1
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Gemmell MR, Jayawardana T, Koentgen S, Brooks E, Kennedy N, Berry S, Lees C, Hold GL. Optimised human stool sample collection for multi-omic microbiota analysis. Sci Rep 2024; 14:16816. [PMID: 39039185 PMCID: PMC11263584 DOI: 10.1038/s41598-024-67499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024] Open
Abstract
To accurately define the role of the gut microbiota in health and disease pathogenesis, the preservation of stool sample integrity, in terms of microbial community composition and metabolic function, is critical. This presents a challenge for any studies which rely on participants self-collecting and returning stool samples as this introduces variability and uncertainty of sample storage/handling. Here, we tested the performance of three stool sample collection/preservation buffers when storing human stool samples at different temperatures (room temperature [20 °C], 4 °C and - 80 °C) for up to three days. We compared and quantified differences in 16S rRNA sequencing composition and short-chain fatty acid profiles compared against immediately snap-frozen stool. We found that the choice of preservation buffer had the largest effect on the resulting microbial community and metabolomic profiles. Collectively analysis confirmed that PSP and RNAlater buffered samples most closely recapitulated the microbial diversity profile of the original (immediately - 80 °C frozen) sample and should be prioritised for human stool microbiome studies.
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Affiliation(s)
| | - Thisun Jayawardana
- School of Clinical Medicine, Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Sabrina Koentgen
- School of Clinical Medicine, Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Ella Brooks
- School of Clinical Medicine, Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Nicholas Kennedy
- University of Exeter, Exeter, Devon, UK
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
| | - Susan Berry
- School of Medicine, Medical Sciences & Dentistry, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Charlie Lees
- Western General Hospital, Edinburgh, UK
- University of Edinburgh Centre for Genomic and Experimental Medicine, Edinburgh, UK
| | - Georgina L Hold
- School of Clinical Medicine, Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia.
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3
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Mehra P, Kumar A. Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology. Cell Biochem Funct 2024; 42:e4063. [PMID: 38961596 DOI: 10.1002/cbf.4063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/12/2024] [Accepted: 05/18/2024] [Indexed: 07/05/2024]
Abstract
The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.
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Affiliation(s)
- Parul Mehra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
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4
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Li XM, Shi X, Yao Y, Shen YC, Wu XL, Cai T, Liang LX, Wang F. Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis. Microbiol Spectr 2023; 11:e0429722. [PMID: 37093040 PMCID: PMC10269478 DOI: 10.1128/spectrum.04297-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/16/2023] [Indexed: 04/25/2023] Open
Abstract
Here, we aimed to compare the effects of different preservation methods on outcomes of fecal microbiota. We evaluated the effects of different preservation methods using stool sample preservation experiments for up to 1 year. The stool samples from feces of healthy volunteers were grouped based on whether absolute ethanol was added and whether they were hypothermically preserved. Besides, we performed a systematic review to combine current fecal microbiota preservation evidence. We found that Proteobacteria changed significantly and Veillonellaceae decreased significantly in the 12th month in the room temperature + absolute ethanol group. The four cryopreservation groups have more similarities with fresh sample in the 12 months; however, different cryopreservation methods have different effects on several phyla, families, and genera. A systematic review showed that the Shannon diversity and Simpson index of samples stored in RNAlater for 1 month were not statistically significant compared with those stored immediately at -80°C (P = 0.220 and P = 0.123, respectively). The -80°C refrigerator and liquid nitrogen cryopreservation with 10% glycerine can both maintain stable microbiota of stool samples for long-term preservation. The addition of absolute ethanol to cryopreserved samples had no significant difference in the effect of preserving fecal microbial characteristics. Our study provides empirical insights into preservation details for future studies of the long-term preservation of fecal microbiota. Systematic review and meta-analysis found that the gut microbiota structure, composition, and diversity of samples preserved by storage methods, such as preservation solution, are relatively stable, which were suitable for short-term storage at room temperature. IMPORTANCE The study of gut bacteria has become increasingly popular, and fecal sample preservation methods and times need to be standardized. Here, we detail a 12-month study of fecal sample preservation, and our study provides an empirical reference about experimental details for long-term high-quality storage of fecal samples in the field of gut microbiology research. The results showed that the combination of -80°C/liquid nitrogen deep cryopreservation and 10% glycerol was the most effective method for the preservation of stool samples, which is suitable for long-term storage for at least 12 months. The addition of anhydrous ethanol to the deep cryopreserved samples did not make a significant difference in the preservation of fecal microbiological characteristics. Combined with the results of systematic reviews and meta-analyses, we believe that, when researchers preserve fecal specimens, it is essential to select the proper preservation method and time period in accordance with the goal of the study.
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Affiliation(s)
- Xin-meng Li
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Xiao Shi
- Department of Dermatology, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Yao Yao
- Department of Gastroenterology, Zhangjiajie People’s Hospital, Zhangjiajie, Hunan, China
| | - Yi-cun Shen
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Xiang-ling Wu
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Ting Cai
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Lun-xi Liang
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
- Department of Gastroenterology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Fen Wang
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
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5
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Hughes RL, Frankenfeld CL, Gohl DM, Huttenhower C, Jackson SA, Vandeputte D, Vogtmann E, Comstock SS, Kable ME. Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022]. Nutrients 2023; 15:nu15112451. [PMID: 37299414 DOI: 10.3390/nu15112451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/14/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The microbial cells colonizing the human body form an ecosystem that is integral to the regulation and maintenance of human health. Elucidation of specific associations between the human microbiome and health outcomes is facilitating the development of microbiome-targeted recommendations and treatments (e.g., fecal microbiota transplant; pre-, pro-, and post-biotics) to help prevent and treat disease. However, the potential of such recommendations and treatments to improve human health has yet to be fully realized. Technological advances have led to the development and proliferation of a wide range of tools and methods to collect, store, sequence, and analyze microbiome samples. However, differences in methodology at each step in these analytic processes can lead to variability in results due to the unique biases and limitations of each component. This technical variability hampers the detection and validation of associations with small to medium effect sizes. Therefore, the American Society for Nutrition (ASN) Nutritional Microbiology Group Engaging Members (GEM), sponsored by the Institute for the Advancement of Food and Nutrition Sciences (IAFNS), hosted a satellite session on methods in nutrition and gut microbiome research to review currently available methods for microbiome research, best practices, as well as tools and standards to aid in comparability of methods and results. This manuscript summarizes the topics and research discussed at the session. Consideration of the guidelines and principles reviewed in this session will increase the accuracy, precision, and comparability of microbiome research and ultimately the understanding of the associations between the human microbiome and health.
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Affiliation(s)
| | | | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Curtis Huttenhower
- Department of Biostatistics and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Scott A Jackson
- Complex Microbial Systems Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Doris Vandeputte
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA
| | - Mary E Kable
- USDA-ARS Western Human Nutrition Research Center, University of California-Davis, Davis, CA 95616, USA
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6
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Bolt Botnen A, Bjørnsen MB, Alberdi A, Gilbert MTP, Aizpurua O. A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies. Heliyon 2023; 9:e12861. [PMID: 36699263 PMCID: PMC9868478 DOI: 10.1016/j.heliyon.2023.e12861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.
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Affiliation(s)
- Amanda Bolt Botnen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - Mads Bjørn Bjørnsen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
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7
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Fachrul M, Méric G, Inouye M, Pamp SJ, Salim A. Assessing and removing the effect of unwanted technical variations in microbiome data. Sci Rep 2022; 12:22236. [PMID: 36564466 PMCID: PMC9789116 DOI: 10.1038/s41598-022-26141-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Varying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations. Such variations, often unaccounted for and of unknown source, may interfere with true biological signals, resulting in misleading biological conclusions. In this work, we aim to characterize the major sources of technical variations in microbiome data and demonstrate how in-silico approaches can minimize their impact. We analyzed 184 pig faecal metagenomes encompassing 21 specific combinations of deliberately introduced factors of technical and biological variations. Using the novel Removing Unwanted Variations-III-Negative Binomial (RUV-III-NB), we identified several known experimental factors, specifically storage conditions and freeze-thaw cycles, as likely major sources of unwanted variation in metagenomes. We also observed that these unwanted technical variations do not affect taxa uniformly, with freezing samples affecting taxa of class Bacteroidia the most, for example. Additionally, we benchmarked the performances of different correction methods, including ComBat, ComBat-seq, RUVg, RUVs, and RUV-III-NB. While RUV-III-NB performed consistently robust across our sensitivity and specificity metrics, most other methods did not remove unwanted variations optimally. Our analyses suggest that a careful consideration of possible technical confounders is critical during experimental design of microbiome studies, and that the inclusion of technical replicates is necessary to efficiently remove unwanted variations computationally.
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Affiliation(s)
- Muhamad Fachrul
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Sünje Johanna Pamp
- National Food Institute, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Agus Salim
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia.
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3010, Australia.
- Department of Population Health, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.
- Department Mathematics and Statistics, La Trobe University, Bundoora, VIC, 3086, Australia.
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8
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Al-Musharaf S, Aljuraiban GS, Al-Ajllan L, Al-Khaldi N, Aljazairy EA, Hussain SD, Alnaami AM, Sabico S, Al-Daghri N. Vitamin B12 Status and Gut Microbiota among Saudi Females with Obesity. Foods 2022; 11:foods11244007. [PMID: 36553749 PMCID: PMC9778531 DOI: 10.3390/foods11244007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Previous studies have suggested that dietary habits and dysbiosis of gut microbiota contributed to obesity development. Vitamin B12 is produced by microbes; however, the relationships between vitamin B12, gut microbiome, and obesity are understudied. We aimed to determine the association between vitamin B12 status and gut microbiota relative to obesity in 92 Saudi Arabian females aged 19-25 years who were obese (n = 44) or normal weight (n = 48). Anthropometric, biochemical data, and dietary data were collected. The microbial communities of stool samples were characterized using the shotgun metagenomic sequencing technique. The relationship between vitamin B12 status and gut microbiota composition was identified using Pearson correlation analysis. A statistically significant difference was found in bacterial α- and β-diversity between the groups relative to median serum vitamin B12 level (404.0 pg/mL) and body weight. In the total participants, dietary vitamin B12 intake was inversely correlated with Bifidobacterium kashiwanohense and Blautia wexlerae species. In obese participants, dietary vitamin B12 intake was inversely correlated with Akkermansia muciniphila species and species from the Verrucomicrobia phylum, whereas it was positively correlated with Bacteroides species. Our findings indicate that the abundance (frequency) and diversity (richness) of gut microbiota are associated with vitamin B12 levels and obesity in young females.
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Affiliation(s)
- Sara Al-Musharaf
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: ; Tel.: +096-655-4243-033
| | - Ghadeer S. Aljuraiban
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Lama Al-Ajllan
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Noura Al-Khaldi
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Esra’a A. Aljazairy
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Syed Danish Hussain
- Chair for Biomarkers of Chronic Diseases, Riyadh Biochemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah M. Alnaami
- Chair for Biomarkers of Chronic Diseases, Riyadh Biochemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Shaun Sabico
- Chair for Biomarkers of Chronic Diseases, Riyadh Biochemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nasser Al-Daghri
- Chair for Biomarkers of Chronic Diseases, Riyadh Biochemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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9
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Reusing a prepaid health plan's fecal immunochemical tests for microbiome associations with colorectal adenoma. Sci Rep 2022; 12:14801. [PMID: 36045142 PMCID: PMC9433441 DOI: 10.1038/s41598-022-18870-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
An altered colonic microbiota probably increases colorectal adenoma (CRA) and cancer (CRC) risk, but large, unbiased fecal collections are needed to examine the relationship of gut microbiota diversity and composition to colorectal carcinogenesis. This study assessed whether fecal immunochemical tests (FITs) from CRA/CRC screening may fulfill this requirement. Using FIT, self-collected by members of Kaiser Permanente Hawaii (KPH), as well as interspersed quality control (QC) specimens, DNA was extracted and amplified to generate 16S rRNA microbiome profiles rarified at 10,000 reads. CRA/CRC were diagnosed by colonoscopy and histopathology. Covariates were from electronic KPH records. Of 921 participants’ FIT devices, 538 (58%) yielded at least 10,000 rRNA reads and 1016 species-level variants mapped to 46 genera. Of the 538 evaluable participants, 63 (11.7%) were FIT-negative per protocol, and they were considered negative for CRA/CRC. Of the 475 FIT + participants, colonoscopy and pathologic review revealed that 8 (1.7%) had CRC, 71 (14.9%) had high-risk CRA, 107 (22.5%) had low-risk CRA, and 289 (60.8%) did not have CRA/CRC. Men were 2.27-fold [95% confidence interval (CI) 1.32–3.91] more likely than women to be FIT+ . Men also had 1.96-fold (CI 1.24–3.07) higher odds of low-risk CRA, with similar trends for high-risk CRA and CRC. CRA/CRC were not associated with overweight, obesity, diabetes, or antibiotic prescriptions in this study. QC analysis across 24 batches of FIT devices revealed QC outliers in four batches. With or without exclusion of the four QC-outlier batches, as well as lenient (1000-read) rarefaction, CRA/CRC had no consistent, statistically significant associations with fecal microbiome alpha diversity, beta diversity or genera relative abundance. CRA/CRC had expected associations with male sex but not with microbiome metrics. Fecal microbiome profiling using DNA extracted from at-home collected, re-used FIT devices is feasible, albeit with substantial challenges. Using FITs for prospective microbiome studies of CRA/CRC risk should consider the impact of the current findings on statistical power and requisite sample sizes.
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10
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Microbiome in cancer: Role in carcinogenesis and impact in therapeutic strategies. Biomed Pharmacother 2022; 149:112898. [PMID: 35381448 DOI: 10.1016/j.biopha.2022.112898] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 11/21/2022] Open
Abstract
Cancer is the world's second-leading cause of death, and the involvement of microbes in a range of diseases, including cancer, is well established. The gut microbiota is known to play an important role in the host's health and physiology. The gut microbiota and its metabolites may activate immunological and cellular pathways that kill invading pathogens and initiate a cancer-fighting immune response. Cancer is a multiplex illness, characterized by the persistence of several genetic and physiological anomalies in malignant tissue, complicating disease therapy and control. Humans have coevolved with a complex bacterial, fungal, and viral microbiome over millions of years. Specific long-known epidemiological links between certain bacteria and cancer have recently been grasped at the molecular level. Similarly, advances in next-generation sequencing technology have enabled detailed research of microbiomes, such as the human gut microbiome, allowing for the finding of taxonomic and metabolomic linkages between the microbiome and cancer. These investigations have found causative pathways for both microorganisms within tumors and bacteria in various host habitats far from tumors using direct and immunological procedures. Anticancer diagnostic and therapeutic solutions could be developed using this review to tackle the threat of anti-cancer medication resistance as well through the wide-ranging involvement of the microbiota in regulating host metabolic and immunological homeostasis. We reviewed the significance of gut microbiota in cancer initiation as well as cancer prevention. We look at certain microorganisms that may play a role in the development of cancer. Several bacteria with probiotic qualities may be employed as bio-therapeutic agents to re-establish the microbial population and trigger a strong immune response to remove malignancies, and further study into this should be conducted.
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11
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Zouiouich S, Mariadassou M, Rué O, Vogtmann E, Huybrechts I, Severi G, Boutron-Ruault MC, Senore C, Naccarati A, Mengozzi G, Kozlakidis Z, Jenab M, Sinha R, Gunter MJ, Leclerc M. Comparison of Fecal Sample Collection Methods for Microbial Analysis Embedded within Colorectal Cancer Screening Programs. Cancer Epidemiol Biomarkers Prev 2022; 31:305-314. [PMID: 34782392 PMCID: PMC10416615 DOI: 10.1158/1055-9965.epi-21-0188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/26/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Colorectal cancer screening programs with fecal sample collection may provide a platform for population-based gut microbiome disease research. We investigated sample collection and storage method impact on the accuracy and stability of the V3-V4 region of the 16S rRNA genes and bacterial quantity across seven different collection methods [i.e., no solution, two specimen collection cards, and four types of fecal immunochemical test (FIT) used in four countries] among 19 healthy volunteers. METHODS Intraclass correlation coefficients (ICC) were calculated for the relative abundance of the top three phyla, the most abundant genera, alpha diversity metrics, and the first principal coordinates of the beta diversity matrices to estimate the stability of microbial profiles after storage for 7 days at room temperature, 4°C or 30°C, and after screening for the presence of occult blood in the stool. In addition, accuracy was estimated for samples frozen immediately compared to samples with no solution (i.e., the putative gold standard). RESULTS When compared with the putative gold standard, we observed significant variation for all collection methods. However, interindividual variability was much higher than the variability introduced by the collection method. Stability ICCs were high (≥0.75) for FIT tubes that underwent colorectal cancer screening procedures. The relative abundance of Actinobacteria (0.65) was an exception and was lower for different FIT tubes stored at 30°C (range, 0.41-0.90) and room temperature (range, 0.06-0.94). CONCLUSIONS Paper-based collection cards and different types of FIT are acceptable tools for microbiome measurements. IMPACT Our findings inform on the utility of commonly used fecal sample collection methods for developing microbiome-focused cohorts nested within screening programs.
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Affiliation(s)
- Semi Zouiouich
- Nutrition and Metabolism Section, International Agency for Research on Cancer-WHO, Lyon, France.
| | - Mahendra Mariadassou
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, France
| | - Olivier Rué
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, France
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Inge Huybrechts
- Nutrition and Metabolism Section, International Agency for Research on Cancer-WHO, Lyon, France
| | - Gianluca Severi
- Université Paris-Saclay, Université Paris-Sud, Université de Versailles Saint-Quentin-en-Yvelines, Centre de Recherche en Epidémiologie et Santé des Populations, National Institute for Health and Medical Research (INSERM), Villejuif, France
- Department of Statistics, Computer Science and Applications "G. Parenti," University of Florence, Florence, Italy
| | - Marie-Christine Boutron-Ruault
- Université Paris-Saclay, Université Paris-Sud, Université de Versailles Saint-Quentin-en-Yvelines, Centre de Recherche en Epidémiologie et Santé des Populations, National Institute for Health and Medical Research (INSERM), Villejuif, France
| | - Carlo Senore
- Epidemiology and Screening Unit-CPO, University Hospital Città della Salute e della Scienza, Torino, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy
- Candiolo Cancer Institute - FPO IRCCS, Candiolo, Turin, Italy
| | - Giulio Mengozzi
- Clinical biochemistry Unit, University Hospital Città della Salute e della Scienza, Turin, Italy
| | - Zisis Kozlakidis
- Laboratory Services and Biobank, International Agency for Research on Cancer-WHO, Lyon, France
| | - Mazda Jenab
- Nutrition and Metabolism Section, International Agency for Research on Cancer-WHO, Lyon, France
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer-WHO, Lyon, France
| | - Marion Leclerc
- Université Paris Saclay, INRAe, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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12
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Nieuwenburg SAV, Mommersteeg MC, Wolters LMM, van Vuuren AJ, Erler N, Peppelenbosch MP, Fuhler GM, Bruno MJ, Kuipers EJ, Spaander MCW. Accuracy of H. pylori fecal antigen test using fecal immunochemical test (FIT). Gastric Cancer 2022; 25:375-381. [PMID: 34792700 PMCID: PMC8882108 DOI: 10.1007/s10120-021-01264-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/24/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric and colorectal cancer (CRC) are both one of the most common cancers worldwide. In many countries fecal immunochemical tests (FIT)-based CRC screening has been implemented. We investigated if FIT can also be applied for detection of H. pylori, the main risk factor for gastric cancer. METHODS This prospective study included participants over 18 years of age referred for urea breath test (UBT). Patients were excluded if they had used antibiotics/bismuth in the past 4 weeks, or a proton pomp inhibitor (PPI) in the past 2 weeks. Participants underwent UBT, ELISA stool antigen test in standard feces tube (SAT), ELISA stool antigen test in FIT tube (Hp-FIT), and blood sampling, and completed a questionnaire on user friendliness. UBT results were used as reference. RESULTS A total of 182 patients were included (37.4% male, median age 52.4 years (IQR 22.4)). Of these, 60 (33.0%) tested H. pylori positive. SAT and Hp-FIT showed comparable overall accuracy 71.1% (95%CI 63.2-78.3) vs. 77.6% (95%CI 70.4-83.8), respectively (p = 0.97). Sensitivity of SAT was 91.8% (95%CI 80.4-97.7) versus 94.2% (95%CI 84.1-98.9) of Hp-FIT (p = 0.98). Serology scored low with an overall accuracy of 49.7% (95%CI 41.7-57.7). Hp-FIT showed the highest overall user convenience. CONCLUSIONS FIT can be used with high accuracy and sensitivity for diagnosis of H. pylori and is rated as the most convenient test. Non-invasive Hp-FIT test is highly promising for combined upper and lower gastrointestinal (pre-) cancerous screening. Further research should investigate the clinical implications, benefits and cost-effectiveness of such an approach.
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Affiliation(s)
- S. A. V. Nieuwenburg
- Departments of Gastroenterology and Hepatology, Erasmus MC University Medical Center’s, (Room Na-610) Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - M. C. Mommersteeg
- Departments of Gastroenterology and Hepatology, Erasmus MC University Medical Center’s, (Room Na-610) Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - L. M. M. Wolters
- Department of Gastroenterology and Hepatology, Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | - A. J. van Vuuren
- Departments of Gastroenterology and Hepatology, Erasmus MC University Medical Center’s, (Room Na-610) Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - N. Erler
- Department of Biostatistics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - M. P. Peppelenbosch
- Departments of Gastroenterology and Hepatology, Erasmus MC University Medical Center’s, (Room Na-610) Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - G. M. Fuhler
- Departments of Gastroenterology and Hepatology, Erasmus MC University Medical Center’s, (Room Na-610) Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - M. J. Bruno
- Departments of Gastroenterology and Hepatology, Erasmus MC University Medical Center’s, (Room Na-610) Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - E. J. Kuipers
- Departments of Gastroenterology and Hepatology, Erasmus MC University Medical Center’s, (Room Na-610) Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - M. C. W. Spaander
- Departments of Gastroenterology and Hepatology, Erasmus MC University Medical Center’s, (Room Na-610) Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
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13
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Abstract
Integrative analysis of high-quality metagenomics and metabolomics data from fecal samples provides novel clues for the mechanism underpinning gut microbe-human interactions. However, data regarding the influence of fecal collection methods on both metagenomics and metabolomics are sparse. Six fecal collection methods (the gold standard [GS] [i.e., immediate freezing at −80°C with no solution], 95% ethanol, RNAlater, OMNIgene Gut, fecal occult blood test [FOBT] cards, and Microlution) were used to collect 88 fecal samples from eight healthy volunteers for whole-genome shotgun sequencing (WGSS) and untargeted metabolomic profiling. Metrics assessed included the abundances of predominant phyla and α- and β-diversity at the species, gene, and pathway levels. Intraclass correlation coefficients (ICCs) were calculated for microbes and metabolites to estimate (i) stability (day 4 versus day 0 within each method), (ii) concordance (day 0 for each method versus the GS), and (iii) reliability (day 4 for each method versus the GS). For the top 4 phyla and microbial diversity metrics at the species, gene, and pathway levels, generally high stability and reliability were observed for most methods except for 95% ethanol; similar concordances were seen for different methods. For metabolomics data, 95% ethanol showed the highest stability, concordance, and reliability (median ICCs = 0.71, 0.71, and 0.65, respectively). Taken together, OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles. We recommend using separate collecting methods for gut metagenomic sequencing and fecal metabolomic profiling in large population studies. IMPORTANCE The choice of fecal collection method is essential for studying gut microbe-human interactions in large-scale population-based research. In this study, we examined the effects of fecal collection methods and storage time at ambient temperature on variations in the gut microbiome community composition; microbial diversity metrics at the species, gene, and pathway levels; antibiotic resistance genes; and metabolome profiling. Our findings suggest using different fecal sample collection methods for different data generation purposes. OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles.
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14
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Mining the Microbiome and Microbiota-Derived Molecules in Inflammatory Bowel Disease. Int J Mol Sci 2021; 22:ijms222011243. [PMID: 34681902 PMCID: PMC8540913 DOI: 10.3390/ijms222011243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal microbiota is a complex community that consists of an ecosystem with a dynamic interplay between bacteria, fungi, archaea, and viruses. Recent advances in model systems have revealed that the gut microbiome is critical for maintaining homeostasis through metabolic digestive function, immune regulation, and intestinal barrier integrity. Taxonomic shifts in the intestinal microbiota are strongly correlated with a multitude of human diseases, including inflammatory bowel disease (IBD). However, many of these studies have been descriptive, and thus the understanding of the cause and effect relationship often remains unclear. Using non-human experimental model systems such as gnotobiotic mice, probiotic mono-colonization, or prebiotic supplementation, researchers have defined numerous species-level functions of the intestinal microbiota that have produced therapeutic candidates for IBD. Despite these advances, the molecular mechanisms responsible for the function of much of the microbiota and the interplay with host cellular processes remain areas of tremendous research potential. In particular, future research will need to unlock the functional molecular units of the microbiota in order to utilize this untapped resource of bioactive molecules for therapy. This review will highlight the advances and remaining challenges of microbiota-based functional studies and therapeutic discovery, specifically in IBD. One of the limiting factors for reviewing this topic is the nascent development of this area with information on some drug candidates still under early commercial development. We will also highlight the current and evolving strategies, including in the biotech industry, used for the discovery of microbiota-derived bioactive molecules in health and disease.
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15
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Insights into epidemiologic assessments of the microbiome and challenges in identifying microbiome relationships with adverse pregnancy outcomes. CURR EPIDEMIOL REP 2021; 8:143-150. [PMID: 34458070 DOI: 10.1007/s40471-021-00263-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Purpose of review We describe different methods for microbiome assessment and analysis and highlight some of the challenges of using omics data in epidemiologic studies of adverse pregnancy outcomes. Recent findings Human microbiomes are dynamic and vary by ancestry and geography. The composition and dynamics of the vaginal microbiome has been associated with risk of preterm birth. Summary There are several different methods for characterizing the microbiome. Choice of method depends on the research question and resources available. Added to known challenges of conducting and analyzing epidemiologic studies are the unique challenges associated with microbiome detection and analysis. The resulting omics assessments of human microbial communities have great potential to identify prognostics, diagnostics and potentially therapeutics for adverse pregnancy outcomes.
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16
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Ishaq SL, Parada FJ, Wolf PG, Bonilla CY, Carney MA, Benezra A, Wissel E, Friedman M, DeAngelis KM, Robinson JM, Fahimipour AK, Manus MB, Grieneisen L, Dietz LG, Pathak A, Chauhan A, Kuthyar S, Stewart JD, Dasari MR, Nonnamaker E, Choudoir M, Horve PF, Zimmerman NB, Kozik AJ, Darling KW, Romero-Olivares AL, Hariharan J, Farmer N, Maki KA, Collier JL, O’Doherty KC, Letourneau J, Kline J, Moses PL, Morar N. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. mSystems 2021; 6:e0047121. [PMID: 34313460 PMCID: PMC8407420 DOI: 10.1128/msystems.00471-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Humans are inextricably linked to each other and our natural world, and microorganisms lie at the nexus of those interactions. Microorganisms form genetically flexible, taxonomically diverse, and biochemically rich communities, i.e., microbiomes that are integral to the health and development of macroorganisms, societies, and ecosystems. Yet engagement with beneficial microbiomes is dictated by access to public resources, such as nutritious food, clean water and air, safe shelter, social interactions, and effective medicine. In this way, microbiomes have sociopolitical contexts that must be considered. The Microbes and Social Equity (MSE) Working Group connects microbiology with social equity research, education, policy, and practice to understand the interplay of microorganisms, individuals, societies, and ecosystems. Here, we outline opportunities for integrating microbiology and social equity work through broadening education and training; diversifying research topics, methods, and perspectives; and advocating for evidence-based public policy that supports sustainable, equitable, and microbial wealth for all.
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Affiliation(s)
- Suzanne L. Ishaq
- University of Maine, School of Food and Agriculture, Orono, Maine, USA
| | - Francisco J. Parada
- Centro de Estudios en Neurociencia Humana y Neuropsicología, Facultad de Psicología, Universidad Diego Portales, Santiago, Chile
| | - Patricia G. Wolf
- Institute for Health Research and Policy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Carla Y. Bonilla
- Gonzaga University, Department of Biology, Spokane, Washington, USA
| | - Megan A. Carney
- University of Arizona, School of Anthropology, Tucson, Arizona, USA
| | - Amber Benezra
- Stevens Institute of Technology, Science and Technology Studies, Hoboken, New Jersey, USA
| | | | - Michael Friedman
- American International College of Arts and Sciences of Antigua, Antigua, Antigua and Barbuda, West Indies
| | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jake M. Robinson
- University of Sheffield, Department of Landscape Architecture, Sheffield, United Kingdom
| | - Ashkaan K. Fahimipour
- Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, California, USA
- National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, Santa Cruz, California, USA
| | - Melissa B. Manus
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Laura Grieneisen
- Department of Genetics, Cell, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Leslie G. Dietz
- University of Oregon, Biology and the Built Environment Center, Eugene, Oregon, USA
| | - Ashish Pathak
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, Florida, USA
| | - Ashvini Chauhan
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, Florida, USA
| | - Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Justin D. Stewart
- Department of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mauna R. Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Emily Nonnamaker
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Mallory Choudoir
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Patrick F. Horve
- University of Oregon, Biology and the Built Environment Center, Eugene, Oregon, USA
| | - Naupaka B. Zimmerman
- University of San Francisco, Department of Biology, San Francisco, California, USA
| | - Ariangela J. Kozik
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Katherine Weatherford Darling
- Social Science Program, University of Maine at Augusta, Augusta, Maine, USA
- University of Maine, Graduate School of Biomedical Science & Engineering, Bangor, Maine, USA
| | | | - Janani Hariharan
- Field of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Nicole Farmer
- National Institutes of Health, Clinical Center, Bethesda, Maryland, USA
| | - Katherine A. Maki
- National Institutes of Health, Clinical Center, Bethesda, Maryland, USA
| | - Jackie L. Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | | | - Jeffrey Letourneau
- Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | | | - Peter L. Moses
- Robert Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
- Finch Therapeutics, Somerville, Massachusetts, USA
| | - Nicolae Morar
- Environmental Studies Program, University of Oregon, Eugene, Oregon, USA
- Department of Philosophy, University of Oregon, Eugene, Oregon, USA
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17
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The maintenance of microbial community in human fecal samples by a cost effective preservation buffer. Sci Rep 2021; 11:13453. [PMID: 34188136 PMCID: PMC8242035 DOI: 10.1038/s41598-021-92869-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/16/2021] [Indexed: 12/25/2022] Open
Abstract
In the burgeoning microbiome field, powerful sequencing approaches and accompanied bioanalytical methods have made tremendous contributions to the discoveries of breakthroughs, which favor to unravel the intimate interplay between gut microbiota and human health. The proper preservation of samples before being processed is essential to guarantee the authenticity and reliability of microbiome studies. Hence, the development of preservation methods is extremely important to hold samples eligible for the consequent analysis, especially population cohort-based investigations or those spanning species or geography, which frequently facing difficulties in suppling freezing conditions. Although there are several commercial products available, the exploration of cost-efficient and ready-to-use preservation methods are still in a large demand. Here, we performed shotgun metagenomic sequencing and demonstrated that microbial consortia in human fecal samples were substantially preserved within a temporary storage of 4 h, independent of the storage temperature. We also verified a previous reported self-made preservation buffer (PB buffer) could not only preserve fecal microbiota at room temperature up to 4 weeks but also enable samples to endure a high temperature condition which mimics temperature variations in summer logistics. Moreover, PB buffer exhibited suitability for human saliva as well. Collectively, PB buffer may be a valuable choice to stabilize samples if neither freezing facilities nor liquid nitrogen is available.
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18
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Pribyl AL, Parks DH, Angel NZ, Boyd JA, Hasson AG, Fang L, MacDonald SL, Wills BA, Wood DLA, Krause L, Tyson GW, Hugenholtz P. Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME COMMUNICATIONS 2021; 1:14. [PMID: 37938632 PMCID: PMC9645250 DOI: 10.1038/s43705-021-00014-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/14/2021] [Accepted: 04/06/2021] [Indexed: 05/04/2023]
Abstract
The ability to preserve microbial communities in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal samples, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal samples from five participants, totalling 180 samples. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 samples across 10 individuals after storage at -20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.
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Affiliation(s)
| | | | | | - Joel A Boyd
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | - Liang Fang
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | | | | | - Lutz Krause
- Microba Life Sciences, Brisbane, QLD, Australia
| | - Gene W Tyson
- Microba Life Sciences, Brisbane, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Science, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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19
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Young C, Wood HM, Fuentes Balaguer A, Bottomley D, Gallop N, Wilkinson L, Benton SC, Brealey M, John C, Burtonwood C, Thompson KN, Yan Y, Barrett JH, Morris EJA, Huttenhower C, Quirke P. Microbiome Analysis of More Than 2,000 NHS Bowel Cancer Screening Programme Samples Shows the Potential to Improve Screening Accuracy. Clin Cancer Res 2021; 27:2246-2254. [PMID: 33658300 PMCID: PMC7610626 DOI: 10.1158/1078-0432.ccr-20-3807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/05/2020] [Accepted: 02/12/2021] [Indexed: 02/03/2023]
Abstract
PURPOSE There is potential for fecal microbiome profiling to improve colorectal cancer screening. This has been demonstrated by research studies, but it has not been quantified at scale using samples collected and processed routinely by a national screening program. EXPERIMENTAL DESIGN Between 2016 and 2019, the largest of the NHS Bowel Cancer Screening Programme hubs prospectively collected processed guaiac fecal occult blood test (gFOBT) samples with subsequent colonoscopy outcomes: blood-negative [n = 491 (22%)]; colorectal cancer [n = 430 (19%)]; adenoma [n = 665 (30%)]; colonoscopy-normal [n = 300 (13%)]; nonneoplastic [n = 366 (16%)]. Samples were transported and stored at room temperature. DNA underwent 16S rRNA gene V4 amplicon sequencing. Taxonomic profiling was performed to provide features for classification via random forests (RF). RESULTS Samples provided 16S amplicon-based microbial profiles, which confirmed previously described colorectal cancer-microbiome associations. Microbiome-based RF models showed potential as a first-tier screen, distinguishing colorectal cancer or neoplasm (colorectal cancer or adenoma) from blood-negative with AUC 0.86 (0.82-0.89) and AUC 0.78 (0.74-0.82), respectively. Microbiome-based models also showed potential as a second-tier screen, distinguishing from among gFOBT blood-positive samples, colorectal cancer or neoplasm from colonoscopy-normal with AUC 0.79 (0.74-0.83) and AUC 0.73 (0.68-0.77), respectively. Models remained robust when restricted to 15 taxa, and performed similarly during external validation with metagenomic datasets. CONCLUSIONS Microbiome features can be assessed using gFOBT samples collected and processed routinely by a national colorectal cancer screening program to improve accuracy as a first- or second-tier screen. The models required as few as 15 taxa, raising the potential of an inexpensive qPCR test. This could reduce the number of colonoscopies in countries that use fecal occult blood test screening.
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Affiliation(s)
- Caroline Young
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom.
| | - Henry M Wood
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Alba Fuentes Balaguer
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Daniel Bottomley
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Niall Gallop
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Lyndsay Wilkinson
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Sally C Benton
- NHS Bowel Cancer Screening Programme - Southern Hub, Surrey Research Park, Guildford, United Kingdom
| | - Martin Brealey
- NHS Bowel Cancer Screening Programme - Southern Hub, Surrey Research Park, Guildford, United Kingdom
| | - Cerin John
- NHS Bowel Cancer Screening Programme - Southern Hub, Surrey Research Park, Guildford, United Kingdom
| | - Carole Burtonwood
- NHS Bowel Cancer Screening Programme - Southern Hub, Surrey Research Park, Guildford, United Kingdom
| | - Kelsey N Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Jennifer H Barrett
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Eva J A Morris
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
- Big Data Institute, Nuffield Department of Population Health, Old Road Campus, University of Oxford, Oxford, United Kingdom
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Philip Quirke
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
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20
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Young C, Wood HM, Seshadri RA, Van Nang P, Vaccaro C, Melendez LC, Bose M, Van Doi M, Piñero TA, Valladares CT, Arguero J, Balaguer AF, Thompson KN, Yan Y, Huttenhower C, Quirke P. The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries. Genome Med 2021; 13:27. [PMID: 33593386 PMCID: PMC7887780 DOI: 10.1186/s13073-021-00844-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The incidence of colorectal cancer (CRC) is increasing in developing countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facilities, and the difficulty of fresh or frozen stool storage/transport. Here, we aimed (1) to establish a broad representation of diverse developing countries (Argentina, Chile, India, and Vietnam); (2) to validate a 'resource-light' sample-collection protocol translatable in these settings using guaiac faecal occult blood test (gFOBT) cards stored and, importantly, shipped internationally at room temperature; (3) to perform initial profiling of the collective CRC-associated microbiome of these developing countries; and (4) to compare this quantitatively with established CRC biomarkers from developed countries. METHODS We assessed the effect of international storage and transport at room temperature by replicating gFOBT from five UK volunteers, storing two in the UK, and sending replicates to institutes in the four countries. Next, to determine the effect of prolonged UK storage, DNA extraction replicates for a subset of samples were performed up to 252 days apart. To profile the CRC-associated microbiome of developing countries, gFOBT were collected from 41 treatment-naïve CRC patients and 40 non-CRC controls from across the four institutes, and V4 16S rRNA gene sequencing was performed. Finally, we constructed a random forest (RF) model that was trained and tested against existing datasets from developed countries. RESULTS The microbiome was stably assayed when samples were stored/transported at room temperature and after prolonged UK storage. Large-scale microbiome structure was separated by country and continent, with a smaller effect from CRC. Importantly, the RF model performed similarly to models trained using external datasets and identified similar taxa of importance (Parvimonas, Peptostreptococcus, Fusobacterium, Alistipes, and Escherichia). CONCLUSIONS This study demonstrates that gFOBT, stored and transported at room temperature, represents a suitable method of faecal sample collection for amplicon-based microbiome biomarkers in developing countries and suggests a CRC-faecal microbiome association that is consistent between developed and developing countries.
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Affiliation(s)
- Caroline Young
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Level 4 Wellcome Trust Brenner Building, Leeds, LS9 7TF, UK.
| | - Henry M Wood
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Level 4 Wellcome Trust Brenner Building, Leeds, LS9 7TF, UK
| | | | - Pham Van Nang
- Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Carlos Vaccaro
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de buenos Aires (HIBA), Buenos Aires, Argentina
| | | | | | - Mai Van Doi
- Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Tamara Alejandra Piñero
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de buenos Aires (HIBA), Buenos Aires, Argentina
| | | | - Julieta Arguero
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de buenos Aires (HIBA), Buenos Aires, Argentina
| | - Alba Fuentes Balaguer
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Level 4 Wellcome Trust Brenner Building, Leeds, LS9 7TF, UK
| | - Kelsey N Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Philip Quirke
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Level 4 Wellcome Trust Brenner Building, Leeds, LS9 7TF, UK
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21
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Masi AC, Koo S, Lamb CA, Hull MA, Sharp L, Nelson A, Hampton JS, Rees CJ, Stewart CJ. Using faecal immunochemical test (FIT) undertaken in a national screening programme for large-scale gut microbiota analysis. Gut 2021; 70:429-431. [PMID: 32430347 DOI: 10.1136/gutjnl-2020-321594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/01/2020] [Indexed: 12/08/2022]
Affiliation(s)
- Andrea C Masi
- Gastroenterology, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Sara Koo
- Gastroenterology, South Tyneside General Hospital, South Shields, UK.,Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher A Lamb
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.,Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Mark A Hull
- Leeds Institute of Biomedical & Clinical Sciences, St James's University Hospital, Leeds, UK
| | - Linda Sharp
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - James S Hampton
- Gastroenterology, South Tyneside General Hospital, South Shields, UK.,Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Colin J Rees
- Gastroenterology, South Tyneside General Hospital, South Shields, UK .,Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
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22
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Aslam H, Marx W, Rocks T, Loughman A, Chandrasekaran V, Ruusunen A, Dawson SL, West M, Mullarkey E, Pasco JA, Jacka FN. The effects of dairy and dairy derivatives on the gut microbiota: a systematic literature review. Gut Microbes 2020; 12:1799533. [PMID: 32835617 PMCID: PMC7524346 DOI: 10.1080/19490976.2020.1799533] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The effects of dairy and dairy-derived products on the human gut microbiota remains understudied. A systematic literature search was conducted using Medline, CINAHL, Embase, Scopus, and PubMed databases with the aim of collating evidence on the intakes of all types of dairy and their effects on the gut microbiota in adults. Risk of bias was assessed using the Cochrane risk-of-bias tool.The search resulted in 6,592 studies, of which eight randomized controlled trials (RCTs) met pre-determined eligibility criteria for inclusion, consisting of a total of 468 participants. Seven studies assessed the effect of type of dairy (milk, yogurt, and kefir) and dairy derivatives (whey and casein) on the gut microbiota, and one study assessed the effect of the quantity of dairy (high dairy vs low dairy). Three studies showed that dairy types consumed (milk, yogurt, and kefir) increased the abundance of beneficial genera Lactobacillus and Bifidobacterium. One study showed that yogurt reduced the abundance of Bacteroides fragilis, a pathogenic strain. Whey and casein isolates and the quantity of dairy consumed did not prompt changes to the gut microbiota composition. All but one study reported no changes to bacterial diversity in response to dairy interventions and one study reported reduction in bacterial diversity in response to milk intake.In conclusion, the results of this review suggest that dairy products such as milk, yogurt, and kefir may modulate the gut microbiota composition in favor to the host. However, the broader health implications of these findings remain unclear and warrant further studies.
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Affiliation(s)
- Hajara Aslam
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia,CONTACT Hajara Aslam IMPACT – the Institute for Mental and Physical Health and Clinical Translation, Food & Mood Centre, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria3220, Australia
| | - Wolfgang Marx
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Tetyana Rocks
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Amy Loughman
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Vinoomika Chandrasekaran
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Anu Ruusunen
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia,Department of Psychiatry, Kuopio University Hospital, Kuopio, Finland,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Samantha L. Dawson
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia,Environmental & Genetic Epidemiology Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Australia
| | - Madeline West
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Eva Mullarkey
- Psychology Department, Wellesley College, Wellesley, MA, USA
| | - Julie A. Pasco
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia,Department of Medicine – Western Health, Melbourne Medical School, The University of Melbourne, St Albans, Victoria, Australia,Department of Epidemiology and Preventive Medicine, Monash University, Prahran, Victoria, Australia,Barwon Health, Geelong, Victoria, Australia
| | - Felice N. Jacka
- IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia,Department of Psychiatry, University of Melbourne, Victoria, Australia,Centre for Adolescent Health, Murdoch Children’s Research Institute, Victoria, Australia
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23
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Parida S, Sharma D. The Microbiome and Cancer: Creating Friendly Neighborhoods and Removing the Foes Within. Cancer Res 2020; 81:790-800. [PMID: 33148661 DOI: 10.1158/0008-5472.can-20-2629] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/01/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022]
Abstract
The human body is colonized by the microbial cells that are estimated to be as abundant as human cells, yet their genome is roughly 100 times the human genome, providing significantly more genetic diversity. The past decade has observed an explosion of interest in examining the existence of microbiota in the human body and understanding its role in various diseases including inflammatory bowel disease, neurologic diseases, cardiovascular disorders, and cancer. Many studies have demonstrated differential community composition between normal tissue and cancerous tissue, paving the way for investigations focused on deciphering the cause-and-effect relationships between specific microbes and initiation and progression of various cancers. Also, evolving are the strategies to alter tumor-associated dysbiosis and move it toward eubiosis with holistic approaches to change the entire neighborhood or to neutralize pathogenic strains. In this review, we discuss important pathogenic bacteria and the underlying mechanisms by which they affect cancer progression. We summarize key microbiota alterations observed in multiple tumor niches, their association with clinical stages, and their potential use in cancer diagnosis and management. Finally, we discuss microbiota-based therapeutic approaches.
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Affiliation(s)
- Sheetal Parida
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dipali Sharma
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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