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Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. Nat Microbiol 2021; 6:1561-1574. [PMID: 34782724 DOI: 10.1038/s41564-021-00979-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/13/2021] [Indexed: 11/08/2022]
Abstract
The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during the Tara Oceans Polar Circle expedition, to evaluate the ecology, metabolic potential and activity of resident bacteria and archaea. We assembled 530 metagenome-assembled genomes (MAGs) to form the Arctic MAGs catalogue comprising 526 species. A total of 441 MAGs belonged to species that have not previously been reported and 299 genomes showed an exclusively polar distribution. Most Arctic MAGs have large genomes and the potential for fast generation times, both of which may enable adaptation to a copiotrophic lifestyle in nutrient-rich waters. We identified 38 habitat generalists and 111 specialists in the Arctic Ocean. We also found a general prevalence of 14 mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic layer during spring and autumn. We revealed 62 MAGs classified as key Arctic species, found only in the Arctic Ocean, showing the highest gene expression values and predicted to have habitat-specific traits. The Artic MAGs catalogue will inform our understanding of polar microorganisms that drive global biogeochemical cycles.
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Fu K, Zhang D, Song Y, Xu M, Wu R, Xiong X, Liu X, Wu L, Guo Y, Zhou Y, Li X, Wang Z. Tibetan Medicine Qishiwei Zhenzhu Pills Can Reduce Cerebral Ischemia-Reperfusion Injury by Regulating Gut Microbiota and Inhibiting Inflammation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:2251679. [PMID: 34804175 PMCID: PMC8601817 DOI: 10.1155/2021/2251679] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 01/11/2023]
Abstract
Cerebral ischemia is a series of harmful reactions, such as acute necrosis of tissue, inflammation, apoptosis, autophagy, and blood-brain barrier injury, due to the insufficient blood supply to the brain. Inflammatory response and gut microbiota imbalance are important concomitant factors of cerebral ischemia and may increase the severity of cerebral ischemia through the gut-brain axis. Qishiwei Zhenzhu pills (QSW) contain more than 70 kinds of medicinal materials, which have the effects of anti-cerebral infarction, anti-convulsion, anti-dementia, and so on. It is a treasure of Tibetan medicine commonly used in the treatment of cerebral ischemia in Tibetan areas. In this study, we gave rats QSW (66.68 mg/kg) once by gavage in advance and then immediately established the rat middle cerebral artery occlusion (MCAO) model. After 24 hours of treatment, the neuroprotection, intestinal pathology, and gut microbiota were examined. The results showed that QSW could significantly reduce the neurobehavioral abnormalities and cerebral infarction rate in MCAO rats. Furthermore, qPCR, western blot, and immunohistochemistry results showed that QSW could effectively inhibit IL-6, IL-1β, and other inflammatory factors so as to effectively reduce the inflammatory response of MCAO rats. Furthermore, QSW could improve intestinal integrity and reduce intestinal injury. 16S rRNA sequencing showed that QSW could significantly improve the gut microbiota disorder of MCAO rats. Specifically, at the phylum level, it can regulate the abundance of Firmicutes and Proteobacteria in the gut microbiota of rats with MCAO. At the genus level, it can adjust the abundance of Escherichia and Shigella. At the species level, it can adjust the abundance of Lactobacillus johnsonii and Lactobacillus reuteri. All in all, this study is the first to show that QSW can reduce the severity of cerebral ischemia-reperfusion injury by regulating gut microbiota and inhibiting the inflammatory response.
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Affiliation(s)
- Ke Fu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Dewei Zhang
- Wanzhou Institute for Drug and Food Control, Chongqing 404000, China
| | - Yinglian Song
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Min Xu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Ruixia Wu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xueqing Xiong
- Wanzhou Institute for Drug and Food Control, Chongqing 404000, China
| | - Xianwu Liu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lei Wu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Ya Guo
- Wanzhou Institute for Drug and Food Control, Chongqing 404000, China
| | - You Zhou
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaoli Li
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhang Wang
- College of Ethnomedicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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103
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Xue W, Li JJ, Zou Y, Zou B, Wei L. Microbiota and Ocular Diseases. Front Cell Infect Microbiol 2021; 11:759333. [PMID: 34746029 PMCID: PMC8566696 DOI: 10.3389/fcimb.2021.759333] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022] Open
Abstract
Recent advances have identified significant associations between the composition and function of the gut microbiota and various disorders in organ systems other than the digestive tract. Utilizing next-generation sequencing and multiomics approaches, the microbial community that possibly impacts ocular disease has been identified. This review provides an overview of the literature on approaches to microbiota analysis and the roles of commensal microbes in ophthalmic diseases, including autoimmune uveitis, age-related macular degeneration, glaucoma, and other ocular disorders. In addition, this review discusses the hypothesis of the "gut-eye axis" and evaluates the therapeutic potential of targeting commensal microbiota to alleviate ocular inflammation.
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Affiliation(s)
- Wei Xue
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Jing Jing Li
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Yanli Zou
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China.,Department of Ophthalmology, Affiliated Foshan Hospital, Southern Medical University, Foshan, China
| | - Bin Zou
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
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Wang Y, Nguyen LH, Mehta RS, Song M, Huttenhower C, Chan AT. Association Between the Sulfur Microbial Diet and Risk of Colorectal Cancer. JAMA Netw Open 2021; 4:e2134308. [PMID: 34767023 PMCID: PMC8590167 DOI: 10.1001/jamanetworkopen.2021.34308] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
IMPORTANCE Sulfur-metabolizing bacteria that reduce dietary sulfur to hydrogen sulfide have been associated with colorectal cancer (CRC). However, there are limited studies investigating the association between diet and sulfur-metabolizing bacteria in the development of CRC. OBJECTIVE To develop a dietary score that correlates with gut sulfur-metabolizing bacteria and to examine its association with CRC risk. DESIGN, SETTING, AND PARTICIPANTS This prospective cohort study included data from the Health Professionals Follow-up Study (1986-2014), Nurses' Health Study (1984-2016), and Nurses' Health Study II (1991-2017). Participants were US male health professionals and female registered nurses who were free of inflammatory bowel disease and cancer at baseline, with a subsample of participants who provided stool samples from 2012 to 2014. Statistical analysis was conducted from September 1, 2020, to June 1, 2021. EXPOSURE A dietary pattern, assessed by a food-frequency questionnaire, that most correlated with 43 sulfur-metabolizing bacteria identified through taxonomic and functional profiling of gut metagenome data. MAIN OUTCOMES AND MEASURES Incident CRC. RESULTS Among 214 797 participants comprising 46 550 men (mean [SD] age at baseline, 54.3 [9.7] years) and 168 247 women (mean [SD] age at baseline, 43.0 [9.2] years), 3217 incident cases of CRC (1.5%) were documented during 5 278 048 person-years of follow-up. The sulfur microbial diet, developed in a subsample of 307 men (mean [SD] age, 70.5 [4.3] years) and 212 women (mean [SD] age, 61.0 [3.8] years), was characterized by high intakes of low-calorie beverages, french fries, red meats, and processed meats and low intakes of fruits, yellow vegetables, whole grains, legumes, leafy vegetables, and cruciferous vegetables. After adjustment for other risk factors, greater adherence to the sulfur microbial diet was associated with an increased risk of CRC, with a hazard ratio (HR) of 1.27 (95% CI, 1.12-1.44) comparing the highest vs the lowest quintile of the diet score (linear trend of diet score quintiles; P < .001 for trend). When assessed by anatomical subsites, greater adherence to the sulfur microbial diet was positively associated with distal CRC (HR, 1.25; 95% CI, 1.05-1.50; P = .02 for trend) but not proximal colon cancer (HR, 1.13; 95% CI, 0.93-1.39; P = .19 for trend). CONCLUSIONS AND RELEVANCE Adherence to the sulfur microbial diet was associated with an increased risk of CRC, suggesting a potential mediating role of sulfur-metabolizing bacteria in the associaton between diet and CRC. Further research is needed to confirm these findings and to determine the underlying mechanisms.
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Affiliation(s)
- Yiqing Wang
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Long H. Nguyen
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Raaj S. Mehta
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Mingyang Song
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Andrew T. Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
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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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Zheng Y, Ran Y, Zhang H, Wang B, Zhou L. The Microbiome in Autoimmune Liver Diseases: Metagenomic and Metabolomic Changes. Front Physiol 2021; 12:715852. [PMID: 34690796 PMCID: PMC8531204 DOI: 10.3389/fphys.2021.715852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022] Open
Abstract
Recent studies have identified the critical role of microbiota in the pathophysiology of autoimmune liver diseases (AILDs), including autoimmune hepatitis (AIH), primary biliary cholangitis (PBC), and primary sclerosing cholangitis (PSC). Metagenomic studies reveal significant decrease of gut bacterial diversity in AILDs. Although profiles of metagenomic vary widely, Veillonella is commonly enriched in AIH, PBC, and PSC. Apart from gut microbiome, the oral and bile microbiome seem to be associated with these diseases as well. The functional analysis of metagenomics suggests that metabolic pathways changed in the gut microbiome of the patients. Microbial metabolites, including short-chain fatty acids (SCFAs) and microbial bile acid metabolites, have been shown to modulate innate immunity, adaptive immunity, and inflammation. Taken together, the evidence of host–microbiome interactions and in-depth mechanistic studies needs further accumulation, which will offer more possibilities to clarify the mechanisms of AILDs and provide potential molecular targets for the prevention and treatment in the future.
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Affiliation(s)
- Yanping Zheng
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ying Ran
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongxia Zhang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Lu Zhou
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China.,Department of Gastroenterology and Hepatology, Hotan People's Hospital, Xinjiang, China
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107
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Ackland J, Watson A, Wilkinson TMA, Staples KJ. Interrupting the Conversation: Implications for Crosstalk Between Viral and Bacterial Infections in the Asthmatic Airway. FRONTIERS IN ALLERGY 2021; 2:738987. [PMID: 35386999 PMCID: PMC8974750 DOI: 10.3389/falgy.2021.738987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022] Open
Abstract
Asthma is a heterogeneous, chronic respiratory disease affecting 300 million people and is thought to be driven by different inflammatory endotypes influenced by a myriad of genetic and environmental factors. The complexity of asthma has rendered it challenging to develop preventative and disease modifying therapies and it remains an unmet clinical need. Whilst many factors have been implicated in asthma pathogenesis and exacerbations, evidence indicates a prominent role for respiratory viruses. However, advances in culture-independent detection methods and extensive microbial profiling of the lung, have also demonstrated a role for respiratory bacteria in asthma. In particular, airway colonization by the Proteobacteria species Nontypeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat) is associated with increased risk of developing recurrent wheeze and asthma in early life, poor clinical outcomes in established adult asthma and the development of more severe inflammatory phenotypes. Furthermore, emerging evidence indicates that bacterial-viral interactions may influence exacerbation risk and disease severity, highlighting the need to consider the impact chronic airway colonization by respiratory bacteria has on influencing host responses to viral infection. In this review, we first outline the currently understood role of viral and bacterial infections in precipitating asthma exacerbations and discuss the underappreciated potential impact of bacteria-virus crosstalk in modulating host responses. We discuss the mechanisms by which early life infection may predispose to asthma development. Finally, we consider how infection and persistent airway colonization may drive different asthma phenotypes, with a view to identifying pathophysiological mechanisms that may prove tractable to new treatment modalities.
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Affiliation(s)
- Jodie Ackland
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
| | - Alastair Watson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Tom M. A. Wilkinson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
| | - Karl J. Staples
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
- *Correspondence: Karl J. Staples
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108
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No evidence for colonization of oral bacteria in the distal gut in healthy adults. Proc Natl Acad Sci U S A 2021; 118:2114152118. [PMID: 34610963 PMCID: PMC8594488 DOI: 10.1073/pnas.2114152118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
The microbial communities in the mouth and colon are anatomically connected via the saliva. However, the extent to which oral microbes reach and successfully colonize the distal gut has been debated. To resolve this long-standing controversy, we used exact amplicon sequence variants generated from concurrently collected saliva/stool microbiota in 66 healthy adults from two countries to show that, with one exception (Dialister invisus), the two niches are completely distinct. Thus, there is no evidence for colonization of oral bacteria in the distal gut. This defines the healthy state to which pathological states could be compared. Finding the same bacteria in the mouth and stool may warrant clinical investigation for an underlying pathology.
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109
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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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110
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Jia S, Li T, Zhang XX. Integrated metagenomic and metatranscriptomic analyses of ultraviolet disinfection effects on antibiotic resistance genes and bacterial communities during wastewater treatment. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1610-1619. [PMID: 33278015 DOI: 10.1007/s10646-020-02313-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Ultraviolet (UV) disinfection is now widely implemented in wastewater treatment plants (WWTPs) worldwide, but its effect on antibiotic resistome of the surviving bacteria remains unclear. In this study, we employed high-throughput sequencing-based metagenomic and metatranscriptomic approaches to comprehensively elucidate the effects of UV disinfection on the shifts of bacterial community and antibiotic resistance genes (ARGs) on both DNA and mRNA levels in one WWTP. Metagenomic analyses revealed an insignificant change in the bacterial community after UV disinfection, while metatranscriptomic analyses showed that UV disinfection significantly changed the abundance of 13.79% of phyla and 10.32% of genera. In total, 38 ARG-like open reading frames (ORFs) and 327 ARG-like transcripts were identified in the DNA and RNA samples, respectively. The relative abundances of the total ARGs, each ARG type, and each ARG subtype also varied after UV disinfection. Additionally, UV disinfection significantly reduced the expression of total ARGs from 49.40 transcripts per kilobase of exon model per million mapped reads (TPM) to 47.62 TPM, and significantly changed the expression of 10.75% of ARG subtypes in wastewater (p < 0.05). Notably, the significant increase in the expression and obvious increase in the relative abundance of macrolide-lincosamide-streptogramin B (MLSB) resistance genes revealed that UV disinfection increases the potential health risk of MLSB resistance genes in wastewater. Moreover, potential host analyses of ARGs revealed the different preferences of antibiotic resistant bacteria (ARB) to ARGs. This study may shed new light on the underlying mechanism of the UV disinfection effect on antibiotic resistance.
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Affiliation(s)
- Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Tong Li
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing, 210023, China.
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111
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Cascarano MC, Stavrakidis-Zachou O, Mladineo I, Thompson KD, Papandroulakis N, Katharios P. Mediterranean Aquaculture in a Changing Climate: Temperature Effects on Pathogens and Diseases of Three Farmed Fish Species. Pathogens 2021; 10:1205. [PMID: 34578236 PMCID: PMC8466566 DOI: 10.3390/pathogens10091205] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 02/07/2023] Open
Abstract
Climate change is expected to have a drastic effect on aquaculture worldwide. As we move forward with the agenda to increase and diversify aquaculture production, rising temperatures will have a progressively relevant impact on fish farming, linked to a multitude of issues associated with fish welfare. Temperature affects the physiology of both fish and pathogens, and has the potential to lead to significant increases in disease outbreaks within aquaculture systems, resulting in severe financial impacts. Significant shifts in future temperature regimes are projected for the Mediterranean Sea. We therefore aim to review and discuss the existing knowledge relating to disease outbreaks in the context of climate change in Mediterranean finfish aquaculture. The objective is to describe the effects of temperature on the physiology of both fish and pathogens, and moreover to list and discuss the principal diseases of the three main fish species farmed in the Mediterranean, namely gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), and meagre (Argyrosomus regius). We will attempt to link the pathology of each disease to a specific temperature range, while discussing potential future disease threats associated with the available climate change trends for the Mediterranean Sea.
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Affiliation(s)
- Maria Chiara Cascarano
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
- Department of Biology, University of Crete, 71003 Heraklion, Greece
| | - Orestis Stavrakidis-Zachou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
- Department of Biology, University of Crete, 71003 Heraklion, Greece
| | - Ivona Mladineo
- Biology Center of Czech Academy of Sciences, Laboratory of Functional Helminthology, Institute of Parasitology, 370 05 Ceske Budejovice, Czech Republic;
| | - Kim D. Thompson
- Vaccines and Diagnostics, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, UK;
| | - Nikos Papandroulakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
| | - Pantelis Katharios
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
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112
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Ezzamouri B, Shoaie S, Ledesma-Amaro R. Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies. Front Microbiol 2021; 12:681982. [PMID: 34531833 PMCID: PMC8438329 DOI: 10.3389/fmicb.2021.681982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/31/2021] [Indexed: 12/26/2022] Open
Abstract
A number of studies have shown that the microbial communities of the human body are integral for the maintenance of human health. Advances in next-generation sequencing have enabled rapid and large-scale quantification of the composition of microbial communities in health and disease. Microorganisms mediate diverse host responses including metabolic pathways and immune responses. Using a system biology approach to further understand the underlying alterations of the microbiota in physiological and pathological states can help reveal potential novel therapeutic and diagnostic interventions within the field of synthetic biology. Tools such as biosensors, memory arrays, and engineered bacteria can rewire the microbiome environment. In this article, we review the computational tools used to study microbiome communities and the current limitations of these methods. We evaluate how genome-scale metabolic models (GEMs) can advance our understanding of the microbe-microbe and microbe-host interactions. Moreover, we present how synergies between these system biology approaches and synthetic biology can be harnessed in human microbiome studies to improve future therapeutics and diagnostics and highlight important knowledge gaps for future research in these rapidly evolving fields.
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Affiliation(s)
- Bouchra Ezzamouri
- Unit for Population-Based Dermatology Research, St John’s Institute of Dermatology, Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kindom
- Faculty of Dentistry, Centre for Host-Microbiome Interactions, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Saeed Shoaie
- Faculty of Dentistry, Centre for Host-Microbiome Interactions, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
- Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, Sweden
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
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113
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Zhou W, Liao Z, Wu Z, Suyama T, Zhang W. Analysis of the difference between aged and degenerated pit mud microbiome in fermentation cellars for Chinese Luzhou-flavor baijiu by metatranscriptomics. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:4621-4631. [PMID: 33474773 DOI: 10.1002/jsfa.11105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/10/2021] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUD Chinese Luzhou-flavor baijiu (LFB) was fermented in an underground cellar, and the bottom and side of the cellar were covered with pit muds (PMs), where the metabolic activity of the microorganisms had a significant effect on the LFB quality. PMs can be divided into aged pit mud (AP) and degenerated pit mud (DP), thus, the qualities of LFB generated from AP and DP were different. In this essay, metatranscriptomics method was applied to illustrate the differences of the two PMs, as well as to search out the pivotal microorganisms and genes influencing the quality of LFB. RESULTS Archaea, Clostridium and some thermophilic microorganisms might bring significant effect in AP, while the active eukaryota and Anaeromyxobacter would cause degeneration in PM. Also, the metabolism of carbohydrate and amino acid were more active in AP. What is more, carbohydrate, amino acid and their derivant can produce important organic acids via the activity of the microorganisms in PMs. There were eight critical enzymes noticed in the organic acids metabolic pathway, which were more actively expressed in AP, demonstrating active expression of the critical genes related to organic acid metabolism could have a positive effect on LFB quality. CONCLUSION This study identified specific differences in active microorganisms, active expressed genes and the expression levels of key genes in vital metabolic pathway between AP and DP. Which may be the actual reason for the differences in the quality of LFB made from different PMs. Mastering these results will provide assistance to improve the quality of LFB. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Wen Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Department of Liquor and Food Engineering, Sichuan Technology and Business College, Dujiangyan, China
| | - Zuomin Liao
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Zhengyun Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Taikei Suyama
- Akashi National College of Technology, Akashi, Japan
| | - Wenxue Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- School of Liquor-Making Engineering, Sichuan University Jinjiang College, Meishan, China
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114
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Henry LP, Bruijning M, Forsberg SKG, Ayroles JF. The microbiome extends host evolutionary potential. Nat Commun 2021; 12:5141. [PMID: 34446709 PMCID: PMC8390463 DOI: 10.1038/s41467-021-25315-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
The microbiome shapes many host traits, yet the biology of microbiomes challenges traditional evolutionary models. Here, we illustrate how integrating the microbiome into quantitative genetics can help untangle complexities of host-microbiome evolution. We describe two general ways in which the microbiome may affect host evolutionary potential: by shifting the mean host phenotype and by changing the variance in host phenotype in the population. We synthesize the literature across diverse taxa and discuss how these scenarios could shape the host response to selection. We conclude by outlining key avenues of research to improve our understanding of the complex interplay between hosts and microbiomes.
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Affiliation(s)
- Lucas P. Henry
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
| | - Marjolein Bruijning
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA
| | - Simon K. G. Forsberg
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA ,grid.8993.b0000 0004 1936 9457Dept. of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Julien F. Ayroles
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
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115
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Gopar-Cuevas Y, Duarte-Jurado AP, Diaz-Perez RN, Saucedo-Cardenas O, Loera-Arias MJ, Montes-de-Oca-Luna R, Rodriguez-Rocha H, Garcia-Garcia A. Pursuing Multiple Biomarkers for Early Idiopathic Parkinson's Disease Diagnosis. Mol Neurobiol 2021; 58:5517-5532. [PMID: 34350555 DOI: 10.1007/s12035-021-02500-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/16/2021] [Indexed: 12/21/2022]
Abstract
Parkinson's disease (PD) ranks first in the world as a neurodegenerative movement disorder and occurs most commonly in an idiopathic form. PD patients may have motor symptoms, non-motor symptoms, including cognitive and behavioral changes, and symptoms related to autonomic nervous system (ANS) failures, such as gastrointestinal, urinary, and cardiovascular symptoms. Unfortunately, the diagnostic accuracy of PD by general neurologists is relatively low. Currently, there is no objective molecular or biochemical test for PD; its diagnosis is based on clinical criteria, mainly by cardinal motor symptoms, which manifest when patients have lost about 60-80% of dopaminergic neurons. Therefore, it is urgent to establish a panel of biomarkers for the early and accurate diagnosis of PD. Once the disease is accurately diagnosed, it may be easier to unravel idiopathic PD's pathogenesis, and ultimately, finding a cure. This review discusses several biomarkers' potential to set a panel for early idiopathic PD diagnosis and future directions.
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Affiliation(s)
- Yareth Gopar-Cuevas
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, 64460, Monterrey, Mexico
| | - Ana P Duarte-Jurado
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, 64460, Monterrey, Mexico
| | - Rosa N Diaz-Perez
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, 64460, Monterrey, Mexico
| | - Odila Saucedo-Cardenas
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, 64460, Monterrey, Mexico.,Departamento de Genética Molecular, Centro de Investigación Biomédica del Noreste, Delegación Nuevo León, Instituto Mexicano del Seguro Social, Monterrey, Mexico
| | - Maria J Loera-Arias
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, 64460, Monterrey, Mexico
| | - Roberto Montes-de-Oca-Luna
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, 64460, Monterrey, Mexico
| | - Humberto Rodriguez-Rocha
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, 64460, Monterrey, Mexico.
| | - Aracely Garcia-Garcia
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, 64460, Monterrey, Mexico.
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116
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Wei LQ, Cheong IH, Yang GH, Li XG, Kozlakidis Z, Ding L, Liu NN, Wang H. The Application of High-Throughput Technologies for the Study of Microbiome and Cancer. Front Genet 2021; 12:699793. [PMID: 34394190 PMCID: PMC8355622 DOI: 10.3389/fgene.2021.699793] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022] Open
Abstract
Human gut microbiome research, especially gut microbiome, has been developing at a considerable pace over the last decades, driven by a rapid technological advancement. The emergence of high-throughput technologies, such as genomics, transcriptomics, and others, has afforded the generation of large volumes of data, and in relation to specific pathologies such as different cancer types. The current review identifies high-throughput technologies as they have been implemented in the study of microbiome and cancer. Four main thematic areas have emerged: the characterization of microbial diversity and composition, microbial functional analyses, biomarker prediction, and, lastly, potential therapeutic applications. The majority of studies identified focus on the microbiome diversity characterization, which is reaching technological maturity, while the remaining three thematic areas could be described as emerging.
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Affiliation(s)
- Lu Qi Wei
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Io Hong Cheong
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Huan Yang
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Guang Li
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zisis Kozlakidis
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Lei Ding
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ning Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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117
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Zhang Y, Thompson KN, Branck T, Yan Yan, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci 2021; 4:279-311. [PMID: 34465175 DOI: 10.1146/annurev-biodatasci-031121-103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tobyn Branck
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Yan
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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118
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Zhang Y, Thompson KN, Huttenhower C, Franzosa EA. Statistical approaches for differential expression analysis in metatranscriptomics. Bioinformatics 2021; 37:i34-i41. [PMID: 34252963 PMCID: PMC8275336 DOI: 10.1093/bioinformatics/btab327] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Motivation Metatranscriptomics (MTX) has become an increasingly practical way to profile the functional activity of microbial communities in situ. However, MTX remains underutilized due to experimental and computational limitations. The latter are complicated by non-independent changes in both RNA transcript levels and their underlying genomic DNA copies (as microbes simultaneously change their overall abundance in the population and regulate individual transcripts), genetic plasticity (as whole loci are frequently gained and lost in microbial lineages) and measurement compositionality and zero-inflation. Here, we present a systematic evaluation of and recommendations for differential expression (DE) analysis in MTX. Results We designed and assessed six statistical models for DE discovery in MTX that incorporate different combinations of DNA and RNA normalization and assumptions about the underlying changes of gene copies or species abundance within communities. We evaluated these models on multiple simulated and real multi-omic datasets. Models adjusting transcripts relative to their encoding gene copies as a covariate were significantly more accurate in identifying DE from MTX in both simulated and real datasets. Moreover, we show that when paired DNA measurements (metagenomic data) are not available, models normalizing MTX measurements within-species while also adjusting for total-species RNA balance sensitivity, specificity and interpretability of DE detection, as does filtering likely technical zeros. The efficiency and accuracy of these models pave the way for more effective MTX-based DE discovery in microbial communities. Availability and implementation The analysis code and synthetic datasets used in this evaluation are available online at http://huttenhower.sph.harvard.edu/mtx2021. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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119
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Bassey AP, Ye K, Li C, Zhou G. Transcriptomic-proteomic integration: A powerful synergy to elucidate the mechanisms of meat spoilage in the cold chain. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.02.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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120
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Wang J, Zhang J, Liu W, Zhang H, Sun Z. Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut. NPJ Biofilms Microbiomes 2021; 7:55. [PMID: 34210980 PMCID: PMC8249650 DOI: 10.1038/s41522-021-00227-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
Little is known about the replication and dynamic transcription of probiotics during their “passenger” journey in the human GI tract, which has therefore limited the understanding of their probiotic mechanisms. Here, metagenomic and metatranscriptomic sequencing was used to expose the in vivo expression patterns of the probiotic Lactobacillus casei Zhang (LcZ), which was compared with its in vitro growth transcriptomes, as well as the dynamics of the indigenous microbiome response to probiotic consumption. Extraction of the strain-specific reads revealed that replication and transcripts from the ingested LcZ were increased, while those from the resident L. casei strains remained unchanged. Mapping of all sequencing reads to LcZ genome showed that gene expression in vitro and in vivo differed dramatically. Approximately 39% of mRNAs and 45% of sRNAs of LcZ well-expressed were repressed after ingestion into human gut. The expression of ABC transporter genes and amino acid metabolism genes was induced at day 14 of ingestion, and genes for sugar and SCFA metabolism were activated at day 28 of ingestion. Expression of rli28c sRNA with peaked expression during the in vitro stationary phase was also activated in the human gut; this sRNA repressed LcZ growth and lactic acid production in vitro. However, the response of the human gut microbiome to LcZ was limited and heterogeneous. These findings implicate the ingested probiotic has to change its transcription patterns to survive and adapt in the human gut, and the time-dependent activation patterns indicate highly dynamic cross-talk between the probiotic and human gut microbes.
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Affiliation(s)
- Jicheng Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C., Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs China, Inner Mongolia Agricultural University, Hohhot, China
| | - Jiachao Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C., Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs China, Inner Mongolia Agricultural University, Hohhot, China.,School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, Hainan, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C., Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs China, Inner Mongolia Agricultural University, Hohhot, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C., Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs China, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C., Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs China, Inner Mongolia Agricultural University, Hohhot, China.
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121
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Eskind CC, Shilts MH, Shaver CM, Das SR, Satyanarayana G. The respiratory microbiome after lung transplantation: Reflection or driver of respiratory disease? Am J Transplant 2021; 21:2333-2340. [PMID: 33749996 PMCID: PMC8926303 DOI: 10.1111/ajt.16568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 02/17/2021] [Accepted: 03/05/2021] [Indexed: 01/25/2023]
Abstract
With the introduction of high-throughput sequencing methods, our understanding of the human lower respiratory tract's inhabitants has expanded significantly in recent years. What is now termed the "lung microbiome" has been described for healthy patients, as well as people with chronic lung diseases and lung transplants. The lung microbiome of lung transplant recipients (LTRs) has proven to be unique compared with nontransplant patients, with characteristic findings associated with disease states, such as pneumonia, acute rejection, and graft failure. In this review, we summarize the current understanding of the lung microbiome in LTRs, not only focusing on bacteria but also highlighting key findings of the viral and the fungal community. Based on our knowledge of the lung microbiome in LTRs, we propose multiple opportunities for clinical use of the microbiome to improve outcomes in this population.
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Affiliation(s)
- Caroline Cohen Eskind
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Meghan H. Shilts
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ciara M. Shaver
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman R. Das
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Otolaryngology and Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gowri Satyanarayana
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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122
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Young RB, Marcelino VR, Chonwerawong M, Gulliver EL, Forster SC. Key Technologies for Progressing Discovery of Microbiome-Based Medicines. Front Microbiol 2021; 12:685935. [PMID: 34239510 PMCID: PMC8258393 DOI: 10.3389/fmicb.2021.685935] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/25/2021] [Indexed: 12/22/2022] Open
Abstract
A growing number of experimental and computational approaches are illuminating the “microbial dark matter” and uncovering the integral role of commensal microbes in human health. Through this work, it is now clear that the human microbiome presents great potential as a therapeutic target for a plethora of diseases, including inflammatory bowel disease, diabetes and obesity. The development of more efficacious and targeted treatments relies on identification of causal links between the microbiome and disease; with future progress dependent on effective links between state-of-the-art sequencing approaches, computational analyses and experimental assays. We argue determining causation is essential, which can be attained by generating hypotheses using multi-omic functional analyses and validating these hypotheses in complex, biologically relevant experimental models. In this review we discuss existing analysis and validation methods, and propose best-practice approaches required to enable the next phase of microbiome research.
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Affiliation(s)
- Remy B Young
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Emily L Gulliver
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
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123
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Yin C, Chen J, Wu X, Liu Y, He Q, Cao Y, Huang YE, Liu S. Preterm Birth Is Correlated With Increased Oral Originated Microbiome in the Gut. Front Cell Infect Microbiol 2021; 11:579766. [PMID: 34222033 PMCID: PMC8248533 DOI: 10.3389/fcimb.2021.579766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 05/31/2021] [Indexed: 01/12/2023] Open
Abstract
Background Preterm birth is one of the leading causes of perinatal morbidity and mortality. Gut microbiome dysbiosis is closely related to adverse pregnancy outcomes. However, the role of the gut microbiome in the pathogenesis of preterm birth remains poorly studied. Method We collected fecal samples from 41 women (cases presenting with threatened preterm labor =19, 11 of which delivered preterm; gestational age-matched no-labor controls, all of which delivered at term = 22) were recruited for the study. We performed 16S rRNA amplicon sequencing to compare the composition of the gut microbiome in threatened preterm labor cases and controls and among women who delivered preterm and at term. By annotating taxonomic biomarkers with the Human Oral Microbiome Database, we observed an increased abundance of potential oral-to-gut bacteria in preterm patients. Results Patients with preterm birth showed a distinct gut microbiome dysbiosis compared with those who delivered at term. Opportunistic pathogens, particularly Porphyromonas, Streptococcus, Fusobacterium, and Veillonella, were enriched, whereas Coprococcus and Gemmiger were markedly depleted in the preterm group. Most of the enriched bacteria were annotated oral bacteria using the Human Oral Microbiome Database. These potential oral-to-gut bacteria were correlated with clinical parameters that reflected maternal and fetal status. Conclusions This study suggests that patients who deliver preterm demonstrate altered gut microbiome that may contain higher common oral bacteria.
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Affiliation(s)
- Chunhua Yin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jingrui Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xuena Wu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yeling Liu
- Anatomy and Pathology Department, Jiangxi Health Vocational College, Nanchang, China
| | - Quan He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ying Cao
- Nursing Department, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yi-E Huang
- Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Sisun Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Ma W, Nguyen LH, Song M, Wang DD, Franzosa EA, Cao Y, Joshi A, Drew DA, Mehta R, Ivey KL, Strate LL, Giovannucci EL, Izard J, Garrett W, Rimm EB, Huttenhower C, Chan AT. Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. Genome Med 2021; 13:102. [PMID: 34140026 PMCID: PMC8212460 DOI: 10.1186/s13073-021-00921-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/08/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A higher intake of dietary fiber is associated with a decreased risk of chronic inflammatory diseases such as cardiovascular disease and inflammatory bowel disease. This may function in part due to abrogation of chronic systemic inflammation induced by factors such as dysbiotic gut communities. Data regarding the detailed influences of long-term and recent intake of differing dietary fiber sources on the human gut microbiome are lacking. METHODS In a cohort of 307 generally healthy men, we examined gut microbiomes, profiled by shotgun metagenomic and metatranscriptomic sequencing, and long-term and recent dietary fiber intake in relation to plasma levels of C-reactive protein (CRP), an established biomarker for chronic inflammation. Data were analyzed using multivariate linear mixed models. RESULTS We found that inflammation-associated gut microbial configurations corresponded with higher CRP levels. A greater intake of dietary fiber was associated with shifts in gut microbiome composition, particularly Clostridiales, and their potential for carbohydrate utilization via polysaccharide degradation. This was particularly true for fruit fiber sources (i.e., pectin). Most striking, fiber intake was associated with significantly greater CRP reduction in individuals without substantial Prevotella copri carriage in the gut, whereas those with P. copri carriage maintained stable CRP levels regardless of fiber intake. CONCLUSIONS Our findings offer human evidence supporting a fiber-gut microbiota interaction, as well as a potential specific mechanism by which gut-mediated systemic inflammation may be mitigated.
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Affiliation(s)
- Wenjie Ma
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Dong D Wang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Amit Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raaj Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kerry L Ivey
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Microbiome and Host Health Programme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, 5000, Australia
- Department of Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, Australia
| | - Lisa L Strate
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA, USA
| | - Edward L Giovannucci
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jacques Izard
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Wendy Garrett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Eric B Rimm
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Ye F, Gao X, Wang Z, Cao S, Liang G, He D, Lv Z, Wang L, Xu P, Zhang Q. Comparison of gut microbiota in autism spectrum disorders and neurotypical boys in China: A case-control study. Synth Syst Biotechnol 2021; 6:120-126. [PMID: 34095558 PMCID: PMC8163862 DOI: 10.1016/j.synbio.2021.03.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/15/2021] [Accepted: 03/30/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Autism spectrum disorders (ASDs) are a set of complex neurobiological disorders. Growing evidence has shown that the microbiota that resides in the gut can modulate brain development via the gut-brain axis. However, direct clinical evidence of the role of the microbiota-gut-brain axis in ASD is relatively limited. METHODS A case-control study of 71 boys with ASD and 18 neurotypical controls was conducted at China-Japan Friendship Hospital. Demographic information and fecal samples were collected, and the gut microbiome was evaluated and compared by 16S ribosomal RNA gene sequencing and metagenomic sequencing. RESULTS A higher abundance of operational taxonomic units (OTUs) based on fecal bacterial profiling was observed in the ASD group. Significantly different microbiome profiles were observed between the two groups. At the genus level, we observed a decrease in the relative abundance of Escherichia, Shigella, Veillonella, Akkermansia, Provindencia, Dialister, Bifidobacterium, Streptococcus, Ruminococcaceae UCG_002, Megasphaera, Eubacterium_coprostanol, Citrobacter, Ruminiclostridium_5, and Ruminiclostridium_6 in the ASD cohort, while Eisenbergiella, Klebsiella, Faecalibacterium, and Blautia were significantly increased. Ten bacterial strains were selected for clinical discrimination between those with ASD and the neurotypical controls. The highest AUC value of the model was 0.947. CONCLUSION Significant differences were observed in the composition of the gut microbiome between boys with ASD and neurotypical controls. These findings contribute to the knowledge of the alteration of the gut microbiome in ASD patients, which opens the possibility for early identification of this disease.
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Affiliation(s)
- Fang Ye
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Xinying Gao
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Zhiyi Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuman Cao
- College of Life Sciences, Institute of Life Science and Green Development, Key Lab of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding, China
| | - Guangcai Liang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Danni He
- Clinical Research Institute, China-Japan Friendship Hospital, Beijing, China
| | - Zhitang Lv
- College of Life Sciences, Institute of Life Science and Green Development, Key Lab of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding, China
| | - Liming Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Pengfei Xu
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Qi Zhang
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
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Jeganathan P, Holmes SP. A Statistical Perspective on the Challenges in Molecular Microbial Biology. JOURNAL OF AGRICULTURAL, BIOLOGICAL, AND ENVIRONMENTAL STATISTICS 2021; 26:131-160. [PMID: 36398283 PMCID: PMC9667415 DOI: 10.1007/s13253-021-00447-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022]
Abstract
High throughput sequencing (HTS)-based technology enables identifying and quantifying non-culturable microbial organisms in all environments. Microbial sequences have enhanced our understanding of the human microbiome, the soil and plant environment, and the marine environment. All molecular microbial data pose statistical challenges due to contamination sequences from reagents, batch effects, unequal sampling, and undetected taxa. Technical biases and heteroscedasticity have the strongest effects, but different strains across subjects and environments also make direct differential abundance testing unwieldy. We provide an introduction to a few statistical tools that can overcome some of these difficulties and demonstrate those tools on an example. We show how standard statistical methods, such as simple hierarchical mixture and topic models, can facilitate inferences on latent microbial communities. We also review some nonparametric Bayesian approaches that combine visualization and uncertainty quantification. The intersection of molecular microbial biology and statistics is an exciting new venue. Finally, we list some of the important open problems that would benefit from more careful statistical method development.
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Affiliation(s)
- Pratheepa Jeganathan
- Department of Statistics, Stanford University, Sequoia Hall, 390 Jane Stanford Way, Stanford, CA 94305, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Sequoia Hall, 390 Jane Stanford Way, Stanford, CA 94305, USA
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Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids. Nat Microbiol 2021; 6:792-805. [PMID: 33846627 DOI: 10.1038/s41564-021-00887-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/01/2021] [Indexed: 02/01/2023]
Abstract
Human physiology is regulated by endogenous signalling compounds, including fatty acid amides (FAAs), chemical mimics of which are made by bacteria. The molecules produced by human-associated microbes are difficult to identify because they may only be made in a local niche or they require a substrate sourced from the host, diet or other microbes. We identified a set of uncharacterized gene clusters in metagenomics data from the human gut microbiome. These clusters were discovered to make FAAs by fusing exogenous fatty acids with amines. Using an in vitro assay, we tested their ability to incorporate 25 fatty acids and 53 amines known to be present in the human gut, from which the production of six FAAs was deduced (oleoyl dopamine, oleoyl tyramine, lauroyl tryptamine, oleoyl aminovaleric acid, α-linolenoyl phenylethylamine and caproyl tryptamine). These molecules were screened against panels of human G-protein-coupled receptors to deduce their putative human targets. Lauroyl tryptamine is found to be an antagonist to the immunomodulatory receptor EBI2 against its native oxysterol ligand (0.98 μM half-maximal inhibitory concentration), is produced in culture by Eubacterium rectale and is present in human faecal samples. FAAs produced by Clostridia may serve as a mechanism to modulate their host by mimicking human signalling molecules.
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128
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Kazantseva J, Malv E, Kaleda A, Kallastu A, Meikas A. Optimisation of sample storage and DNA extraction for human gut microbiota studies. BMC Microbiol 2021; 21:158. [PMID: 34051731 PMCID: PMC8164492 DOI: 10.1186/s12866-021-02233-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023] Open
Abstract
Background New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important. Results Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusions Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02233-y.
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Affiliation(s)
- Jekaterina Kazantseva
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia.
| | - Esther Malv
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Aleksei Kaleda
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Aili Kallastu
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Anne Meikas
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
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Oral Microbiota and Salivary Levels of Oral Pathogens in Gastro-Intestinal Diseases: Current Knowledge and Exploratory Study. Microorganisms 2021; 9:microorganisms9051064. [PMID: 34069179 PMCID: PMC8156550 DOI: 10.3390/microorganisms9051064] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/23/2022] Open
Abstract
Various bi-directional associations exist between oral health and gastro-intestinal diseases. The oral microbiome plays a role in the gastro-intestinal carcinogenesis and fusobacteria are the most investigated bacteria involved. This paper aims to review the current knowledge and report the preliminary data on salivary levels of Fusobacterium nucleatum, Porphyromonas gingivalis and Candida albicans in subjects with different gastro-intestinal conditions or pathologies, in order to determine any differences. The null hypothesis was “subjects with different gastro-intestinal diseases do not show significant differences in the composition of the oral microbiota”. Twenty-one subjects undergoing esophagastroduodenoscopy or colonscopy were recruited. For each subject, a salivary sample was collected before the endoscopy procedure, immediately stored at −20 °C and subsequently used for genomic bacterial DNA extraction by real-time PCR. Low levels of F. nucleatum and P. gingivalis were peculiar in the oral microbiota in subjects affected by Helicobater pylori-negative chronic gastritis without cancerization and future studies will elucidate this association. The level of C. albicans did not statistically differ among groups. This preliminary study could be used in the future, following further investigation, as a non-invasive method for the search of gastrointestinal diseases and associated markers.
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Naidoo CC, Nyawo GR, Sulaiman I, Wu BG, Turner CT, Bu K, Palmer Z, Li Y, Reeve BWP, Moodley S, Jackson JG, Limberis J, Diacon AH, van Helden PD, Clemente JC, Warren RM, Noursadeghi M, Segal LN, Theron G. Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis. EBioMedicine 2021; 67:103374. [PMID: 33975252 PMCID: PMC8122180 DOI: 10.1016/j.ebiom.2021.103374] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/07/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The relationship between tuberculosis (TB), one of the leading infectious causes of death worldwide, and the microbiome, which is critical for health, is poorly understood. METHODS To identify potential microbiome-host interactions, profiling of the oral, sputum and stool microbiota [n = 58 cases, n = 47 culture-negative symptomatic controls (SCs)] and whole blood transcriptome were done in pre-treatment presumptive pulmonary TB patients. This was a cross-sectional study. Microbiota were also characterised in close contacts of cases (CCCs, n = 73) and close contacts of SCs (CCSCs, n = 82) without active TB. FINDINGS Cases and SCs each had similar α- and β-diversities in oral washes and sputum, however, β-diversity differed in stool (PERMANOVA p = 0•035). Cases were enriched with anaerobes in oral washes, sputum (Paludibacter, Lautropia in both) and stool (Erysipelotrichaceae, Blautia, Anaerostipes) and their stools enriched in microbial genes annotated as amino acid and carbohydrate metabolic pathways. In pairwise comparisons with their CCCs, cases had Megasphaera-enriched oral and sputum microbiota and Bifidobacterium-, Roseburia-, and Dorea-depleted stools. Compared to their CCSCs, SCs had reduced α-diversities and many differential taxa per specimen type. Cases differed transcriptionally from SCs in peripheral blood (PERMANOVA p = 0•001). A co-occurrence network analysis showed stool taxa, Erysipelotrichaceae and Blautia, to negatively co-correlate with enriched "death receptor" and "EIF2 signalling" pathways whereas Anaerostipes positively correlated with enriched "interferon signalling", "Nur77 signalling" and "inflammasome" pathways; all of which are host pathways associated with disease severity. In contrast, none of the taxa enriched in SCs correlated with host pathways. INTERPRETATION TB-specific microbial relationships were identified in oral washes, induced sputum, and stool from cases before the confounding effects of antibiotics. Specific anaerobes in cases' stool predict upregulation of pro-inflammatory immunological pathways, supporting the gut microbiota's role in TB. FUNDING European & Developing Countries Clinical Trials Partnership, South African-Medical Research Council, National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Charissa C Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Georgina R Nyawo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, United States
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, United States
| | - Carolin T Turner
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Kevin Bu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zaida Palmer
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, United States
| | - Byron W P Reeve
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Suventha Moodley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Jennifer G Jackson
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Jason Limberis
- Division of Experimental Medicine, University of California, San Francisco, United States
| | - Andreas H Diacon
- Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Paul D van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, United States
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.
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Melkonian C, Fillinger L, Atashgahi S, da Rocha UN, Kuiper E, Olivier B, Braster M, Gottstein W, Helmus R, Parsons JR, Smidt H, van der Waals M, Gerritse J, Brandt BW, Röling WFM, Molenaar D, van Spanning RJM. High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. Commun Biol 2021; 4:530. [PMID: 33953314 PMCID: PMC8099898 DOI: 10.1038/s42003-021-01948-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.
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Affiliation(s)
- Chrats Melkonian
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Lucas Fillinger
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Esther Kuiper
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Brett Olivier
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Martin Braster
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Willi Gottstein
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Jan Gerritse
- Unit Subsurface and Groundwater Systems, Deltares, Utrecht, The Netherlands
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wilfred F M Röling
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rob J M van Spanning
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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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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Sugihara K, Kamada N. Diet-Microbiota Interactions in Inflammatory Bowel Disease. Nutrients 2021; 13:1533. [PMID: 34062869 PMCID: PMC8147260 DOI: 10.3390/nu13051533] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract. Although the precise etiology of IBD is largely unknown, it is widely thought that diet contributes to the development of IBD. Diet shapes the composition of the gut microbiota, which plays critical roles in intestinal homeostasis. In contrast, intestinal inflammation induces gut dysbiosis and may affect the use of dietary nutrients by host cells and the gut microbiota. The interaction of diet and the gut microbiota is perturbed in patients with IBD. Herein, we review the current knowledge of diet and gut microbiota interaction in intestinal homeostasis. We also discuss alterations of diet and gut microbiota interaction that influence the outcome and the nutritional treatment of IBD. Understanding the complex relationships between diet and the gut microbiota provides crucial insight into the pathogenesis of IBD and advances the development of new therapeutic approaches.
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Affiliation(s)
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA;
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134
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Liu X, Ma Y, Wang J. Genetic variation and function: revealing potential factors associated with microbial phenotypes. BIOPHYSICS REPORTS 2021; 7:111-126. [PMID: 37288143 PMCID: PMC10235906 DOI: 10.52601/bpr.2021.200040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/09/2021] [Indexed: 06/09/2023] Open
Abstract
Innovations in sequencing technology have generated voluminous microbial and host genomic data, making it possible to detect these genetic variations and analyze the function influenced by them. Recently, many studies have linked such genetic variations to phenotypes through association or comparative analysis, which have further advanced our understanding of multiple microbial functions. In this review, we summarized the application of association analysis in microbes like Mycobacterium tuberculosis, focusing on screening of microbial genetic variants potentially associated with phenotypes such as drug resistance, pathogenesis and novel drug targets etc.; reviewed the application of additional comparative genomic or transcriptomic methods to identify genetic factors associated with functions in microbes; expanded the scope of our study to focus on host genetic factors associated with certain microbes or microbiome and summarized the recent host genetic variations associated with microbial phenotypes, including susceptibility and load after infection of HIV, presence/absence of different taxa, and quantitative traits of microbiome, and lastly, discussed the challenges that may be encountered and the apparent or potential viable solutions. Gene-function analysis of microbe and microbiome is still in its infancy, and in order to unleash its full potential, it is necessary to understand its history, current status, and the challenges hindering its development.
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Affiliation(s)
- Xiaolin Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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135
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Everett C, Li C, Wilkinson JE, Nguyen LH, McIver LJ, Ivey K, Izard J, Palacios N, Eliassen AH, Willett WC, Ascherio A, Sun Q, Tworoger SS, Chan AT, Garrett WS, Huttenhower C, Rimm EB, Song M. Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies. Nat Protoc 2021; 16:2724-2731. [PMID: 33883746 DOI: 10.1038/s41596-021-00519-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/16/2021] [Indexed: 02/06/2023]
Abstract
A lack of prospective studies has been a major barrier for assessing the role of the microbiome in human health and disease on a population-wide scale. To address this significant knowledge gap, we have launched a large-scale collection targeting fecal and oral microbiome specimens from 20,000 women within the Nurses' Health Study II cohort (the Microbiome Among Nurses study, or Micro-N). Leveraging the rich epidemiologic data that have been repeatedly collected from this cohort since 1989; the established biorepository of archived blood, urine, buccal cell, and tumor tissue specimens; the available genetic and biomarker data; the cohort's ongoing follow-up; and the BIOM-Mass microbiome research platform, Micro-N furnishes unparalleled resources for future prospective studies to interrogate the interplay between host, environmental factors, and the microbiome in human health. These prospectively collected materials will provide much-needed evidence to infer causality in microbiome-associated outcomes, paving the way toward development of microbiota-targeted modulators, preventives, diagnostics and therapeutics. Here, we describe a generalizable, scalable and cost-effective platform used for stool and oral microbiome specimen and metadata collection in the Micro-N study as an example of how prospective studies of the microbiome may be carried out.
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Affiliation(s)
- Christine Everett
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Chengchen Li
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jeremy E Wilkinson
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lauren J McIver
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kerry Ivey
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,South Australian Health and Medical Research Institute, Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia.,Department of Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Jacques Izard
- Food Science and Technology Department, Institute of Agriculture and Natural Resources, University of Nebraska, Lincoln, NE, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Natalia Palacios
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Public Health, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - A Heather Eliassen
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Walter C Willett
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Alberto Ascherio
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Qi Sun
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Shelley S Tworoger
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Andrew T Chan
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Wendy S Garrett
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric B Rimm
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mingyang Song
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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136
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Xu L, Wu Z, Wang Y, Wang S, Shu C, Duan Z, Deng S. High-throughput sequencing identifies salivary microbiota in Chinese caries-free preschool children with primary dentition. J Zhejiang Univ Sci B 2021; 22:285-294. [PMID: 33835762 DOI: 10.1631/jzus.b2000554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
OBJECTIVES The study aimed at identifying salivary microbiota in caries-free Chinese preschool children using high-throughput sequencing. METHODS Saliva samples were obtained from 35 caries-free preschool children (18 boys and 17 girls) with primary dentition, and 16S ribosomal DNA (rDNA) V3-V4 hypervariable regions of the microorganisms were analyzed using Illumina MiSeq. RESULTS At 97% similarity level, all of these reads were clustered into 334 operational taxonomic units (OTUs). Among these, five phyla (Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Candidate division TM7) and 13 genera (Streptococcus, Rothia, Granulicatella, Prevotella, Enterobacter, Veillonella, Neisseria, Staphylococcus, Janthinobacterium, Pseudomonas, Brevundimonas, Devosia, and Gemella) were the most dominant, constituting 99.4% and 89.9% of the salivary microbiota, respectively. The core salivary microbiome comprised nine genera (Actinomyces, Capnocytophaga, Gemella, Granulicatella, Lachnoanaerobaculum, Neisseria, Porphyromonas, Rothia,and Streptococcus). Analysis of microbial diversity and community structure revealed a similar pattern between male and female subjects. The difference in microbial community composition between them was mainly attributed to Neisseria (P=0.023). Furthermore, functional prediction revealed that the most abundant genes were related to amino acid transport and metabolism. CONCLUSIONS Our results revealed the diversity and composition of salivary microbiota in caries-free preschool children, with little difference between male and female subjects. Identity of the core microbiome, coupled with prediction of gene function, deepens our understanding of oral microbiota in caries-free populations and provides basic information for associating salivary microecology and oral health.
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Affiliation(s)
- Lei Xu
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou 310006, China
| | - Zhifang Wu
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou 310006, China
| | - Yuan Wang
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou 310006, China
| | - Sa Wang
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou 310006, China
| | - Chang Shu
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou 310006, China
| | - Zhuhui Duan
- Department of Stomatology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang 471009, China
| | - Shuli Deng
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou 310006, China.
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137
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Yaghjyan L, Mai V, Wang X, Ukhanova M, Tagliamonte M, Martinez YC, Rich SN, Egan KM. Gut microbiome, body weight, and mammographic breast density in healthy postmenopausal women. Cancer Causes Control 2021; 32:681-692. [PMID: 33772705 DOI: 10.1007/s10552-021-01420-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/16/2021] [Indexed: 12/17/2022]
Abstract
PURPOSE We examined gut microbiome (GM) profiles in relation to mammographic breast density (BD) and body mass index (BMI) in healthy postmenopausal women. METHODS Eligible women were postmenopausal, had a BMI ≤ 35 kg/m2, and had not recently taken oral/IV antibiotics. All women provided a fecal sample and information on breast cancer risk factors. Mammographic BD was classified with the American College of Radiology's BI-RADS BD classification system. Bacterial DNA was isolated from fecal samples and the V1-V2 hypervariable regions of 16S rRNA were sequenced on the Illumina MiSeq platform. We examined associations of GM with indices of within-sample (alpha) diversity and the ratio of the two main phyla (Firmicutes and Bacteroidetes; F/B ratio) with BD and BMI. RESULTS Among 69 women with BD data, 39 had low BD (BI-RADS I/II) and 30 had high BD (BI-RADS III/IV). BMI was inversely associated with BD (mean BMI = 23.8 and 28.0 in women with high and low BD, respectively, p = 1.07 × 10-5). Similar levels of GM diversity were found across weight groups according to Shannon (p = 0.83); Inverse Simpson (p = 0.97); and Chao1 (p = 0.31) indices. F/B ratio and microbiota diversity were suggestively greater in women with high vs. low BD (p = 0.35, 0.14, 0.15, and 0.17 for F/B ratio, Shannon, Inverse Simpson and Chao1, respectively). CONCLUSION Suggestive differences observed in women with high and low BD with respect to GM alpha diversity and prevalence of specific GM taxa need to be confirmed in larger studies.
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Affiliation(s)
- Lusine Yaghjyan
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | - Maria Ukhanova
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | | | - Shannan N Rich
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Kathleen M Egan
- H. Lee Moffitt Cancer Center, Tampa, FL, USA. .,Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA.
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138
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Liu M, Devlin JC, Hu J, Volkova A, Battaglia TW, Ho M, Asplin JR, Byrd A, Loke P, Li H, Ruggles KV, Tsirigos A, Blaser MJ, Nazzal L. Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. eLife 2021; 10:e63642. [PMID: 33769280 PMCID: PMC8062136 DOI: 10.7554/elife.63642] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Furthermore, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with inflammatory bowel disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn's disease (CD) patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.
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Affiliation(s)
- Menghan Liu
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | - Joseph C Devlin
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | - Jiyuan Hu
- NYU Langone HealthNew YorkUnited States
| | - Angelina Volkova
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | | | - Melody Ho
- NYU Langone HealthNew YorkUnited States
| | - John R Asplin
- Litholink Corporation, Laboratory Corporation of America HoldingsChicagoUnited States
| | - Allyson Byrd
- Department of Cancer Immunology, Genentech IncSouth San FranciscoUnited States
| | - P'ng Loke
- NYU Langone HealthNew YorkUnited States
| | - Huilin Li
- NYU Langone HealthNew YorkUnited States
| | | | | | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers UniversityNew YorkUnited States
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139
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Becattini S, Sorbara MT, Kim SG, Littmann EL, Dong Q, Walsh G, Wright R, Amoretti L, Fontana E, Hohl TM, Pamer EG. Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation. Cell Host Microbe 2021; 29:378-393.e5. [PMID: 33539766 PMCID: PMC7954923 DOI: 10.1016/j.chom.2021.01.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/08/2020] [Accepted: 01/07/2021] [Indexed: 12/17/2022]
Abstract
The gut microbiota produces metabolites that regulate host immunity, thereby impacting disease resistance and susceptibility. The extent to which commensal bacteria reciprocally respond to immune activation, however, remains largely unexplored. Herein, we colonized mice with four anaerobic symbionts and show that acute immune responses result in dramatic transcriptional reprogramming of these commensals with minimal changes in their relative abundance. Transcriptomic changes include induction of stress-response mediators and downregulation of carbohydrate-degrading factors such as polysaccharide utilization loci (PULs). Flagellin and anti-CD3 antibody, two distinct immune stimuli, induced similar transcriptional profiles, suggesting that commensal bacteria detect common effectors or activate shared pathways when facing different host responses. Immune activation altered the intestinal metabolome within 6 hours, decreasing luminal short-chain fatty acid and increasing aromatic metabolite concentrations. Thus, intestinal bacteria, prior to detectable shifts in community composition, respond to acute host immune activation by rapidly changing gene transcription and immunomodulatory metabolite production.
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Affiliation(s)
- Simone Becattini
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology and Immunology, School of Medicine, University of Geneva, 1206 Geneva, Switzerland.
| | - Matthew T Sorbara
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Sohn G Kim
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eric L Littmann
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Qiwen Dong
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Gavin Walsh
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Roberta Wright
- Center for Microbes Inflammation and Cancer, Molecular Microbiology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Luigi Amoretti
- Center for Microbes Inflammation and Cancer, Molecular Microbiology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Emily Fontana
- Center for Microbes Inflammation and Cancer, Molecular Microbiology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Tobias M Hohl
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Infectious Diseases Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA.
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140
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Daliri EBM, Ofosu FK, Xiuqin C, Chelliah R, Oh DH. Probiotic Effector Compounds: Current Knowledge and Future Perspectives. Front Microbiol 2021; 12:655705. [PMID: 33746935 PMCID: PMC7965967 DOI: 10.3389/fmicb.2021.655705] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/12/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the mechanism behind probiotic action will enable a rational selection of probiotics, increase the chances of success in clinical studies and make it easy to substantiate health claims. However, most probiotic studies over the years have rather focused on the effects of probiotics in health and disease, whereas little is known about the specific molecules that trigger effects in hosts. This makes it difficult to describe the detailed mechanism by which a given probiotic functions. Probiotics communicate with their hosts through molecular signaling. Meanwhile, since the molecules produced by probiotics under in vitro conditions may differ from those produced in vivo, in vitro mechanistic studies would have to be conducted under conditions that mimic gastrointestinal conditions as much as possible. The ideal situation would, however, be to carry out well-designed clinical trials in humans (or the target animal) using adequate quantities of the suspected probiotic molecule(s) or adequate quantities of isogenic knock-out or knock-in probiotic mutants. In this review, we discuss our current knowledge about probiotic bacteria and yeast molecules that are involved in molecular signaling with the host. We also discuss the challenges and future perspectives in the search for probiotic effector molecules.
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Affiliation(s)
- Eric Banan-Mwine Daliri
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | - Fred Kwame Ofosu
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | - Chen Xiuqin
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | - Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon, South Korea
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141
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The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling. Int J Mol Sci 2021; 22:ijms22041965. [PMID: 33671197 PMCID: PMC7922330 DOI: 10.3390/ijms22041965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/15/2022] Open
Abstract
Gastrointestinal (GIT) diseases have risen globally in recent years, and early detection of the host’s gut microbiota, typically through fecal material, has become a crucial component for rapid diagnosis of such diseases. Human fecal material is a complex substance composed of undigested macromolecules and particles, and the processing of such matter is a challenge due to the unstable nature of its products and the complexity of the matrix. The identification of these products can be used as an indication for present and future diseases; however, many researchers focus on one variable or marker looking for specific biomarkers of disease. Therefore, the combination of genomics, transcriptomics, proteomics and metabonomics can give a detailed and complete insight into the gut environment. The proper sample collection, sample preparation and accurate analytical methods play a crucial role in generating precise microbial data and hypotheses in gut microbiome research, as well as multivariate data analysis in determining the gut microbiome functionality in regard to diseases. This review summarizes fecal sample protocols involved in profiling coeliac disease.
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142
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Westermann AJ, Vogel J. Cross-species RNA-seq for deciphering host-microbe interactions. Nat Rev Genet 2021; 22:361-378. [PMID: 33597744 DOI: 10.1038/s41576-021-00326-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2021] [Indexed: 02/08/2023]
Abstract
The human body is constantly exposed to microorganisms, which entails manifold interactions between human cells and diverse commensal or pathogenic bacteria. The cellular states of the interacting cells are decisive for the outcome of these encounters such as whether bacterial virulence programmes and host defence or tolerance mechanisms are induced. This Review summarizes how next-generation RNA sequencing (RNA-seq) has become a primary technology to study host-microbe interactions with high resolution, improving our understanding of the physiological consequences and the mechanisms at play. We illustrate how the discriminatory power and sensitivity of RNA-seq helps to dissect increasingly complex cellular interactions in time and space down to the single-cell level. We also outline how future transcriptomics may answer currently open questions in host-microbe interactions and inform treatment schemes for microbial disorders.
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Affiliation(s)
- Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany. .,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany. .,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
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143
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Daliri EBM, Ofosu FK, Chelliah R, Lee BH, Oh DH. Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies. Biomolecules 2021; 11:300. [PMID: 33671370 PMCID: PMC7922017 DOI: 10.3390/biom11020300] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/10/2021] [Accepted: 02/14/2021] [Indexed: 12/14/2022] Open
Abstract
The advent of omic technology has made it possible to identify viable but unculturable micro-organisms in the gut. Therefore, application of multi-omic technologies in gut microbiome studies has become invaluable for unveiling a comprehensive interaction between these commensals in health and disease. Meanwhile, despite the successful identification of many microbial and host-microbial cometabolites that have been reported so far, it remains difficult to clearly identify the origin and function of some proteins and metabolites that are detected in gut samples. However, the application of single omic techniques for studying the gut microbiome comes with its own challenges which may be overcome if a number of different omics techniques are combined. In this review, we discuss our current knowledge about multi-omic techniques, their challenges and future perspective in this field of gut microbiome studies.
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Affiliation(s)
- Eric Banan-Mwine Daliri
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
| | - Fred Kwame Ofosu
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
| | - Ramachandran Chelliah
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
| | - Byong H. Lee
- SportBiomics, Sacramento Inc., California, CA 95660, USA;
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
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144
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The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. Nat Med 2021; 27:333-343. [PMID: 33574608 DOI: 10.1038/s41591-020-01223-3] [Citation(s) in RCA: 179] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022]
Abstract
To address how the microbiome might modify the interaction between diet and cardiometabolic health, we analyzed longitudinal microbiome data from 307 male participants in the Health Professionals Follow-Up Study, together with long-term dietary information and measurements of biomarkers of glucose homeostasis, lipid metabolism and inflammation from blood samples. Here, we demonstrate that a healthy Mediterranean-style dietary pattern is associated with specific functional and taxonomic components of the gut microbiome, and that its protective associations with cardiometabolic health vary depending on microbial composition. In particular, the protective association between adherence to the Mediterranean diet and cardiometabolic disease risk was significantly stronger among participants with decreased abundance of Prevotella copri. Our findings advance the concept of precision nutrition and have the potential to inform more effective and precise dietary approaches for the prevention of cardiometabolic disease mediated through alterations in the gut microbiome.
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145
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Gwak HJ, Lee SJ, Rho M. Application of computational approaches to analyze metagenomic data. J Microbiol 2021; 59:233-241. [DOI: 10.1007/s12275-021-0632-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/04/2023]
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146
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Salvador R, Zhang A, Horai R, Caspi RR. Microbiota as Drivers and as Therapeutic Targets in Ocular and Tissue Specific Autoimmunity. Front Cell Dev Biol 2021; 8:606751. [PMID: 33614621 PMCID: PMC7893107 DOI: 10.3389/fcell.2020.606751] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/17/2020] [Indexed: 12/16/2022] Open
Abstract
Autoimmune uveitis is a major cause of blindness in humans. Activation of retina-specific autoreactive T cells by commensal microbiota has been shown to trigger uveitis in mice. Although a culprit microbe and/or its immunogenic antigen remains to be identified, studies from inducible and spontaneous mouse models suggest the potential of microbiota-modulating therapies for treating ocular autoimmune disease. In this review, we summarize recent findings on the contribution of microbiota to T cell-driven, tissue-specific autoimmunity, with an emphasis on autoimmune uveitis, and analyze microbiota-altering interventions, including antibiotics, probiotics, and microbiota-derived metabolites (e.g., short-chain fatty acids), which have been shown to be effective in other autoimmune diseases. We also discuss the need to explore more translational animal models as well as to integrate various datasets (microbiomic, transcriptomic, proteomic, metabolomic, and other cellular measurements) to gain a better understanding of how microbiota can directly or indirectly modulate the immune system and contribute to the onset of disease. It is hoped that deeper understanding of these interactions may lead to more effective treatment interventions.
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Affiliation(s)
- Ryan Salvador
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Amy Zhang
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Reiko Horai
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Rachel R Caspi
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
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147
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Taguer M, Shapiro BJ, Maurice CF. Translational activity is uncoupled from nucleic acid content in bacterial cells of the human gut microbiota. Gut Microbes 2021; 13:1-15. [PMID: 33779505 PMCID: PMC8009119 DOI: 10.1080/19490976.2021.1903289] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/12/2021] [Accepted: 03/02/2021] [Indexed: 02/04/2023] Open
Abstract
Changes in bacterial diversity in the human gut have been associated with many conditions, despite not always reflecting changes in bacterial activity. Methods linking bacterial identity to function are needed for improved understanding of how bacterial communities adapt and respond to their environment, including the gut. Here, we optimized bioorthogonal non-canonical amino acid tagging (BONCAT) for the gut microbiota and combined it with fluorescently activated cell sorting and sequencing (FACS-Seq) to identify the translationally active members of the community. We then used this novel technique to compare with other bulk community measurements of activity and viability: relative nucleic acid content and membrane damage. The translationally active bacteria represent about half of the gut microbiota, and are not distinct from the whole community. The high nucleic acid content bacteria also represent half of the gut microbiota, but are distinct from the whole community and correlate with the damaged subset. Perturbing the community with xenobiotics previously shown to alter bacterial activity but not diversity resulted in stronger changes in the distinct physiological fractions than in the whole community. BONCAT is a suitable method to probe the translationally active members of the gut microbiota, and combined with FACS-Seq, allows for their identification. The high nucleic acid content bacteria are not necessarily the protein-producing bacteria in the community; thus, further work is needed to understand the relationship between nucleic acid content and bacterial metabolism in the human gut. Considering physiologically distinct subsets of the gut microbiota may be more informative than whole-community profiling.
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Affiliation(s)
- Mariia Taguer
- Department of Microbiology & Immunology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - B. Jesse Shapiro
- Department of Microbiology & Immunology, McGill Genome Centre, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Corinne F. Maurice
- Department of Microbiology & Immunology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
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148
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Copeland JK, Chao G, Vanderhout S, Acton E, Wang PW, Benchimol EI, El-Sohemy A, Croitoru K, Gommerman JL, Guttman DS. The Impact of Migration on the Gut Metagenome of South Asian Canadians. Gut Microbes 2021; 13:1-29. [PMID: 33794735 PMCID: PMC8023248 DOI: 10.1080/19490976.2021.1902705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 02/04/2023] Open
Abstract
South Asian (SA) Canadian immigrants have a higher risk of developing certain immune-mediated inflammatory diseases compared to non-migrant SAs. We sought to investigate the effect of migration on the gut metagenome and to identify microbiological associations between migration and conditions that may influence the development of immune-mediated inflammatory diseases. Metagenomic analysis of 58 first-generation (GEN1) SA immigrants and 38 unrelated Canadian born children-of-immigrants (GEN2) determined that the time lived in Canada was associated with continued changes in gut microbial communities. Migration of GEN1 to Canada early in life results in a gut community with similarities to GEN2 SA Canadians and non-SA North Americans. Conversely, GEN1 immigrants who arrived recently to Canada exhibited pronounced differences from GEN2, while displaying microbial similarities to a non-migrating SA cohort. Multivariate analysis identified that community composition was primarily influenced by high abundance taxa. Prevotella copri dominated in GEN1 and non-migrant SAs. Clostridia and functionally related Bacteroidia spp. replaced P. copri dominance over generations in Canada. Mutually exclusive Dialister species occurred at differing relative abundances over time and generations in Canada. This shift in species composition is accompanied by a change in genes associated with carbohydrate utilization and short-chain fatty acid production. Total energy derived from carbohydrates compared to protein consumption was significantly higher for GEN1 recent immigrants, which may influence the functional requirements of the gut community. This study demonstrates the associations between migration and the gut microbiome, which may be further associated with the altered risk of immune-mediated inflammatory diseases observed for SA Canadians.
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Affiliation(s)
- Julia K. Copeland
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, CA, Canada
| | - Gary Chao
- Department of Immunology, University of Toronto, Toronto, CA, Canada
| | - Shelley Vanderhout
- Nutrigenomix, Department of Nutritional Sciences, University of Toronto, Toronto, CA, Canada
| | - Erica Acton
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, CA, Canada
| | - Pauline W. Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, CA, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, CA, Canada
| | - Eric I. Benchimol
- Department of Pediatrics, and School of Epidemiology and Public Health, University of Ottawa, Ottawa, CA, Canada
| | - Ahmed El-Sohemy
- Department of Nutritional Sciences, University of Toronto, Toronto, CA, Canada
| | - Ken Croitoru
- Department of Medicine, University of Toronto and Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, CA, Canada
| | | | - David S. Guttman
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, CA, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, CA, Canada
| | - the GEMINI Research Team
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, CA, Canada
- Department of Immunology, University of Toronto, Toronto, CA, Canada
- Nutrigenomix, Department of Nutritional Sciences, University of Toronto, Toronto, CA, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, CA, Canada
- Department of Pediatrics, and School of Epidemiology and Public Health, University of Ottawa, Ottawa, CA, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, CA, Canada
- Department of Medicine, University of Toronto and Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, CA, Canada
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149
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D’Souza AW, Moodley-Govender E, Berla B, Kelkar T, Wang B, Sun X, Daniels B, Coutsoudis A, Trehan I, Dantas G. Cotrimoxazole Prophylaxis Increases Resistance Gene Prevalence and α-Diversity but Decreases β-Diversity in the Gut Microbiome of Human Immunodeficiency Virus-Exposed, Uninfected Infants. Clin Infect Dis 2020; 71:2858-2868. [PMID: 31832638 PMCID: PMC7778358 DOI: 10.1093/cid/ciz1186] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Prophylactic cotrimoxazole treatment is recommended in human immunodeficiency virus (HIV)-exposed, uninfected (HEU) infants, but the effects of this treatment on developing HEU infant gut microbiotas and resistomes are largely undefined. METHODS We analyzed whole-metagenome sequencing data from 163 longitudinally collected stool samples from 63 HEU infants randomized to receive (n = 34; CTX-T) or to not receive (n = 29; CTX-N) prophylactic cotrimoxazole treatment. We generated taxonomic, functional pathway, and resistance gene profiles for each sample and compared microbiome signatures between the CTX-T and CTX-N infants. RESULTS Metagenomic analysis did not reveal significant differences in taxonomic or functional pathway α-diversity between CTX-T and CTX-N infants. In contrast, resistance gene prevalence (P = .00719) and α-diversity (P = .0045) increased in CTX-T infants. These differences increased over time for both resistance gene prevalence measured by log-normalized abundance (4-month mean, 0.71 [95% confidence interval {CI}, .2-1.2] and 6-month mean, 0.85 [95% CI, .1-1.7]) and α-diversity (P = .0045). Unlike α-diversity, interindividual gut microbiome taxonomic (mean, -0.11 [95% CI, -.15 to -.077]), functional taxonomic (mean, -0.050 [95% CI, -.084 to -.017]), and resistance gene (mean, -0.13 [95% CI, -.17 to -.099]) β-diversity decreased in CTX-T infants compared with CTX-N infants. These results are consistent with persistent antibiotic selection pressure. CONCLUSIONS Cotrimoxazole prophylaxis in HEU infants decreased gut microbiome β-diversity and increased antibiotic resistance gene α-diversity and prevalence. Antibiotic resistance is a growing threat, especially in low- and middle-income countries where the higher perinatal HIV exposure rates result in cotrimoxazole prophylaxis. Understanding effects from current HEU infant antibiotic prophylaxis guidelines will inform guideline revisions and efforts to reduce increasing antibiotic resistance.
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Affiliation(s)
- Alaric W D’Souza
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Eshia Moodley-Govender
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
| | - Bertram Berla
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Tejas Kelkar
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Bin Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Xiaoqing Sun
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Brodie Daniels
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
- HIV Preventin Research Unit, South African Medical Research Council, Durban, South Africa
| | - Anna Coutsoudis
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
| | - Indi Trehan
- HIV Preventin Research Unit, South African Medical Research Council, Durban, South Africa
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Gautam Dantas
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, Missouri, USA
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150
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Damhorst GL, Adelman MW, Woodworth MH, Kraft CS. Current Capabilities of Gut Microbiome-Based Diagnostics and the Promise of Clinical Application. J Infect Dis 2020; 223:S270-S275. [PMID: 33330938 DOI: 10.1093/infdis/jiaa689] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There is increasing evidence for the importance of the gut microbiome in human health and disease. Traditional and modern technologies - from cell culture to next generation sequencing - have facilitated these advances in knowledge. Each of the tools employed in measuring the microbiome exhibits unique capabilities that may be leveraged for clinical diagnostics. However, much still needs to be done to standardize the language and metrics by which a microbiome is characterized. Here we review the capabilities of gut microbiome-based diagnostics, review selected examples, and discuss the outlook towards clinical application.
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Affiliation(s)
- Gregory L Damhorst
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA
| | - Max W Adelman
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA
| | - Michael H Woodworth
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA.,Department of Pathology and Laboratory Medicine; Department of Medicine; Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
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