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, TX, USA
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35
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Hollister EB, Brooks JP, Gentry TJ. Bioinformation and ’Omic Approaches for Characterization of Environmental Microorganisms. Environ Microbiol 2015. [DOI: 10.1016/b978-0-12-394626-3.00021-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Spinler JK, Sontakke A, Hollister EB, Venable SF, Oh PL, Balderas MA, Saulnier DMA, Mistretta TA, Devaraj S, Walter J, Versalovic J, Highlander SK. From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. Genome Biol Evol 2014; 6:1772-89. [PMID: 24951561 PMCID: PMC4122935 DOI: 10.1093/gbe/evu137] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The vertebrate gut symbiont Lactobacillus reuteri has diversified into separate clades reflecting host origin. Strains show evidence of host adaptation, but how host–microbe coevolution influences microbial-derived effects on hosts is poorly understood. Emphasizing human-derived strains of L. reuteri, we combined comparative genomic analyses with functional assays to examine variations in host interaction among genetically distinct ecotypes. Within clade II or VI, the genomes of human-derived L. reuteri strains are highly conserved in gene content and at the nucleotide level. Nevertheless, they share only 70–90% of total gene content, indicating differences in functional capacity. Human-associated lineages are distinguished by genes related to bacteriophages, vitamin biosynthesis, antimicrobial production, and immunomodulation. Differential production of reuterin, histamine, and folate by 23 clade II and VI strains was demonstrated. These strains also differed with respect to their ability to modulate human cytokine production (tumor necrosis factor, monocyte chemoattractant protein-1, interleukin [IL]-1β, IL-5, IL-7, IL-12, and IL-13) by myeloid cells. Microarray analysis of representative clade II and clade VI strains revealed global regulation of genes within the reuterin, vitamin B12, folate, and arginine catabolism gene clusters by the AraC family transcriptional regulator, PocR. Thus, human-derived L. reuteri clade II and VI strains are genetically distinct and their differences affect their functional repertoires and probiotic features. These findings highlight the biological impact of microbe:host coevolution and illustrate the functional significance of subspecies differences in the human microbiome. Consideration of host origin and functional differences at the subspecies level may have major impacts on probiotic strain selection and considerations of microbial ecology in mammalian species.
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Affiliation(s)
- Jennifer K Spinler
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Amrita Sontakke
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Emily B Hollister
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Susan F Venable
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Phaik Lyn Oh
- Department of Food Science and Technology, University of Nebraska, Lincoln
| | - Miriam A Balderas
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX
| | - Delphine M A Saulnier
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TXPresent address: Department of Gastrointestinal Microbiology, German Institute of Human Nutrition, Nuthetal, Germany
| | - Toni-Ann Mistretta
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Sridevi Devaraj
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Jens Walter
- Department of Food Science and Technology, University of Nebraska, LincolnPresent address: Departments of Agricultural, Food, & Nutritional Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - James Versalovic
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TXDepartment of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX
| | - Sarah K Highlander
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TXHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TXPresent address: Genomic Medicine, J. Craig Venter Institute, La Jolla, CA
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Hollister EB, Gao C, Versalovic J. Compositional and functional features of the gastrointestinal microbiome and their effects on human health. Gastroenterology 2014; 146:1449-58. [PMID: 24486050 PMCID: PMC4181834 DOI: 10.1053/j.gastro.2014.01.052] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/13/2014] [Accepted: 01/24/2014] [Indexed: 12/13/2022]
Abstract
The human gastrointestinal tract contains distinct microbial communities that differ in composition and function based on their location, as well as age, sex, race/ethnicity, and diet of their host. We describe the bacterial taxa present in different locations of the GI tract, and their specific metabolic features. The distinct features of these specific microbial communities might affect human health and disease. Several bacterial taxa and metabolic modules (biochemical functions) have been associated with human health and the absence of disease. Core features of the healthy microbiome might be defined and targeted to prevent disease and optimize human health.
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Affiliation(s)
- Emily B. Hollister
- Department of Pathology & Immunology, Baylor College of Medicine,Department of Pathology, Texas Children’s Hospital
| | - Chunxu Gao
- Department of Pathology & Immunology, Baylor College of Medicine,Department of Molecular Virology & Microbiology, Baylor College of Medicine,Department of Pathology, Texas Children’s Hospital
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas.
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38
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Chumpitazi BP, Hollister EB, Oezguen N, Tsai CM, McMeans AR, Luna RA, Savidge TC, Versalovic J, Shulman RJ. Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome. Gut Microbes 2014; 5:165-75. [PMID: 24637601 PMCID: PMC4063841 DOI: 10.4161/gmic.27923] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We sought to determine whether a low fermentable substrate diet (LFSD) decreases abdominal pain frequency in children with irritable bowel syndrome (IBS) and to identify potential microbial factors related to diet efficacy. Pain symptoms, stooling characteristics, breath hydrogen and methane, whole intestinal transit time, stool microbiome, and metabolite composition were collected and/or documented in eight children with IBS at baseline and during one week of an LFSD intervention. Pain frequency (P<0.05), pain severity (P<0.05), and pain-related interference with activities (P<0.05) decreased in the subjects while on the LFSD. Responders vs. non-responders: four children (50%) were identified as responders (> 50% decrease in abdominal pain frequency while on the LFSD). There were no differences between responders and non-responders with respect to hydrogen production, methane production, stooling characteristics, or gut transit time. Responders were characterized by increased pre-LFSD abundance of bacterial taxa belonging to the genera Sporobacter (P<0.05) and Subdoligranulum (P<0.02) and decreased abundance of taxa belonging to Bacteroides (P<0.05) relative to non-responders. In parallel, stool metabolites differed between responders and non-responders and were associated with differences in microbiome composition. These pilot study results suggest that an LFSD may be effective in decreasing GI symptoms in children with IBS. Microbial factors such as gut microbiome composition and stool metabolites while on the diet may relate to LFSD efficacy.
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Affiliation(s)
- Bruno P Chumpitazi
- Department of Pediatrics; Baylor College of Medicine; Houston, TX USA,Section of Pediatric Gastroenterology, Hepatology, and Nutrition; Texas Children’s Hospital; Houston, TX USA,Correspondence to: Bruno P Chumpitazi,
| | - Emily B Hollister
- Department of Pathology and Immunology; Baylor College of Medicine; Houston, TX USA,Texas Children’s Microbiome Center; Department of Pathology; Texas Children’s Hospital; Houston, TX USA
| | - Numan Oezguen
- Department of Pathology and Immunology; Baylor College of Medicine; Houston, TX USA,Texas Children’s Microbiome Center; Department of Pathology; Texas Children’s Hospital; Houston, TX USA
| | - Cynthia M Tsai
- Department of Pediatrics; Baylor College of Medicine; Houston, TX USA,Section of Pediatric Gastroenterology, Hepatology, and Nutrition; Texas Children’s Hospital; Houston, TX USA
| | - Ann R McMeans
- Children’s Nutrition Research Center; Houston, TX USA
| | - Ruth A Luna
- Department of Pathology and Immunology; Baylor College of Medicine; Houston, TX USA,Texas Children’s Microbiome Center; Department of Pathology; Texas Children’s Hospital; Houston, TX USA
| | - Tor C Savidge
- Department of Pathology and Immunology; Baylor College of Medicine; Houston, TX USA,Texas Children’s Microbiome Center; Department of Pathology; Texas Children’s Hospital; Houston, TX USA
| | - James Versalovic
- Department of Pediatrics; Baylor College of Medicine; Houston, TX USA,Department of Pathology and Immunology; Baylor College of Medicine; Houston, TX USA,Texas Children’s Microbiome Center; Department of Pathology; Texas Children’s Hospital; Houston, TX USA
| | - Robert J Shulman
- Department of Pediatrics; Baylor College of Medicine; Houston, TX USA,Section of Pediatric Gastroenterology, Hepatology, and Nutrition; Texas Children’s Hospital; Houston, TX USA,Children’s Nutrition Research Center; Houston, TX USA
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Cope JL, Hammett AJM, Kolomiets EA, Forrest AK, Golub KW, Hollister EB, DeWitt TJ, Gentry TJ, Holtzapple MT, Wilkinson HH. Evaluating the performance of carboxylate platform fermentations across diverse inocula originating as sediments from extreme environments. Bioresour Technol 2014; 155:388-394. [PMID: 24502857 DOI: 10.1016/j.biortech.2013.12.105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 12/22/2013] [Accepted: 12/24/2013] [Indexed: 06/03/2023]
Abstract
To test the hypothesis that microbial communities from saline and thermal sediment environments are pre-adapted to exhibit superior fermentation performances, 501 saline and thermal samples were collected from a wide geographic range. Each sediment sample was screened as inoculum in a 30-day batch fermentation. Using multivariate statistics, the capacity of each community was assessed to determine its ability to degrade a cellulosic substrate and produce carboxylic acids in the context of the inoculum sediment chemistry. Conductance of soils was positively associated with production of particular acids, but negatively associated with conversion efficiency. In situ sediment temperature and conversion efficiency were consistently positively related. Because inoculum characteristics influence carboxylate platform productivity, optimization of the inoculum is an important and realistic goal.
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Affiliation(s)
- Julia L Cope
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030-2617, USA
| | - Amy Jo M Hammett
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, USA
| | - Elena A Kolomiets
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, USA
| | - Andrea K Forrest
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Kristina W Golub
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Emily B Hollister
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030-2617, USA
| | - Thomas J DeWitt
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, USA
| | - Terry J Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA
| | - Mark T Holtzapple
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Heather H Wilkinson
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, USA.
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Nagy-Szakal D, Hollister EB, Luna RA, Szigeti R, Tatevian N, Smith CW, Versalovic J, Kellermayer R. Cellulose supplementation early in life ameliorates colitis in adult mice. PLoS One 2013; 8:e56685. [PMID: 23437211 PMCID: PMC3577696 DOI: 10.1371/journal.pone.0056685] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/14/2013] [Indexed: 01/19/2023] Open
Abstract
Decreased consumption of dietary fibers, such as cellulose, has been proposed to promote the emergence of inflammatory bowel diseases (IBD: Crohn disease [CD] and ulcerative colitis [UC]) where intestinal microbes are recognized to play an etiologic role. However, it is not known if transient fiber consumption during critical developmental periods may prevent consecutive intestinal inflammation. The incidence of IBD peaks in young adulthood indicating that pediatric environmental exposures may be important in the etiology of this disease group. We studied the effects of transient dietary cellulose supplementation on dextran sulfate sodium (DSS) colitis susceptibility during the pediatric period in mice. Cellulose supplementation stimulated substantial shifts in the colonic mucosal microbiome. Several bacterial taxa decreased in relative abundance (e.g., Coriobacteriaceae [p = 0.001]), and other taxa increased in abundance (e.g., Peptostreptococcaceae [p = 0.008] and Clostridiaceae [p = 0.048]). Some of these shifts persisted for 10 days following the cessation of cellulose supplementation. The changes in the gut microbiome were associated with transient trophic and anticolitic effects 10 days following the cessation of a cellulose-enriched diet, but these changes diminished by 40 days following reversal to a low cellulose diet. These findings emphasize the transient protective effect of dietary cellulose in the mammalian large bowel and highlight the potential role of dietary fibers in amelioration of intestinal inflammation.
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Affiliation(s)
- Dorottya Nagy-Szakal
- Section of Pediatric Gastroenterology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- USDA/ARS Children's Nutrition Research Center, Houston, Texas, United States of America
| | - Emily B. Hollister
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Ruth Ann Luna
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Reka Szigeti
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nina Tatevian
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - C. Wayne Smith
- USDA/ARS Children's Nutrition Research Center, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - James Versalovic
- Department of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- USDA/ARS Children's Nutrition Research Center, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
- * E-mail:
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Hollister EB, Hu P, Wang AS, Hons FM, Gentry TJ. Differential impacts of brassicaceous and nonbrassicaceous oilseed meals on soil bacterial and fungal communities. FEMS Microbiol Ecol 2012; 83:632-41. [PMID: 23025785 DOI: 10.1111/1574-6941.12020] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/21/2012] [Accepted: 09/25/2012] [Indexed: 12/01/2022] Open
Abstract
Demand for alternative fuels has sparked renewed interest in the production of biodiesel from oil-rich seeds. Oilseed meals are a byproduct of this process, and given their relatively high nutrient content, land application represents a potential value-added use. In this microcosm-based study, soil microbial community responses to amendments of a glucosinolate-containing brassicaceous oilseed meal (Brassica juncea, mustard), a non-glucosinolate-containing, nonbrassicaceous oilseed meal (Linum usitatissimum, flax), and a nonoilseed biomass (Sorghum bicolor) were characterized using a 28-day time series of replicated 16S rRNA gene and fungal ITS gene sequence libraries. We hypothesized that biomass type and glucosinolate content would alter community composition but that effects would diminish over time. Distinct separation occurred by amendment type, with mustard inducing large increases in the abundance of bacterial taxa associated with fungal disease suppression (e.g. Bacillus, Pseudomonas, and Streptomyces spp.). Dramatic shifts were seen among the fungi, too, with phylotype richness decreasing by > 60% following mustard addition. Changes in bacterial and fungal community composition were rapid, and distinct community types persisted throughout the study. Oilseed amendment, and mustard in particular, has the potential to alter soil microbial community structure substantially, and such changes are likely to be important in the context of ecosystem health.
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Affiliation(s)
- Emily B Hollister
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA.
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Forrest AK, Hollister EB, Gentry TJ, Wilkinson HH, Holtzapple MT. Comparison of mixed-acid fermentations inoculated with six different mixed cultures. Bioresour Technol 2012; 118:343-349. [PMID: 22705541 DOI: 10.1016/j.biortech.2012.05.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/05/2012] [Accepted: 05/11/2012] [Indexed: 06/01/2023]
Abstract
The MixAlco™ process biologically converts biomass to carboxylate salts that may be converted to a variety of chemicals and fuels. This study examines the fermentation performance of six different mixed cultures, and how the performance was affected by the bacterial composition of each community. All six countercurrent fermentations had very similar performance, but were dissimilar in microbial community composition. The acid concentrations varied by only 12% between fermentation trains and the conversions varied only by 6%. The microbial communities were profiled using 16S rRNA tag-pyrosequencing, which revealed the presence of dynamic communities that were dominated by bacteria resembling Clostridia, but they shared few taxa in common. Yue-Clayton similarity calculations of the communities revealed that they were extremely different. The presence of different but functionally similar microbial communities in this study suggests that it is the operating parameters that determine the fermentation end-products.
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Affiliation(s)
- Andrea K Forrest
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.
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Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Tringe SG, Malfatti SA, Holtzapple MT, Gentry TJ. Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One 2012; 7:e39689. [PMID: 22761870 PMCID: PMC3382152 DOI: 10.1371/journal.pone.0039689] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 05/29/2012] [Indexed: 11/19/2022] Open
Abstract
The carboxylate platform is a flexible, cost-effective means of converting lignocellulosic materials into chemicals and liquid fuels. Although the platform's chemistry and engineering are well studied, relatively little is known about the mixed microbial communities underlying its conversion processes. In this study, we examined the metagenomes of two actively fermenting platform communities incubated under contrasting temperature conditions (mesophilic 40°C; thermophilic 55 °C), but utilizing the same inoculum and lignocellulosic feedstock. Community composition segregated by temperature. The thermophilic community harbored genes affiliated with Clostridia, Bacilli, and a Thermoanaerobacterium sp, whereas the mesophilic community metagenome was composed of genes affiliated with other Clostridia and Bacilli, Bacteriodia, γ-Proteobacteria, and Actinobacteria. Although both communities were able to metabolize cellulosic materials and shared many core functions, significant differences were detected with respect to the abundances of multiple Pfams, COGs, and enzyme families. The mesophilic metagenome was enriched in genes related to the degradation of arabinose and other hemicellulose-derived oligosaccharides, and the production of valerate and caproate. In contrast, the thermophilic community was enriched in genes related to the uptake of cellobiose and the transfer of genetic material. Functions assigned to taxonomic bins indicated that multiple community members at either temperature had the potential to degrade cellulose, cellobiose, or xylose and produce acetate, ethanol, and propionate. The results of this study suggest that both metabolic flexibility and functional redundancy contribute to the platform's ability to process lignocellulosic substrates and are likely to provide a degree of stability to the platform's fermentation processes.
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Affiliation(s)
- Emily B Hollister
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America.
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Ng JP, Hollister EB, González-Chávez MDCA, Hons FM, Zuberer DA, Aitkenhead-Peterson JA, Loeppert R, Gentry TJ. Impacts of Cropping Systems and Long-Term Tillage on Soil Microbial Population Levels and Community Composition in Dryland Agricultural Setting. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/487370] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Few studies have used molecular methods to correlate the abundance of specific microbial taxonomic groups with changes in soil properties impacted by long-term agriculture. Community qPCR with 16S rRNA gene sequencing to examine the effects of long-term crop-management practices (no-till vs. conventional tillage, and continuous wheat (Triticum aestivum L.) vs. sorghum-wheat-soybean rotation (Sorghum bicolor L. Moench-Triticum aestivum L.-Glycine max L. Merr) on bacterial and fungal relative abundances and identify the dominant members of the soil microbial community. The qPCR assays revealed that crop rotation decreased bacterial copy numbers, but no-till practices did not significantly alter bacteria or fungi relative to conventional tillage. Cyanobacteria were more abundant while Actinobacteria were less numerous under continuous wheat. Acidobacteria and Planctomycetes were positively correlated with soil microbial biomass C and N. This study highlights ways cropping systems affect microbial communities and aids the development of sustainable agriculture.
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Affiliation(s)
- Justin P. Ng
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
- Programa de Edafología, Colegio de Postgraduados en Ciencias Agrícolas, Campus Montecillo, Carr. México-Texcoco, 56230 Montecillo, MEX, Mexico
| | - Emily B. Hollister
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
| | - Ma. del Carmen A. González-Chávez
- Programa de Edafología, Colegio de Postgraduados en Ciencias Agrícolas, Campus Montecillo, Carr. México-Texcoco, 56230 Montecillo, MEX, Mexico
| | - Frank M. Hons
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
| | - David A. Zuberer
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
| | | | - Richard Loeppert
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
| | - Terry J. Gentry
- Soil and Crop Sciences Department, Texas A&M University, College Station, TX 77843-2474, USA
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Somenahally AC, Hollister EB, Yan W, Gentry TJ, Loeppert RH. Water management impacts on arsenic speciation and iron-reducing bacteria in contrasting rice-rhizosphere compartments. Environ Sci Technol 2011; 45:8328-35. [PMID: 21870848 DOI: 10.1021/es2012403] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Rice cultivated on arsenic (As) contaminated-soils will accumulate variable grain-As concentrations, as impacted by varietal differences, soil variables, and crop management. A field-scale experiment was conducted to study the impact of intermittent and continuous flooding on As speciation and microbial populations in rice rhizosphere compartments of soils that were either historically amended with As pesticide or unamended with As. Rhizosphere-soil, root-plaque, pore-water and grain As were quantified and speciated, and microbial populations in rhizosphere soil and root-plaque were characterized. Total-As concentrations in rhizosphere and grain were significantly lower in intermittently flooded compared to the continuously flooded plots (86% lower in pore-water, 55% lower in root-plaque and 41% lower in grain samples). iAs(V), iAs(III), and DMAs(V) were the predominant As species detected in rhizosphere-soil and root-plaque, pore-water and grain samples, respectively. Relative proportions of Archaea and iron-reducing bacteria (FeRB) were higher in rhizosphere soil compared to root-plaque. In rhizosphere soil, the relative abundance of FeRB was lower in intermittently flooded compared to continuously flooded plots, but there were no differences between root-plaque samples. This study has demonstrated that reductions in dissolved As concentrations in the rhizosphere and subsequent decreases in grain-As concentration can be attained through water management.
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Affiliation(s)
- Anil C Somenahally
- Department of Soil and Crop Sciences, Texas A&M University , College Station, Texas, 77843-2474, United States.
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Golub KW, Smith AD, Hollister EB, Gentry TJ, Holtzapple MT. Investigation of intermittent air exposure on four-stage and one-stage anaerobic semi-continuous mixed-acid fermentations. Bioresour Technol 2011; 102:5066-75. [PMID: 21353536 DOI: 10.1016/j.biortech.2011.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/31/2011] [Accepted: 02/01/2011] [Indexed: 05/16/2023]
Abstract
This study evaluated anaerobic mixed-acid countercurrent fermentations in both strict S (minimal oxygen) and relaxed R (high oxygen) conditions. In relaxed fermentations, filter solids and liquids were exposed to air for 90 min every 56 h. The total acid concentrations for four-stage trains were 23.0 (4S) and 22.1 (4R) g/L(Liq), and for one-stage trains were 17.2 (1S) and 18.4 (1R) g/L(Liq). The strict and relaxed trains had statistically similar exit yields. The strict trains had significantly more high-molecular-weight carboxylic acids. The relaxed trains had slightly higher conversion and slightly lower selectivity, but not significantly. Air exposure had no significant effect on the bacterial profiles of the strict and relaxed fermentations. For all fermentations, the most abundant bacterial genus was Prevotella, a strict anaerobe. This study shows that the mixed-culture community is oxygen tolerant because it maintains fermentation performance during oxygen-induced stress.
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Affiliation(s)
- Kristina W Golub
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States.
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Hollister EB, Hammett AM, Holtzapple MT, Gentry TJ, Wilkinson HH. Microbial community composition and dynamics in a semi-industrial-scale facility operating under the MixAlco™ bioconversion platform. J Appl Microbiol 2011; 110:587-96. [PMID: 21199196 DOI: 10.1111/j.1365-2672.2010.04919.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS To monitor microbial community dynamics in a semi-industrial-scale lignocellulosic biofuel reactor system and to improve our understanding of the microbial communities involved in the MixAlco™ biomass conversion process. METHODS AND RESULTS Reactor microbial communities were characterized at six time points over the course of an 80-day, mesophilic, semi-industrial-scale fermentation using community qPCR and 16S rRNA tag-pyrosequencing. We found the communities to be dynamic, bacterially dominated consortia capable of changing quickly in response to reactor conditions. Clostridia- and Bacteroidetes-like organisms dominated the reactor communities, but ultimately the communities established consortia containing complementary functional capacities for the degradation of lignocellulosic materials. Eighteen operational taxonomic units were found to share strong correlations with reactor acid concentration and may represent taxa integral to fermentor performance. CONCLUSIONS The results of this study indicate that the emergence of complementary functional classes within the fermentor consortia may be a trait that is consistent across scales, and they suggest that there may be flexibility with respect to the specific identities of the organisms involved in the fermentor's degradation and fermentation processes. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides new information regarding the composition, dynamics and potential flexibility of the microbial communities associated with the MixAlco™ process and is likely to inform the improvement of this and other applications that employ mixed microbial communities.
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Affiliation(s)
- E B Hollister
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA.
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Gontcharova V, Youn E, Wolcott RD, Hollister EB, Gentry TJ, Dowd SE. Black Box Chimera Check (B2C2): a Windows-Based Software for Batch Depletion of Chimeras from Bacterial 16S rRNA Gene Datasets. Open Microbiol J 2010; 4:47-52. [PMID: 21339894 PMCID: PMC3040993 DOI: 10.2174/1874285801004010047] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 06/25/2010] [Accepted: 06/30/2010] [Indexed: 02/01/2023] Open
Abstract
The existing chimera detection programs are not specifically designed for "next generation" sequence data. Technologies like Roche 454 FLX and Titanium have been adapted over the past years especially with the introduction of bacterial tag-encoded FLX/Titanium amplicon pyrosequencing methodologies to produce over one million 250-600 bp 16S rRNA gene reads that need to be depleted of chimeras prior to downstream analysis. Meeting the needs of basic scientists who are venturing into high-throughput microbial diversity studies such as those based upon pyrosequencing and specifically providing a solution for Windows users, the B2C2 software is designed to be able to accept files containing large multi-FASTA formatted sequences and screen for possible chimeras in a high throughput fashion. The graphical user interface (GUI) is also able to batch process multiple files. When compared to popular chimera screening software the B2C2 performed as well or better while dramatically decreasing the amount of time required generating and screening results. Even average computer users are able to interact with the Windows .Net GUI-based application and define the stringency to which the analysis should be done. B2C2 may be downloaded from http://www.researchandtesting.com/B2C2.
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Hollister EB, Engledow AS, Hammett AJM, Provin TL, Wilkinson HH, Gentry TJ. Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME J 2010; 4:829-38. [DOI: 10.1038/ismej.2010.3] [Citation(s) in RCA: 228] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Lancaster SH, Hollister EB, Senseman SA, Gentry TJ. Effects of repeated glyphosate applications on soil microbial community composition and the mineralization of glyphosate. Pest Manag Sci 2010; 66:59-64. [PMID: 19697445 DOI: 10.1002/ps.1831] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
BACKGROUND Repeated applications may have a greater impact on the soil microbial community than a single application of glyphosate. Experiments were conducted to study the effect of one, two, three, four or five applications of glyphosate on soil microbial community composition and glyphosate mineralization and distribution of (14)C residues in soil. RESULTS Fatty acid methyl esters (FAMEs) common to gram-negative bacteria were present in higher concentrations following five applications relative to one, two, three or four applications both 7 and 14 days after application (DAA). Additionally, sequencing of 16S rRNA bacterial genes indicated that the abundance of the gram-negative Burkholderia spp. was increased following the application of glyphosate. The cumulative percentage (14)C mineralized 14 DAA was reduced when glyphosate was applied 4 or 5 times relative to the amount of (14)C mineralized following one, two or three applications. Incorporation of (14)C residues into soil microbial biomass was greater following five glyphosate applications than following the first application 3 and 7 DAA. CONCLUSION These studies suggest that the changes in the dissipation or distribution of glyphosate following repeated applications of glyphosate may be related to shifts in the soil microbial community composition.
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Affiliation(s)
- Sarah H Lancaster
- Department of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USA.
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