1
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Odendaal ML, de Steenhuijsen Piters WAA, Franz E, Chu MLJN, Groot JA, van Logchem EM, Hasrat R, Kuiling S, Pijnacker R, Mariman R, Trzciński K, van der Klis FRM, Sanders EAM, Smit LAM, Bogaert D, Bosch T. Host and environmental factors shape upper airway microbiota and respiratory health across the human lifespan. Cell 2024:S0092-8674(24)00768-2. [PMID: 39094567 DOI: 10.1016/j.cell.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/22/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024]
Abstract
Our understanding of the normal variation in the upper respiratory tract (URT) microbiota across the human lifespan and how these relate to host, environment, and health is limited. We studied the microbiota of 3,104 saliva (<10 year-olds)/oropharynx (≥10 year-olds) and 2,485 nasopharynx samples of 3,160 Dutch individuals 0-87 years of age, participating in a cross-sectional population-wide study (PIENTER-3) using 16S-rRNA sequencing. The microbiota composition was strongly related to age, especially in the nasopharynx, with maturation occurring throughout childhood and adolescence. Clear niche- and age-specific associations were found between the microbiota composition and host/environmental factors and health outcomes. Among others, social interaction, sex, and season were associated with the nasopharyngeal microbial community. By contrast, the oral microbiota was more related to antibiotics, tobacco, and alcohol use. We present an atlas of the URT microbiota across the lifespan in association with environment and health, establishing a baseline for future research.
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Affiliation(s)
- Mari-Lee Odendaal
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Wouter A A de Steenhuijsen Piters
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Mei Ling J N Chu
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
| | - James A Groot
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Elske M van Logchem
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Raiza Hasrat
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sjoerd Kuiling
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Roan Pijnacker
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Rob Mariman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Krzysztof Trzciński
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
| | - Fiona R M van der Klis
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Elisabeth A M Sanders
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Debby Bogaert
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands; Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
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2
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Chen YC, Destouches L, Cook A, Fedorec AJH. Synthetic microbial ecology: engineering habitats for modular consortia. J Appl Microbiol 2024; 135:lxae158. [PMID: 38936824 DOI: 10.1093/jambio/lxae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]
Abstract
Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.
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Affiliation(s)
- Yue Casey Chen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Louie Destouches
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alice Cook
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
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3
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Hoisington AJ, Stamper CE, Ellis JC, Lowry CA, Brenner LA. Quantifying variation across 16S rRNA gene sequencing runs in human microbiome studies. Appl Microbiol Biotechnol 2024; 108:367. [PMID: 38850297 PMCID: PMC11162379 DOI: 10.1007/s00253-024-13198-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024]
Abstract
Recent microbiome research has incorporated a higher number of samples through more participants in a study, longitudinal studies, and metanalysis between studies. Physical limitations in a sequencing machine can result in samples spread across sequencing runs. Here we present the results of sequencing nearly 1000 16S rRNA gene sequences in fecal (stabilized and swab) and oral (swab) samples from multiple human microbiome studies and positive controls that were conducted with identical standard operating procedures. Sequencing was performed in the same center across 18 different runs. The simplified mock community showed limitations in accuracy, while precision (e.g., technical variation) was robust for the mock community and actual human positive control samples. Technical variation was the lowest for stabilized fecal samples, followed by fecal swab samples, and then oral swab samples. The order of technical variation stability was inverse of DNA concentrations (e.g., highest in stabilized fecal samples), highlighting the importance of DNA concentration in reproducibility and urging caution when analyzing low biomass samples. Coefficients of variation at the genus level also followed the same trend for lower variation with higher DNA concentrations. Technical variation across both sample types and the two human sampling locations was significantly less than the observed biological variation. Overall, this research providing comparisons between technical and biological variation, highlights the importance of using positive controls, and provides semi-quantified data to better understand variation introduced by sequencing runs. KEY POINTS: • Mock community and positive control accuracy were lower than precision. • Samples with lower DNA concentration had increased technical variation across sequencing runs. • Biological variation was significantly higher than technical variation due to sequencing runs.
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Affiliation(s)
- Andrew J Hoisington
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA.
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA.
- Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson Air Force Base, Dayton, OH, USA.
| | - Christopher E Stamper
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA
| | | | - Christopher A Lowry
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA
- Department of Integrative Physiology, Center for Neuroscience, and Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO, USA
| | - Lisa A Brenner
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA
- Department of Psychiatry, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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4
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Ohdera AH, Mansbridge M, Wang M, Naydenkov P, Kamel B, Goentoro L. The microbiome of a Pacific moon jellyfish Aurelia coerulea. PLoS One 2024; 19:e0298002. [PMID: 38635587 PMCID: PMC11025843 DOI: 10.1371/journal.pone.0298002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/16/2024] [Indexed: 04/20/2024] Open
Abstract
The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea, first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca. Mariplasma lunae (Mollicutes) and Ca. Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca. Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.
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Affiliation(s)
- Aki H. Ohdera
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
- National Museum of Natural History, Smithsonian Institute, Washington, D.C., United States of America
| | | | - Matthew Wang
- Flintridge Preparatory School, La Cañada Flintridge, CA, United States of America
| | - Paulina Naydenkov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Bishoy Kamel
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Lea Goentoro
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
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5
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Zong Y, Zhao H, Wang T. mbDecoda: a debiased approach to compositional data analysis for microbiome surveys. Brief Bioinform 2024; 25:bbae205. [PMID: 38701410 PMCID: PMC11066923 DOI: 10.1093/bib/bbae205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Potentially pathogenic or probiotic microbes can be identified by comparing their abundance levels between healthy and diseased populations, or more broadly, by linking microbiome composition with clinical phenotypes or environmental factors. However, in microbiome studies, feature tables provide relative rather than absolute abundance of each feature in each sample, as the microbial loads of the samples and the ratios of sequencing depth to microbial load are both unknown and subject to considerable variation. Moreover, microbiome abundance data are count-valued, often over-dispersed and contain a substantial proportion of zeros. To carry out differential abundance analysis while addressing these challenges, we introduce mbDecoda, a model-based approach for debiased analysis of sparse compositions of microbiomes. mbDecoda employs a zero-inflated negative binomial model, linking mean abundance to the variable of interest through a log link function, and it accommodates the adjustment for confounding factors. To efficiently obtain maximum likelihood estimates of model parameters, an Expectation Maximization algorithm is developed. A minimum coverage interval approach is then proposed to rectify compositional bias, enabling accurate and reliable absolute abundance analysis. Through extensive simulation studies and analysis of real-world microbiome datasets, we demonstrate that mbDecoda compares favorably with state-of-the-art methods in terms of effectiveness, robustness and reproducibility.
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Affiliation(s)
- Yuxuan Zong
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Hongyu Zhao
- SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
- Department of Biostatistics, Yale University, New Haven, CT
| | - Tao Wang
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
- Department of Statistics, Shanghai Jiao Tong University, Shanghai, China
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6
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Metze D, Schnecker J, de Carlan CLN, Bhattarai B, Verbruggen E, Ostonen I, Janssens IA, Sigurdsson BD, Hausmann B, Kaiser C, Richter A. Soil warming increases the number of growing bacterial taxa but not their growth rates. SCIENCE ADVANCES 2024; 10:eadk6295. [PMID: 38394199 PMCID: PMC10889357 DOI: 10.1126/sciadv.adk6295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Biplabi Bhattarai
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Erik Verbruggen
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Ivika Ostonen
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ivan A. Janssens
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Bjarni D. Sigurdsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Hvanneyri, Borgarnes, Iceland
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria
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7
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Wanghu H, Li Y, Huang J, Pu K, Guo F, Zhong P, Wang T, Yuan J, Yu Y, Chen J, Liu J, Chen JJ, Hu C. A novel synthetic nucleic acid mixture for quantification of microbes by mNGS. Microb Genom 2024; 10:001199. [PMID: 38358316 PMCID: PMC10926700 DOI: 10.1099/mgen.0.001199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) provides considerable advantages in identifying emerging and re-emerging, difficult-to-detect and co-infected pathogens; however, the clinical application of mNGS remains limited primarily due to the lack of quantitative capabilities. This study introduces a novel approach, KingCreate-Quantification (KCQ) system, for quantitative analysis of microbes in clinical specimens by mNGS, which co-sequence the target DNA extracted from the specimens along with a set of synthetic dsDNA molecules used as Internal-Standard (IS). The assay facilitates the conversion of microbial reads into their copy numbers based on IS reads utilizing a mathematical model proposed in this study. The performance of KCQ was systemically evaluated using commercial mock microbes with varying IS input amounts, different proportions of human genomic DNA, and at varying amounts of sequence analysis data. Subsequently, KCQ was applied in microbial quantitation in 36 clinical specimens including blood, bronchoalveolar lavage fluid, cerebrospinal fluid and oropharyngeal swabs. A total of 477 microbe genetic fragments were screened using the bioinformatic system. Of these 83 fragments were quantitatively compared with digital droplet PCR (ddPCR), revealing a correlation coefficient of 0.97 between the quantitative results of KCQ and ddPCR. Our study demonstrated that KCQ presents a practical approach for the quantitative analysis of microbes by mNGS in clinical samples.
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Affiliation(s)
- Hailing Wanghu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Yingzhen Li
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jin Huang
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Kangze Pu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Fengming Guo
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Peiwen Zhong
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Ting Wang
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jianying Yuan
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Yan Yu
- Changsha KingMed Diagnostics Group Co., Ltd., Changsha, Huna, 410000, PR China
| | - Jiachang Chen
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jun Liu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jason J. Chen
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, 511436, PR China
| | - Chaohui Hu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, 511436, PR China
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8
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Lyu X, Nuhu M, Candry P, Wolfanger J, Betenbaugh M, Saldivar A, Zuniga C, Wang Y, Shrestha S. Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass. J Ind Microbiol Biotechnol 2024; 51:kuae025. [PMID: 39003244 PMCID: PMC11287213 DOI: 10.1093/jimb/kuae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024]
Abstract
Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted. ONE-SENTENCE SUMMARY This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.
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Affiliation(s)
- Xuejiao Lyu
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mujaheed Nuhu
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Pieter Candry
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Jenna Wolfanger
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexis Saldivar
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Cristal Zuniga
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Ying Wang
- Department of Soil and Crop Sciences, Texas A&M University, TX 77843, USA
| | - Shilva Shrestha
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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9
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McGuinness AJ, Stinson LF, Snelson M, Loughman A, Stringer A, Hannan AJ, Cowan CSM, Jama HA, Caparros-Martin JA, West ML, Wardill HR. From hype to hope: Considerations in conducting robust microbiome science. Brain Behav Immun 2024; 115:120-130. [PMID: 37806533 DOI: 10.1016/j.bbi.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/14/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023] Open
Abstract
Microbiome science has been one of the most exciting and rapidly evolving research fields in the past two decades. Breakthroughs in technologies including DNA sequencing have meant that the trillions of microbes (particularly bacteria) inhabiting human biological niches (particularly the gut) can be profiled and analysed in exquisite detail. This microbiome profiling has profound impacts across many fields of research, especially biomedical science, with implications for how we understand and ultimately treat a wide range of human disorders. However, like many great scientific frontiers in human history, the pioneering nature of microbiome research comes with a multitude of challenges and potential pitfalls. These include the reproducibility and robustness of microbiome science, especially in its applications to human health outcomes. In this article, we address the enormous promise of microbiome science and its many challenges, proposing constructive solutions to enhance the reproducibility and robustness of research in this nascent field. The optimisation of microbiome science spans research design, implementation and analysis, and we discuss specific aspects such as the importance of ecological principals and functionality, challenges with microbiome-modulating therapies and the consideration of confounding, alternative options for microbiome sequencing, and the potential of machine learning and computational science to advance the field. The power of microbiome science promises to revolutionise our understanding of many diseases and provide new approaches to prevention, early diagnosis, and treatment.
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Affiliation(s)
- Amelia J McGuinness
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Matthew Snelson
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC, Australia.
| | - Amy Loughman
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Andrea Stringer
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Anthony J Hannan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Australia
| | | | - Hamdi A Jama
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC, Australia
| | | | - Madeline L West
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Hannah R Wardill
- Supportive Oncology Research Group, Precision Medicine (Cancer), South Australian Health and Medical Research Institute (SAHMRI), University of Adelaide, Adelaide, South Australia, Australia
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10
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Ou Y, Rots E, Belzer C, Smidt H, de Weerth C. Gut microbiota and child behavior in early puberty: does child sex play a role? Gut Microbes 2023; 15:2278222. [PMID: 37943628 PMCID: PMC10731618 DOI: 10.1080/19490976.2023.2278222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
A growing number of studies have indicated relations between the gut microbiota and mental health. However, to date, there is a scarcity of microbiota studies in community samples in early puberty. The current preregistered study (https://osf.io/wu2vt) investigated gut microbiota composition in relation to sex in low-risk children and explored behavioral associations with gut microbiota composition and metabolites in the same samples, together with the potential role of sex. Fecal microbiota composition was analyzed in 12-year-old children (N = 137) by 16S rRNA gene sequencing and quantitative PCR. Modest sex differences were observed in beta diversity. Generalized linear models showed consistent behavioral relations to both relative and absolute abundances of individual taxa, including positive associations between Parasutterella and mother-reported internalizing behavior, and negative associations between Odoribacter and mother-reported externalizing behavior. Additionally, Prevotella 9 was positively related to mother-reported externalizing behavior, confirming earlier findings on the same cohort at 5 years of age. Sex-related differences were found in behavioral relations to Ruminiclostridium 5, Alistipes, Streptococcus, Ruminiclostridium 9, Ruminococcaceae UCG-5, and Dialister, for relative abundances, as well as to Family XIII AD3011 group and an unidentified bacterium within the Tenericutes, for absolute abundances. Limited behavioral relations were observed regarding alpha diversity and fecal metabolites. Our findings describe links between the gut microbiota and child behavior, together with differences between child sexes in these relations, in low-risk early pubertal children. Importantly, this study confirmed earlier findings in this cohort of positive relations between Prevotella 9 and externalizing behavior at age 10 years. Results also show the merit of including absolute abundances in microbiota studies.
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Affiliation(s)
- Yangwenshan Ou
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eline Rots
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Carolina de Weerth
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
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11
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Hellysaz A, Nordgren J, Neijd M, Martí M, Svensson L, Hagbom M. Microbiota do not restrict rotavirus infection of colon. J Virol 2023; 97:e0152623. [PMID: 37905839 PMCID: PMC10688362 DOI: 10.1128/jvi.01526-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Alterations of the gut microbiome can have significant effects on gastrointestinal homeostasis leading to various diseases and symptoms. Increased understanding of rotavirus infection in relation to the microbiota can provide better understanding on how microbiota can be used for clinical prevention as well as treatment strategies. Our volumetric 3D imaging data show that antibiotic treatment and its consequent reduction of the microbial load does not alter the extent of rotavirus infection of enterocytes in the small intestine and that restriction factors other than bacteria limit the infection of colonocytes.
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Affiliation(s)
- Arash Hellysaz
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johan Nordgren
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Magdalena Neijd
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Magalí Martí
- Division of Children’s and Women’s Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lennart Svensson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Division of Infectious Diseases, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Marie Hagbom
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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12
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Sisk-Hackworth L, Brown J, Sau L, Levine AA, Tam LYI, Ramesh A, Shah RS, Kelley-Thackray ET, Wang S, Nguyen A, Kelley ST, Thackray VG. Genetic hypogonadal mouse model reveals niche-specific influence of reproductive axis and sex on intestinal microbial communities. Biol Sex Differ 2023; 14:79. [PMID: 37932822 PMCID: PMC10626657 DOI: 10.1186/s13293-023-00564-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The gut microbiome has been linked to many diseases with sex bias including autoimmune, metabolic, neurological, and reproductive disorders. While numerous studies report sex differences in fecal microbial communities, the role of the reproductive axis in this differentiation is unclear and it is unknown how sex differentiation affects microbial diversity in specific regions of the small and large intestine. METHODS We used a genetic hypogonadal mouse model that does not produce sex steroids or go through puberty to investigate how sex and the reproductive axis impact bacterial diversity within the intestine. Using 16S rRNA gene sequencing, we analyzed alpha and beta diversity and taxonomic composition of fecal and intestinal communities from the lumen and mucosa of the duodenum, ileum, and cecum from adult female (n = 20) and male (n = 20) wild-type mice and female (n = 17) and male (n = 20) hypogonadal mice. RESULTS Both sex and reproductive axis inactivation altered bacterial composition in an intestinal section and niche-specific manner. Hypogonadism was significantly associated with bacteria from the Bacteroidaceae, Eggerthellaceae, Muribaculaceae, and Rikenellaceae families, which have genes for bile acid metabolism and mucin degradation. Microbial balances between males and females and between hypogonadal and wild-type mice were also intestinal section-specific. In addition, we identified 3 bacterial genera (Escherichia Shigella, Lachnoclostridium, and Eggerthellaceae genus) with higher abundance in wild-type female mice throughout the intestinal tract compared to both wild-type male and hypogonadal female mice, indicating that activation of the reproductive axis leads to female-specific differentiation of the gut microbiome. Our results also implicated factors independent of the reproductive axis (i.e., sex chromosomes) in shaping sex differences in intestinal communities. Additionally, our detailed profile of intestinal communities showed that fecal samples do not reflect bacterial diversity in the small intestine. CONCLUSIONS Our results indicate that sex differences in the gut microbiome are intestinal niche-specific and that sampling feces or the large intestine may miss significant sex effects in the small intestine. These results strongly support the need to consider both sex and reproductive status when studying the gut microbiome and while developing microbial-based therapies.
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Affiliation(s)
- Laura Sisk-Hackworth
- University of California San Diego, La Jolla, CA, USA
- San Diego State University, San Diego, CA, USA
| | - Jada Brown
- University of California San Diego, La Jolla, CA, USA
| | - Lillian Sau
- University of California San Diego, La Jolla, CA, USA
| | | | | | | | - Reeya S Shah
- University of California San Diego, La Jolla, CA, USA
| | | | - Sophia Wang
- University of California San Diego, La Jolla, CA, USA
| | - Anita Nguyen
- University of California San Diego, La Jolla, CA, USA
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13
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Epp Schmidt D, Maul JE, Yarwood SA. Quantitative Amplicon Sequencing Is Necessary to Identify Differential Taxa and Correlated Taxa Where Population Sizes Differ. MICROBIAL ECOLOGY 2023; 86:2790-2801. [PMID: 37563275 DOI: 10.1007/s00248-023-02273-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
High-throughput, multiplexed-amplicon sequencing has become a core tool for understanding environmental microbiomes. As researchers have widely adopted sequencing, many open-source analysis pipelines have been developed to compare microbiomes using compositional analysis frameworks. However, there is increasing evidence that compositional analyses do not provide the information necessary to accurately interpret many community assembly processes. This is especially true when there are large gradients that drive distinct community assembly processes. Recently, sequencing has been combined with Q-PCR (among other sources of total quantitation) to generate "Quantitative Sequencing" (QSeq) data. QSeq more accurately estimates the true abundance of taxa, is a more reliable basis for inferring correlation, and, ultimately, can be more reliably related to environmental data to infer community assembly processes. In this paper, we use a combination of published data sets, synthesis, and empirical modeling to offer guidance for which contexts QSeq is advantageous. As little as 5% variation in total abundance among experimental groups resulted in more accurate inference by QSeq than compositional methods. Compositional methods for differential abundance and correlation unreliably detected patterns in abundance and covariance when there was greater than 20% variation in total abundance among experimental groups. Whether QSeq performs better for beta diversity analysis depends on the question being asked, and the analytic strategy (e.g., what distance metric is being used); for many questions and methods, QSeq and compositional analysis are equivalent for beta diversity analysis. QSeq is especially useful for taxon-specific analysis; QSeq transformation and analysis should be the default for answering taxon-specific questions of amplicon sequence data. Publicly available bioinformatics pipelines should incorporate support for QSeq transformation and analysis.
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Affiliation(s)
| | - Jude E Maul
- United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
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14
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Wu-Woods NJ, Barlow JT, Trigodet F, Shaw DG, Romano AE, Jabri B, Eren AM, Ismagilov RF. Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples. Nat Methods 2023; 20:1672-1682. [PMID: 37828152 PMCID: PMC10885704 DOI: 10.1038/s41592-023-02025-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 08/27/2023] [Indexed: 10/14/2023]
Abstract
Host-microbe interactions have been linked to health and disease states through the use of microbial taxonomic profiling, mostly via 16S ribosomal RNA gene sequencing. However, many mechanistic insights remain elusive, in part because studying the genomes of microbes associated with mammalian tissue is difficult due to the high ratio of host to microbial DNA in such samples. Here we describe a microbial-enrichment method (MEM), which we demonstrate on a wide range of sample types, including saliva, stool, intestinal scrapings, and intestinal mucosal biopsies. MEM enabled high-throughput characterization of microbial metagenomes from human intestinal biopsies by reducing host DNA more than 1,000-fold with minimal microbial community changes (roughly 90% of taxa had no significant differences between MEM-treated and untreated control groups). Shotgun sequencing of MEM-treated human intestinal biopsies enabled characterization of both high- and low-abundance microbial taxa, pathways and genes longitudinally along the gastrointestinal tract. We report the construction of metagenome-assembled genomes directly from human intestinal biopsies for bacteria and archaea at relative abundances as low as 1%. Analysis of metagenome-assembled genomes reveals distinct subpopulation structures between the small and large intestine for some taxa. MEM opens a path for the microbiome field to acquire deeper insights into host-microbe interactions by enabling in-depth characterization of host-tissue-associated microbial communities.
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Affiliation(s)
- Natalie J Wu-Woods
- Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Jacob T Barlow
- Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Dustin G Shaw
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Committee on Immunology, The University of Chicago, Chicago, IL, USA
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Anna E Romano
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Committee on Immunology, The University of Chicago, Chicago, IL, USA
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Alfred-Wegener-Institute for Marine and Polar Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Rustem F Ismagilov
- Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA.
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, USA.
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15
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Metze D, Schnecker J, Canarini A, Fuchslueger L, Koch BJ, Stone BW, Hungate BA, Hausmann B, Schmidt H, Schaumberger A, Bahn M, Kaiser C, Richter A. Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions. Nat Commun 2023; 14:5895. [PMID: 37736743 PMCID: PMC10516970 DOI: 10.1038/s41467-023-41524-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Benjamin J Koch
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Schaumberger
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria.
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16
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Abstract
A massive number of microorganisms, belonging to different species, continuously divide inside the guts of animals and humans. The large size of these communities and their rapid division times imply that we should be able to watch microbial evolution in the gut in real time, in a similar manner to what has been done in vitro. Here, we review recent findings on how natural selection shapes intrahost evolution (also known as within-host evolution), with a focus on the intestines of mice and humans. The microbiota of a healthy host is not as static as initially thought from the information measured at only one genomic marker. Rather, the genomes of each gut-colonizing species can be highly dynamic, and such dynamism seems to be related to the microbiota species diversity. Genetic and bioinformatic tools, and analysis of time series data, allow quantification of the selection strength on emerging mutations and horizontal transfer events in gut ecosystems. The drivers and functional consequences of gut evolution can now begin to be grasped. The rules of this intrahost microbiota evolution, and how they depend on the biology of each species, need to be understood for more effective development of microbiota therapies to help maintain or restore host health.
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Affiliation(s)
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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17
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De Tomassi A, Reiter A, Reiger M, Rauer L, Rohayem R, Ck-Care Study Group, Traidl-Hoffmann C, Neumann AU, Hülpüsch C. Combining 16S Sequencing and qPCR Quantification Reveals Staphylococcus aureus Driven Bacterial Overgrowth in the Skin of Severe Atopic Dermatitis Patients. Biomolecules 2023; 13:1030. [PMID: 37509067 PMCID: PMC10377005 DOI: 10.3390/biom13071030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/11/2023] [Accepted: 06/18/2023] [Indexed: 07/30/2023] Open
Abstract
Atopic dermatitis (AD) is an inflammatory skin disease with a microbiome dysbiosis towards a high relative abundance of Staphylococcus aureus. However, information is missing on the actual bacterial load on AD skin, which may affect the cell number driven release of pathogenic factors. Here, we combined the relative abundance results obtained by next-generation sequencing (NGS, 16S V1-V3) with bacterial quantification by targeted qPCR (total bacterial load = 16S, S. aureus = nuc gene). Skin swabs were sampled cross-sectionally (n = 135 AD patients; n = 20 healthy) and longitudinally (n = 6 AD patients; n = 6 healthy). NGS and qPCR yielded highly inter-correlated S. aureus relative abundances and S. aureus cell numbers. Additionally, intra-individual differences between body sides, skin status, and consecutive timepoints were also observed. Interestingly, a significantly higher total bacterial load, in addition to higher S. aureus relative abundance and cell numbers, was observed in AD patients in both lesional and non-lesional skin, as compared to healthy controls. Moreover, in the lesional skin of AD patients, higher S. aureus cell numbers significantly correlated with the higher total bacterial load. Furthermore, significantly more severe AD patients presented with higher S. aureus cell number and total bacterial load compared to patients with mild or moderate AD. Our results indicate that severe AD patients exhibit S. aureus driven increased bacterial skin colonization. Overall, bacterial quantification gives important insights in addition to microbiome composition by sequencing.
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Affiliation(s)
- Amedeo De Tomassi
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
| | - Anna Reiter
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
| | - Matthias Reiger
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
| | - Luise Rauer
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Zentrum München, 86156 Augsburg, Germany
- Environmental Medicine, Technical University of Munich, 86156 Augsburg, Germany
| | - Robin Rohayem
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
| | - Ck-Care Study Group
- CK CARE, Christine-Kühne Center for Allergy Research and Education, 7265 Davos, Switzerland
| | - Claudia Traidl-Hoffmann
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Zentrum München, 86156 Augsburg, Germany
- Environmental Medicine, Technical University of Munich, 86156 Augsburg, Germany
- CK CARE, Christine-Kühne Center for Allergy Research and Education, 7265 Davos, Switzerland
- ZIEL-Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Avidan U Neumann
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Zentrum München, 86156 Augsburg, Germany
- CK CARE, Christine-Kühne Center for Allergy Research and Education, 7265 Davos, Switzerland
| | - Claudia Hülpüsch
- Environmental Medicine, Faculty of Medicine, University of Augsburg, 86156 Augsburg, Germany
- Environmental Medicine, Technical University of Munich, 86156 Augsburg, Germany
- CK CARE, Christine-Kühne Center for Allergy Research and Education, 7265 Davos, Switzerland
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18
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Münch PC, Eberl C, Woelfel S, Ring D, Fritz A, Herp S, Lade I, Geffers R, Franzosa EA, Huttenhower C, McHardy AC, Stecher B. Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects. Cell Host Microbe 2023; 31:1007-1020.e4. [PMID: 37279755 DOI: 10.1016/j.chom.2023.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 03/11/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023]
Abstract
Bacteria can evolve to withstand a wide range of antibiotics (ABs) by using various resistance mechanisms. How ABs affect the ecology of the gut microbiome is still poorly understood. We investigated strain-specific responses and evolution during repeated AB perturbations by three clinically relevant ABs, using gnotobiotic mice colonized with a synthetic bacterial community (oligo-mouse-microbiota). Over 80 days, we observed resilience effects at the strain and community levels, and we found that they were correlated with modulations of the estimated growth rate and levels of prophage induction as determined from metagenomics data. Moreover, we tracked mutational changes in the bacterial populations, and this uncovered clonal expansion and contraction of haplotypes and selection of putative AB resistance-conferring SNPs. We functionally verified these mutations via reisolation of clones with increased minimum inhibitory concentration (MIC) of ciprofloxacin and tetracycline from evolved communities. This demonstrates that host-associated microbial communities employ various mechanisms to respond to selective pressures that maintain community stability.
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Affiliation(s)
- Philipp C Münch
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38124, Germany; Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany; Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Claudia Eberl
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Simon Woelfel
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Diana Ring
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Adrian Fritz
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38124, Germany
| | - Simone Herp
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Iris Lade
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, 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
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38124, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
| | - Bärbel Stecher
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig-Maximilian University of Munich, 80336 Munich, Germany; German Center for Infection Research, Partner site LMU Munich, Munich, Germany.
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19
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Zhang Y, Chen T, Hao X, Hu Y, Chen M, Zhang D, Cai H, Luo J, Kong L, Huang S, Huang Y, Yang N, Liu R, Li Q, Yuan C, Wang C, Zhou H, Huang W, Zhang W. Mapping the regulatory effects of herbal organic compounds on gut bacteria. Pharmacol Res 2023; 193:106804. [PMID: 37244386 DOI: 10.1016/j.phrs.2023.106804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Affiliation(s)
- Yulong Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Ting Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Xiaoqing Hao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, P. R. China; The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, P. R. China
| | - Yuanjia Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, P. R. China; DPM, Faculty of Health Sciences, University of Macau, Macao SAR 999078, P. R. China
| | - Manyun Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Daiyan Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, P. R. China
| | - Hong Cai
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, P. R. China
| | - Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Sutianzi Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, P. R. China
| | - Yuanfei Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, P. R. China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, P. R. China
| | - Nian Yang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, P. R. China
| | - Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, P. R. China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, P. R. China
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, P. R. China; The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, P. R. China
| | - Chunsu Yuan
- Tang Center of Herbal Medicine Research and Department of Anesthesia & Critical Care, University of Chicago, Chicago, IL 60637, USA
| | - Chongzhi Wang
- Tang Center of Herbal Medicine Research and Department of Anesthesia & Critical Care, University of Chicago, Chicago, IL 60637, USA
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, P. R. China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, P. R. China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, P. R. China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, P. R. China.
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, P. R. China; The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, P. R. China; Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha 410006, P. R. China.
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20
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李 政, 彭 显. [Application of Droplet-Based Microfluidics in Microbial Research]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:673-678. [PMID: 37248604 PMCID: PMC10475413 DOI: 10.12182/20230560303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Droplet-based microfluidics is a technology that generates and manipulates highly uniform droplets, ranging from picoliter to nanoliter droplets, in microchannels under precise control. In biological research, each droplet can be used to encapsulate a small group of cells or even a single cell, and then serve as an individual container for biochemical reaction, which is well suited for high-throughput and high-resolution biochemical analysis. In the field of microbial research, from cultivation and identification of microbes to the investigation of the spatiotemporal dynamics of microbial communities, from precise quantitation of microbiota to systematic study of microbial interactions, and from the isolation of rare and unculturable microbes to the development of genetically engineered strains, droplet microfluidic technology has played an important promotional role in all these aspects. Droplet microfluidics shows potential for becoming a basic tool for exploring single-cell microbes in microbiological research. In this review, we gave a brief overview of the technical basis of droplet microfluidics. Then, we presented its latest applications in microbial research and had some discussions, aiming to provide a reference for relevant research on microorganisms.
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Affiliation(s)
- 政毅 李
- 口腔疾病研究国家重点实验室 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 显 彭
- 口腔疾病研究国家重点实验室 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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21
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Couvillion SP, Danczak RE, Cao X, Yang Q, Keerthisinghe TP, McClure RS, Bitounis D, Burnet MC, Fansler SJ, Richardson RE, Fang M, Qian WJ, Demokritou P, Thrall BD. Graphene oxide exposure alters gut microbial community composition and metabolism in an in vitro human model. NANOIMPACT 2023; 30:100463. [PMID: 37060994 DOI: 10.1016/j.impact.2023.100463] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 05/12/2023]
Abstract
Graphene oxide (GO) nanomaterials have unique physicochemical properties that make them highly promising for biomedical, environmental, and agricultural applications. There is growing interest in the use of GO and extensive in vitro and in vivo studies have been conducted to assess its nanotoxicity. Although it is known that GO can alter the composition of the gut microbiota in mice and zebrafish, studies on the potential impacts of GO on the human gut microbiome are largely lacking. This study addresses an important knowledge gap by investigating the impact of GO exposure- at low (25 mg/L) and high (250 mg/L) doses under both fed (nutrient rich) and fasted (nutrient deplete) conditions- on the gut microbial communitys' structure and function, using an in vitro model. This model includes simulated oral, gastric, small intestinal phase digestion of GO followed by incubation in a colon bioreactor. 16S rRNA amplicon sequencing revealed that GO exposure resulted in a restructuring of community composition. 25 mg/L GO induced a marked decrease in the Bacteroidota phylum and increased the ratio of Firmicutes to Bacteroidota (F/B). Untargeted metabolomics on the supernatants indicated that 25 mg/L GO impaired microbial utilization and metabolism of substrates (amino acids, carbohydrate metabolites) and reduced production of beneficial microbial metabolites such as 5-hydroxyindole-3-acetic acid and GABA. Exposure to 250 mg/L GO resulted in community composition and metabolome profiles that were very similar to the controls that lacked both GO and digestive enzymes. Differential abundance analyses revealed that 3 genera from the phylum Bacteroidota (Bacteroides, Dysgonomonas, and Parabacteroides) were more abundant after 250 mg/L GO exposure, irrespective of feed state. Integrative correlation network analysis indicated that the phylum Bacteroidota showed strong positive correlations to multiple microbial metabolites including GABA and 3-indoleacetic acid, are much larger number of correlations compared to other phyla. These results show that GO exposure has a significant impact on gut microbial community composition and metabolism at both low and high GO concentrations.
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Affiliation(s)
- Sneha P Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Robert E Danczak
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xiaoqiong Cao
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA
| | - Qin Yang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Tharushi P Keerthisinghe
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Ryan S McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Dimitrios Bitounis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rachel E Richardson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA.
| | - Brian D Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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22
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Boshuizen HC, Te Beest DE. Pitfalls in the statistical analysis of microbiome amplicon sequencing data. Mol Ecol Resour 2023; 23:539-548. [PMID: 36330663 DOI: 10.1111/1755-0998.13730] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Microbiome data are characterized by several aspects that make them challenging to analyse statistically: they are compositional, high dimensional and rich in zeros. A large array of statistical methods exist to analyse these data. Some are borrowed from other fields, such as ecology or RNA-sequencing, while others are custom-made for microbiome data. The large range of available methods, and which is continuously expanding, means that researchers have to invest considerable effort in choosing what method(s) to apply. In this paper we list 14 statistical methods or approaches that we think should be generally avoided. In several cases this is because we believe the assumptions behind the method are unlikely to be met for microbiome data. In other cases we see methods that are used in ways they are not intended to be used. We believe researchers would be helped by more critical evaluations of existing methods, as not all methods in use are suitable or have been sufficiently reviewed. We hope this paper contributes to a critical discussion on what methods are appropriate to use in the analysis of microbiome data.
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Affiliation(s)
| | - Dennis E Te Beest
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
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23
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Mi K, Xu Y, Li Y, Liu X. QMD: A new method to quantify microbial absolute abundance differences between groups. IMETA 2023; 2:e78. [PMID: 38868342 PMCID: PMC10989753 DOI: 10.1002/imt2.78] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/07/2022] [Accepted: 12/06/2022] [Indexed: 06/14/2024]
Abstract
A new method, quantification of microbial absolute abundance differences (QMD), was proposed to estimate the microbial absolute abundance changes of each taxon under different conditions based on the microbial relative abundance. Compared with other methods, QMD displayed greater confidence in understanding microbiome dynamics between groups. We also provide QMD software to investigate common deviations and achieve a better understanding of microbiota changes under different conditions.
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Affiliation(s)
- Kai Mi
- State Key Laboratory of Reproductive Medicine, Center of Global HealthNanjing Medical UniversityNanjingChina
- Department of Pathogen Biology‐Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province Key Laboratory of Human Functional Genomics of Jiangsu ProvinceNanjing Medical UniversityNanjingChina
| | - Yuyu Xu
- State Key Laboratory of Reproductive Medicine, Center of Global HealthNanjing Medical UniversityNanjingChina
- Department of Pathogen Biology‐Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province Key Laboratory of Human Functional Genomics of Jiangsu ProvinceNanjing Medical UniversityNanjingChina
| | - Yiqing Li
- State Key Laboratory of Reproductive Medicine, Center of Global HealthNanjing Medical UniversityNanjingChina
- Department of Pathogen Biology‐Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province Key Laboratory of Human Functional Genomics of Jiangsu ProvinceNanjing Medical UniversityNanjingChina
| | - Xingyin Liu
- State Key Laboratory of Reproductive Medicine, Center of Global HealthNanjing Medical UniversityNanjingChina
- Department of Pathogen Biology‐Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province Key Laboratory of Human Functional Genomics of Jiangsu ProvinceNanjing Medical UniversityNanjingChina
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversityNanjingChina
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24
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Gaire TN, Scott HM, Noyes NR, Ericsson AC, Tokach MD, Menegat MB, Vinasco J, Roenne B, Ray T, Nagaraja TG, Volkova VV. Age influences the temporal dynamics of microbiome and antimicrobial resistance genes among fecal bacteria in a cohort of production pigs. Anim Microbiome 2023; 5:2. [PMID: 36624546 PMCID: PMC9830919 DOI: 10.1186/s42523-022-00222-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The pig gastrointestinal tract hosts a diverse microbiome, which can serve to select and maintain a reservoir of antimicrobial resistance genes (ARG). Studies suggest that the types and quantities of antimicrobial resistance (AMR) in fecal bacteria change as the animal host ages, yet the temporal dynamics of AMR within communities of bacteria in pigs during a full production cycle remains largely unstudied. RESULTS A longitudinal study was performed to evaluate the dynamics of fecal microbiome and AMR in a cohort of pigs during a production cycle; from birth to market age. Our data showed that piglet fecal microbial communities assemble rapidly after birth and become more diverse with age. Individual piglet fecal microbiomes progressed along similar trajectories with age-specific community types/enterotypes and showed a clear shift from E. coli/Shigella-, Fusobacteria-, Bacteroides-dominant enterotypes to Prevotella-, Megaspheara-, and Lactobacillus-dominated enterotypes with aging. Even when the fecal microbiome was the least diverse, the richness of ARGs, quantities of AMR gene copies, and counts of AMR fecal bacteria were highest in piglets at 2 days of age; subsequently, these declined over time, likely due to age-related competitive changes in the underlying microbiome. ARGs conferring resistance to metals and multi-compound/biocides were detected predominately at the earliest sampled ages. CONCLUSIONS The fecal microbiome and resistome-along with evaluated descriptors of phenotypic antimicrobial susceptibility of fecal bacteria-among a cohort of pigs, demonstrated opposing trajectories in diversity primarily driven by the aging of pigs.
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Affiliation(s)
- Tara N. Gaire
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - H. Morgan Scott
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Noelle R. Noyes
- grid.17635.360000000419368657Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108 USA
| | - Aaron C. Ericsson
- grid.134936.a0000 0001 2162 3504Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211 USA
| | - Michael D. Tokach
- grid.36567.310000 0001 0737 1259Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506 USA
| | - Mariana B. Menegat
- grid.36567.310000 0001 0737 1259Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506 USA
| | - Javier Vinasco
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Boyd Roenne
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - Tui Ray
- grid.17635.360000000419368657Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108 USA
| | - T. G. Nagaraja
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - Victoriya V. Volkova
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
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25
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Earley ZM, Lisicka W, Sifakis JJ, Aguirre-Gamboa R, Kowalczyk A, Barlow JT, Shaw DG, Discepolo V, Tan IL, Gona S, Ernest JD, Matzinger P, Barreiro LB, Morgun A, Bendelac A, Ismagilov RF, Shulzhenko N, Riesenfeld SJ, Jabri B. GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology. Immunity 2023; 56:43-57.e10. [PMID: 36630917 PMCID: PMC10262782 DOI: 10.1016/j.immuni.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023]
Abstract
There is growing recognition that regionalization of bacterial colonization and immunity along the intestinal tract has an important role in health and disease. Yet, the mechanisms underlying intestinal regionalization and its dysregulation in disease are not well understood. This study found that regional epithelial expression of the transcription factor GATA4 controls bacterial colonization and inflammatory tissue immunity in the proximal small intestine by regulating retinol metabolism and luminal IgA. Furthermore, in mice without jejunal GATA4 expression, the commensal segmented filamentous bacteria promoted pathogenic inflammatory immune responses that disrupted barrier function and increased mortality upon Citrobacter rodentium infection. In celiac disease patients, low GATA4 expression was associated with metabolic alterations, mucosal Actinobacillus, and increased IL-17 immunity. Taken together, these results reveal broad impacts of GATA4-regulated intestinal regionalization on bacterial colonization and tissue immunity, highlighting an elaborate interdependence of intestinal metabolism, immunity, and microbiota in homeostasis and disease.
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Affiliation(s)
- Zachary M Earley
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Wioletta Lisicka
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Joseph J Sifakis
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | | | - Anita Kowalczyk
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jacob T Barlow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dustin G Shaw
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Valentina Discepolo
- Department of Medical Translational Sciences and European Laboratory for the Investigation of Food Induced Diseases, University of Federico II, Naples, Italy
| | - Ineke L Tan
- Department of Gastroenterology and Hepatology, University of Groningen and University of Medical Center Groningen, Groningen, the Netherlands
| | - Saideep Gona
- Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Jordan D Ernest
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Polly Matzinger
- Ghost Lab, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Rustem F Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Natalia Shulzhenko
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | - Samantha J Riesenfeld
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| | - Bana Jabri
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Department of Pathology, University of Chicago, Chicago, IL, USA; Department of Pediatrics, University of Chicago, Chicago, IL, USA.
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26
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synDNA-a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing. mSystems 2022; 7:e0044722. [PMID: 36317886 PMCID: PMC9765022 DOI: 10.1128/msystems.00447-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microbiome studies have the common goal of determining which microbial taxa are present, respond to specific conditions, or promote phenotypic changes in the host. Most of these studies rely on relative abundance measurements to drive conclusions. Inherent limitations of relative values are the inability to determine whether an individual taxon is more or less abundant and the magnitude of this change between the two samples. These limitations can be overcome by using absolute abundance quantifications, which can allow for a more complete understanding of community dynamics by measuring variations in total microbial loads. Obtaining absolute abundance measurements is still technically challenging. Here, we developed synthetic DNA (synDNA) spike-ins that enable precise and cost-effective absolute quantification of microbiome data by adding defined amounts of synDNAs to the samples. We designed 10 synDNAs with the following features: 2,000-bp length, variable GC content (26, 36, 46, 56, or 66% GC), and negligible identity to sequences found in the NCBI database. Dilution pools were generated by mixing the 10 synDNAs at different concentrations. Shotgun metagenomic sequencing showed that the pools of synDNAs with different percentages of GC efficiently reproduced the serial dilution, showing high correlation (r = 0.96; R2 ≥ 0.94) and significance (P < 0.01). Furthermore, we demonstrated that the synDNAs can be used as DNA spike-ins to generate linear models and predict with high accuracy the absolute number of bacterial cells in complex microbial communities. IMPORTANCE The synDNAs designed in this study enable accurate and reproducible measurements of absolute amount and fold changes of bacterial species in complex microbial communities. The method proposed here is versatile and promising as it can be applied to bacterial communities or genomic features like genes and operons, in addition to being easily adaptable by other research groups at a low cost. We also made the synDNAs' sequences and the plasmids available to encourage future application of the proposed method in the study of microbial communities.
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27
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Shen J, McFarland AG, Blaustein RA, Rose LJ, Perry-Dow KA, Moghadam AA, Hayden MK, Young VB, Hartmann EM. An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics. MICROBIOME 2022; 10:206. [PMID: 36457108 PMCID: PMC9716758 DOI: 10.1186/s40168-022-01412-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Effective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but are currently challenged by several limitations: (1) they are not powerful enough to extract valid signals out of the background noise for low-biomass samples, (2) they do not distinguish between viable and nonviable organisms, and (3) they do not reveal the microbial load quantitatively. An additional practical challenge towards a robust pipeline is the inability to efficiently allocate sequencing resources a priori. Assessment of sequencing depth is generally practiced post hoc, if at all, for most microbiome studies, regardless of the sample type. This practice is inefficient at best, and at worst, poor sequencing depth jeopardizes the interpretation of study results. To address these challenges, we present a workflow for metagenomics-based environmental surveillance that is appropriate for low-biomass samples, distinguishes viability, is quantitative, and estimates sequencing resources. RESULTS The workflow was developed using a representative microbiome sample, which was created by aggregating 120 surface swabs collected from a medical intensive care unit. Upon evaluating and optimizing techniques as well as developing new modules, we recommend best practices and introduce a well-structured workflow. We recommend adopting liquid-liquid extraction to improve DNA yield and only incorporating whole-cell filtration when the nonbacterial proportion is large. We suggest including propidium monoazide treatment coupled with internal standards and absolute abundance profiling for viability assessment and involving cultivation when demanding comprehensive profiling. We further recommend integrating internal standards for quantification and additionally qPCR when we expect poor taxonomic classification. We also introduce a machine learning-based model to predict required sequencing effort from accessible sample features. The model helps make full use of sequencing resources and achieve desired outcomes. Video Abstract CONCLUSIONS: This workflow will contribute to more accurate and robust environmental surveillance and infection prevention. Lessons gained from this study will also benefit the continuing development of methods in relevant fields.
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Affiliation(s)
- Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA.
| | - Alexander G McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
| | - Ryan A Blaustein
- Department of Nutrition and Food Science, University of Maryland, College Park, USA
| | - Laura J Rose
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Anahid A Moghadam
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, USA
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, The University of Michigan Medical School, Ann Arbor, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
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28
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Yao Z, Zhu Y, Wu Q, Xu Y. Challenges and perspectives of quantitative microbiome profiling in food fermentations. Crit Rev Food Sci Nutr 2022; 64:4995-5015. [PMID: 36412251 DOI: 10.1080/10408398.2022.2147899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.
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Affiliation(s)
- Zhihao Yao
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yang Zhu
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Ma G, Logares R, Xue Y, Yang J. Does filter pore size introduce bias in DNA sequence-based plankton community studies? Front Microbiol 2022; 13:969799. [PMID: 36225356 PMCID: PMC9549009 DOI: 10.3389/fmicb.2022.969799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
The cell size of microbial eukaryotic plankton normally ranges from 0.2 to 200 μm. During the past decade, high-throughput sequencing of DNA has been revolutionizing their study on an unprecedented scale. Nonetheless, it is currently unclear whether we can accurately, effectively, and quantitatively depict the microbial eukaryotic plankton community using size-fractionated filtration combined with environmental DNA (eDNA) molecular methods. Here we assessed the microbial eukaryotic plankton communities with two filtering strategies from two subtropical reservoirs, that is one-step filtration (0.2–200 μm) and size-fractionated filtration (0.2–3 and 3–200 μm). The difference of 18S rRNA gene copy abundance between the two filtering treatments was less than 50% of the 0.2–200 μm microbial eukaryotic community for 95% of the total samples. Although the microbial eukaryotic plankton communities within the 0.2–200 μm and the 0.2–3 and 3–200 μm size fractions had approximately identical 18S rRNA gene copies, there were significant differences in their community composition. Furthermore, our results demonstrate that the systemic bias introduced by size-fractionation filtration has more influence on unique OTUs than shared OTUs, and the significant differences in abundance between the two eukaryotic plankton communities largely occurred in low-abundance OTUs in specific seasons. This work provides new insights into the use of size-fractionation in molecular studies of microbial eukaryotes populating the plankton.
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Affiliation(s)
- Guolin Ma
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Ningbo Observation and Research Station, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Ningbo Observation and Research Station, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
- *Correspondence: Yuanyuan Xue,
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Ningbo Observation and Research Station, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
- Jun Yang,
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Investigating plant-microbe interactions within the root. Arch Microbiol 2022; 204:639. [PMID: 36136275 DOI: 10.1007/s00203-022-03257-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/15/2022] [Accepted: 09/12/2022] [Indexed: 11/02/2022]
Abstract
A diverse lineage of microorganisms inhabits plant roots and interacts with plants in various ways. Further, these microbes communicate and interact with each other within the root microbial community. These symbioses add an array of influences, such as plant growth promotion or indirect protection to the host plant. Omics technology and genetic manipulation have been applied to unravel these interactions. Recent studies probed plants' control over microbes. However, the activity of the root microbial community under host influence has not been elucidated enough. In this mini-review, we discussed the recent advances and limits of omics technology and genetics for dissecting the activity of the root-associated microbial community. These materials may help us formulate the correct experimental plans to capture the entire molecular mechanisms of the plant-microbe interaction.
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Heidrich V, Beule L. Are short-read amplicons suitable for the prediction of microbiome functional potential? A critical perspective. IMETA 2022; 1:e38. [PMID: 38868716 PMCID: PMC10989910 DOI: 10.1002/imt2.38] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/13/2022] [Accepted: 06/18/2022] [Indexed: 06/14/2024]
Abstract
Taxonomic marker gene analysis allows uncovering taxonomic profiles of microbial communities at low cost, making it omnipresent in microbiome research. There is an ever-expanding set of tools to extract further biological information from this kind of data. In this perspective, we enunciate several concerns regarding the biological validity of predicting functional potential from taxonomic profiles, especially when they are generated by short-read sequencing. The taxonomic resolution of marker genes, intragenomic variability of marker genes, and the compositional nature of microbiome data are discussed. Combining actual measurements of microbiome functions with predicted functional potentials is proposed as a powerful approach to better understand microbiome functioning. In this context, the significance of predicted functional potentials for generating and testing hypotheses is highlighted. We argue that functions of microbiomes predicted from microbiome DNA read count data generated by short-read amplicon sequencing should not serve as the only basis to draw biological inferences.
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Affiliation(s)
- Vitor Heidrich
- Centro de Oncologia MolecularHospital Sírio‐LibanêsSão PauloBrazil
- Departamento de Bioquímica, Instituto de QuímicaUniversidade de São PauloSão PauloBrazil
| | - Lukas Beule
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated PlantsInstitute for Ecological Chemistry, Plant Analysis and Stored Product ProtectionBerlinGermany
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Doms S, Fokt H, Rühlemann MC, Chung CJ, Kuenstner A, Ibrahim SM, Franke A, Turner LM, Baines JF. Key features of the genetic architecture and evolution of host-microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice. eLife 2022; 11:75419. [PMID: 35866635 PMCID: PMC9307277 DOI: 10.7554/elife.75419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/14/2022] [Indexed: 12/13/2022] Open
Abstract
Determining the forces that shape diversity in host-associated bacterial communities is critical to understanding the evolution and maintenance of metaorganisms. To gain deeper understanding of the role of host genetics in shaping gut microbial traits, we employed a powerful genetic mapping approach using inbred lines derived from the hybrid zone of two incipient house mouse species. Furthermore, we uniquely performed our analysis on microbial traits measured at the gut mucosal interface, which is in more direct contact with host cells and the immune system. Several mucosa-associated bacterial taxa have high heritability estimates, and interestingly, 16S rRNA transcript-based heritability estimates are positively correlated with cospeciation rate estimates. Genome-wide association mapping identifies 428 loci influencing 120 taxa, with narrow genomic intervals pinpointing promising candidate genes and pathways. Importantly, we identified an enrichment of candidate genes associated with several human diseases, including inflammatory bowel disease, and functional categories including innate immunity and G-protein-coupled receptors. These results highlight key features of the genetic architecture of mammalian host-microbe interactions and how they diverge as new species form. The digestive system, particularly the large intestine, hosts many types of bacteria which together form the gut microbiome. The exact makeup of different bacterial species is specific to an individual, but microbiomes are often more similar between related individuals, and more generally, across related species. Whether this is because individuals share similar environments or similar genetic backgrounds remains unclear. These two factors can be disentangled by breeding different animal lineages – which have different genetic backgrounds while belonging to the same species – and then raising the progeny in the same environment. To investigate this question, Doms et al. studied the genes and microbiomes of mice resulting from breeding strains from multiple locations in a natural hybrid zone between different subspecies. The experiments showed that 428 genetic regions affected the makeup of the microbiome, many of which were known to be associated with human diseases. Further analysis revealed 79 genes that were particularly interesting, as they were involved in recognition and communication with bacteria. These results show how the influence of the host genome on microbiome composition becomes more specialized as animals evolve. Overall, the work by Doms et al. helps to pinpoint the genes that impact the microbiome; this knowledge could be helpful to examine how these interactions contribute to the emergence of conditions such as diabetes or inflammatory bowel disease, which are linked to perturbations in gut bacteria.
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Affiliation(s)
- Shauni Doms
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Hanna Fokt
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Malte Christoph Rühlemann
- Institute for Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany.,Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Cecilia J Chung
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Axel Kuenstner
- Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Saleh M Ibrahim
- Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Sharjah Institute of Medical Research, Sharjah, United Arab Emirates
| | - Andre Franke
- Institute for Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany
| | - Leslie M Turner
- Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
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Roche KE, Mukherjee S. The accuracy of absolute differential abundance analysis from relative count data. PLoS Comput Biol 2022; 18:e1010284. [PMID: 35816553 PMCID: PMC9302745 DOI: 10.1371/journal.pcbi.1010284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/21/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022] Open
Abstract
Concerns have been raised about the use of relative abundance data derived from next generation sequencing as a proxy for absolute abundances. For example, in the differential abundance setting, compositional effects in relative abundance data may give rise to spurious differences (false positives) when considered from the absolute perspective. In practice however, relative abundances are often transformed by renormalization strategies intended to compensate for these effects and the scope of the practical problem remains unclear. We used simulated data to explore the consistency of differential abundance calling on renormalized relative abundances versus absolute abundances and find that, while overall consistency is high, with a median sensitivity (true positive rates) of 0.91 and specificity (1—false positive rates) of 0.89, consistency can be much lower where there is widespread change in the abundance of features across conditions. We confirm these findings on a large number of real data sets drawn from 16S metabarcoding, expression array, bulk RNA-seq, and single-cell RNA-seq experiments, where data sets with the greatest change between experimental conditions are also those with the highest false positive rates. Finally, we evaluate the predictive utility of summary features of relative abundance data themselves. Estimates of sparsity and the prevalence of feature-level change in relative abundance data give reasonable predictions of discrepancy in differential abundance calling in simulated data and can provide useful bounds for worst-case outcomes in real data. Molecular sequence counting is a near-ubituiqous method for taking “snapshots” of the state of biological systems at the molecular level and is applied to problems as diverse as profiling gene expression and characterizing bacterial community composition. However, concerns exist about the interpretation of these data, given they are relative counts. In particular some feature-level differences between samples may be technical, not biological, stemming from compositional effects. Here, we quantify the accuracy of estimates of sample-sample differences made from relative versus “absolute” molecular count data, using a comprehensive simulation strategy and published experimental data. We find the accuracy of difference estimation is high in at least 50% of simulated and real data sets but that low accuracy outcomes are far from rare. Further, we observe similar numbers of these low accuracy cases when using any of several popular methods for estimating differences in biological count data. Our results support the use of complementary reference measures of absolute abundance (like RNA spike-ins) for normalizing next-generation sequencing data. We briefly validate the use of these reference quantities and of stringent effect size thresholds as strategies for mitigating interpretational problems with relative count data.
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Affiliation(s)
- Kimberly E. Roche
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
- * E-mail:
| | - Sayan Mukherjee
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
- Departments of Statistical Science, Mathematics, Computer Science, Biostatistics & Bioinformatics, Duke University, Durham, North Carolina, United States of America
- Center for Scalable Data Analytics and Artificial Intelligence, Universität Leipzig and the Max Planck Institute for Mathematics in the Natural Sciences, Leipzig, Germany
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
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Ramirez-Delgado D, Cicala F, Gonzalez-Sanchez RA, Avalos-Tellez R, Solana-Arellano E, Licea-Navarro A. Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México. PeerJ 2022; 10:e13235. [PMID: 35833012 PMCID: PMC9272818 DOI: 10.7717/peerj.13235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/17/2022] [Indexed: 01/13/2023] Open
Abstract
Background The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities. Methods We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses. Results As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6-V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6-V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.
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Affiliation(s)
| | - Francesco Cicala
- Biomedical Innovation Department, CICESE, Ensenada, Baja California, México
| | | | - Rosalia Avalos-Tellez
- Comisión Nacional de Areas Naturales Protegidas, Secretaría de Medio Ambiente y Recursos Naturales, Bahia de los Angeles, Baja California, México
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35
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Microbial ecology of biofiltration used for producing safe drinking water. Appl Microbiol Biotechnol 2022; 106:4813-4829. [PMID: 35771243 PMCID: PMC9329406 DOI: 10.1007/s00253-022-12013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/24/2022]
Abstract
Abstract
Biofiltration is a water purification technology playing a pivotal role in producing safe drinking water. This technology attracts many interests worldwide due to its advantages, such as no addition of chemicals, a low energy input, and a high removal efficiency of organic compounds, undesirable taste and odours, and pathogens. The current review describes the microbial ecology of three biofiltration processes that are routinely used in drinking water treatment plants, i.e. (i) rapid sand filtration (RSF), (ii) granular activated carbon filtration (GACF), and (iii) slow sand filtration (SSF). We summarised and compared the characteristics, removal performance, and corresponding (newly revealed) mechanisms of the three biofiltration processes. Specifically, the microbial ecology of the different biofilter processes and the role of microbial communities in removing nutrients, organic compounds, and pathogens were reviewed. Finally, we highlight the limitations and challenges in the study of biofiltration in drinking water production, and propose future perspectives for obtaining a comprehensive understanding of the microbial ecology of biofiltration, which is needed to promote and optimise its further application. Key points • Biofilters are composed of complex microbiomes, primarily shaped by water quality. • Conventional biofilters contribute to address safety challenges in drinking water. • Studies may underestimate the active/functional role of microbiomes in biofilters. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12013-x.
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37
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Abstract
We present this protocol using a mouse model to assess the impact of early-life antibiotic exposure on mammalian lifespan and the composition of the gut microbiota over time. We describe longitudinal fecal sampling and health monitoring following early-life antibiotic exposure. We detail DNA extraction and 16S rRNA gene sequencing to longitudinally profile the composition of the fecal microbiota. Finally, we discuss how to address potential confounders such as the stochastic recolonization of the gut microbiota following antibiotic exposure. For complete details on the use and execution of this protocol, please refer to Lynn et al. (2021). We describe a mouse model of early-life antibiotic exposure Bacterial load rapidly depleted following antibiotic exposure but recovers quickly Low diversity, highly variable microbiota colonizes after antibiotic exposure We describe criteria for health monitoring as the mice age
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Yang Y, Che Y, Liu L, Wang C, Yin X, Deng Y, Yang C, Zhang T. Rapid absolute quantification of pathogens and ARGs by nanopore sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:152190. [PMID: 34890655 DOI: 10.1016/j.scitotenv.2021.152190] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
Compositional nature of relative abundance data in the current standard microbiome studies limits microbial dynamics interpretations and cross-sample comparisons. Here, we demonstrate the first rapid (1-h sequencing) method coupling Nanopore metagenomic sequencing with cellular spike-in to facilitate the absolute quantification and removal assessment of pathogens and antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Nanopore sequencing-based quantification results for both simple mock community and complex real environmental samples showed a high consistency with those from the widely-used Illumina and culture-based approaches. Implementing such method, we quantified 46 predominant putative pathogenic species, and 361 ARGs in three WWTP sample sets. Though high log removals of dominant pathogens (2.23 logs) and ARGs (1.98 logs) were achieved, complete removal of all pathogens and ARGs were not achieved. Noticeably, Mycobacterium spp., Clostridium_P perfringens, and Borrelia hermsii exhibited low removal, and 13 ARGs even increased in absolute abundance after the treatment. Our proposed approach manifested its profound ability in providing absolute quantitation information guiding wastewater-based epidemiological surveillance and quantitative risk assessment facilitating microbial hazards management.
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Affiliation(s)
- Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - You Che
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China.
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Pardesi B, Roberton AM, Lee KC, Angert ER, Rosendale DI, Boycheva S, White WL, Clements KD. Distinct microbiota composition and fermentation products indicate functional compartmentalization in the hindgut of a marine herbivorous fish. Mol Ecol 2022; 31:2494-2509. [PMID: 35152505 PMCID: PMC9306998 DOI: 10.1111/mec.16394] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/28/2022]
Abstract
Many marine herbivorous fishes harbour diverse microbial communities in the hindgut that can play important roles in host health and nutrition. Kyphosus sydneyanus is a temperate marine herbivorous fish that feeds predominantly on brown seaweeds. We employed 16S rRNA gene amplicon sequencing and gas chromatography to characterize microbial communities and their metabolites in different hindgut regions of six K. sydneyanus. Measurements were confined to three distal sections of the intestine, labelled III, IV and V from anterior to posterior. A total of 625 operational taxonomic units from 20 phyla and 123 genera were obtained. Bacteroidota, Firmicutes and Proteobacteria were the major phyla in mean relative abundance, which varied along the gut. Firmicutes (76%) was the most dominant group in section III, whereas Bacteroidota (69.3%) dominated section V. Total short‐chain fatty acid (SCFA) concentration was highest in sections IV and V, confirming active fermentation in these two most distal sections. The abundance of Bacteroidota correlated with propionate concentration in section V, while Firmicutes positively correlated with formate in sections III and IV. Acetate levels were highest in sections IV and V, which correlated with abundance of Bacteroidota. Despite differences in gut microbial community composition, SCFA profiles were consistent between individual fish in the different hindgut regions of K. sydneyanus, although proportions of SCFAs differed among gut sections. These findings demonstrate functional compartmentalization of the hindgut microbial community, highlighting the need for regional sampling when interpreting overall microbiome function. These results support previous work suggesting that hindgut microbiota in marine herbivorous fish are important to nutrition in some host species by converting dietary carbohydrates into metabolically useful SCFAs.
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Affiliation(s)
- Bikiran Pardesi
- School of Biological Sciences University of Auckland Auckland New Zealand
| | | | - Kevin C. Lee
- Faculty of Health and Environmental Sciences Auckland University of Technology Auckland New Zealand
| | - Esther R. Angert
- Department of Microbiology Cornell University Ithaca NY 14853 USA
| | - Douglas I. Rosendale
- Plant & Food Research Ltd Palmerston North New Zealand
- Anagenix Ltd Parnell, Auckland 1052 New Zealand
| | - Svetlana Boycheva
- School of Biological Sciences University of Auckland Auckland New Zealand
- Biotelliga, Parnell, Auckland 1052 New Zealand
| | - William Lindsey White
- School of Science Faculty of Health and Environmental Sciences Auckland University of Technology Auckland New Zealand
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Chang H, Yu H, Li X, Zhou Z, Liang H, Song W, Ji H, Liang Y, Vidic RD. Role of biological granular activated carbon in contaminant removal and ultrafiltration membrane performance in a full-scale system. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2021.120122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Bindari YR, Gerber PF. Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance. Poult Sci 2021; 101:101612. [PMID: 34872745 PMCID: PMC8713025 DOI: 10.1016/j.psj.2021.101612] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 02/08/2023] Open
Abstract
Maintenance of "gut health" is considered a priority in commercial chicken farms, although a precise definition of what constitutes gut health and how to evaluate it is still lacking. In research settings, monitoring of gut microbiota has gained great attention as shifts in microbial community composition have been associated with gut health and productive performance. However, microbial signatures associated with productivity remain elusive because of the high variability of the microbiota of individual birds resulting in multiple and sometimes contradictory profiles associated with poor or high performance. The high costs associated with the testing and the need for the terminal sampling of a large number of birds for the collection of gut contents also make this tool of limited use in commercial settings. This review highlights the existing literature on the chicken digestive system and associated microbiota; factors affecting the gut microbiota and emergence of the major chicken enteric diseases coccidiosis and necrotic enteritis; methods to evaluate gut health and their association with performance; main issues in investigating chicken microbial populations; and the relationship of microbial profiles and production outcomes. Emphasis is given to emerging noninvasive and easy-to-collect sampling methods that could be used to monitor gut health and microbiological changes in commercial flocks.
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Affiliation(s)
- Yugal Raj Bindari
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Priscilla F Gerber
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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Barlow JT, Leite G, Romano AE, Sedighi R, Chang C, Celly S, Rezaie A, Mathur R, Pimentel M, Ismagilov RF. Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome. MICROBIOME 2021; 9:214. [PMID: 34724979 PMCID: PMC8561862 DOI: 10.1186/s40168-021-01162-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/14/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Upper gastrointestinal (GI) disorders and abdominal pain afflict between 12 and 30% of the worldwide population and research suggests these conditions are linked to the gut microbiome. Although large-intestine microbiota have been linked to several GI diseases, the microbiota of the human small intestine and its relation to human disease has been understudied. The small intestine is the major site for immune surveillance in the gut, and compared with the large intestine, it has greater than 100 times the surface area and a thinner and more permeable mucus layer. RESULTS Using quantitative sequencing, we evaluated total and taxon-specific absolute microbial loads from 250 duodenal-aspirate samples and 21 paired duodenum-saliva samples from participants in the REIMAGINE study. Log-transformed total microbial loads spanned 5 logs and were normally distributed. Paired saliva-duodenum samples suggested potential transmission of oral microbes to the duodenum, including organisms from the HACEK group. Several taxa, including Klebsiella, Escherichia, Enterococcus, and Clostridium, seemed to displace strict anaerobes common in the duodenum, so we refer to these taxa as disruptors. Disruptor taxa were enriched in samples with high total microbial loads and in individuals with small intestinal bacterial overgrowth (SIBO). Absolute loads of disruptors were associated with more severe GI symptoms, highlighting the value of absolute taxon quantification when studying small-intestine health and function. CONCLUSION This study provides the largest dataset of the absolute abundance of microbiota from the human duodenum to date. The results reveal a clear relationship between the oral microbiota and the duodenal microbiota and suggest an association between the absolute abundance of disruptor taxa, SIBO, and the prevalence of severe GI symptoms. Video Abstract.
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Affiliation(s)
- Jacob T. Barlow
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 USA
| | - Gabriela Leite
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Anna E. Romano
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 USA
| | - Rashin Sedighi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Christine Chang
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Shreya Celly
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Ali Rezaie
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Ruchi Mathur
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
- Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Rustem F. Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 USA
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43
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Bindari YR, Moore RJ, Van TTH, Walkden-Brown SW, Gerber PF. Microbial taxa in dust and excreta associated with the productive performance of commercial meat chicken flocks. Anim Microbiome 2021; 3:66. [PMID: 34600571 PMCID: PMC8487525 DOI: 10.1186/s42523-021-00127-y] [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: 02/18/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND A major focus of research on the gut microbiota of poultry has been to define signatures of a healthy gut and identify microbiota components that correlate with feed conversion. However, there is a high variation in individual gut microbiota profiles and their association with performance. Population level samples such as dust and pooled excreta could be useful to investigate bacterial signatures associated with productivity at the flock-level. This study was designed to investigate the bacterial signatures of high and low-performing commercial meat chicken farms in dust and pooled excreta samples. Poultry house dust and fresh pooled excreta were collected at days 7, 14, 21, 28 and 35 of age from 8 farms of two Australian integrator companies and 389 samples assessed by 16S ribosomal RNA gene amplicon sequencing. The farms were ranked as low (n = 4) or high performers (n = 4) based on feed conversion rate corrected by body weight. RESULTS Permutational analysis of variance based on Bray-Curtis dissimilarities using abundance data for bacterial community structure results showed that company explained the highest variation in the bacterial community structure in excreta (R2 = 0.21, p = 0.001) while age explained the highest variation in the bacterial community structure in dust (R2 = 0.13, p = 0.001). Farm performance explained the least variation in the bacterial community structure in both dust (R2 = 0.03, p = 0.001) and excreta (R2 = 0.01, p = 0.001) samples. However, specific bacterial taxa were found to be associated with high and low performance in both dust and excreta. The bacteria taxa associated with high-performing farms in dust or excreta found in this study were Enterococcus and Candidatus Arthromitus whereas bacterial taxa associated with low-performing farms included Nocardia, Lapillococcus, Brachybacterium, Ruania, Dietzia, Brevibacterium, Jeotgalicoccus, Corynebacterium and Aerococcus. CONCLUSIONS Dust and excreta could be useful for investigating bacterial signatures associated with high and low performance in commercial poultry farms. Further studies on a larger number of farms are needed to determine if the bacterial signatures found in this study are reproducible.
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Affiliation(s)
- Yugal Raj Bindari
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora West Campus, Plenty Rd, Bundoora, VIC, 3083, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora West Campus, Plenty Rd, Bundoora, VIC, 3083, Australia
| | - Stephen W Walkden-Brown
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Priscilla F Gerber
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
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44
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Zhang L, Yin W, Wang C, Zhang A, Zhang H, Zhang T, Ju F. Untangling Microbiota Diversity and Assembly Patterns in the World's Largest Water Diversion Canal. WATER RESEARCH 2021; 204:117617. [PMID: 34555587 DOI: 10.1016/j.watres.2021.117617] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Large water diversion projects are important constructions for reallocation of human-essential water resources. Deciphering microbiota dynamics and assembly mechanisms underlying canal water ecosystem services especially during long-distance diversion is a prerequisite for water quality monitoring, biohazard warning and sustainable management. Using a 1432-km canal of the South-to-North Water Diversion Projects as a model system, we answer three central questions: how bacterial and micro-eukaryotic communities spatio-temporally develop, how much ecological stochasticity contributes to microbiota assembly, and which immigrating populations better survive and navigate across the canal. We applied quantitative ribosomal RNA gene sequence analyses to investigate canal water microbial communities sampled over a year, as well as null model- and neutral model-based approaches to disentangle the microbiota assembly processes. Our results showed clear microbiota dynamics in community composition driven by seasonality more than geographic location, and seasonally dependent influence of environmental parameters. Overall, bacterial community was largely shaped by deterministic processes, whereas stochasticity dominated micro-eukaryotic community assembly. We defined a local growth factor (LGF) and demonstrated its innovative use to quantitatively infer microbial proliferation, unraveling taxonomically dependent population response to local environmental selection across canal sections. Using LGF as a quantitative indicator of immigrating capacities, we also found that most micro-eukaryotic populations (82%) from the source water sustained growth in the canal and better acclimated to the hydrodynamical water environment than bacteria (67%). Taxa inferred to largely propagate include Limnohabitans sp. and Cryptophyceae, potentially contributing to water auto-purification. Combined, our work poses first and unique insights into the microbiota assembly patterns and dynamics in the world's largest water diversion canal, providing important ecological knowledge for long-term sustainable water quality maintenance in such a giant engineered system.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Wei Yin
- Changjiang Water Resources Protection Institute, 515 Qintai Street, Wuhan 430051, Hubei Province, China
| | - Chao Wang
- Changjiang Water Resources Protection Institute, 515 Qintai Street, Wuhan 430051, Hubei Province, China
| | - Aijing Zhang
- Construction and Administration Bureau of South-to-North Water Diversion Middle Route Project, 1 Yuyuantan South Road, Beijing 100038, China
| | - Hong Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, Pokfulam Road, The University of Hong Kong, Hong Kong 999077, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
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45
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Qian Y, Lan F, Venturelli OS. Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models. Curr Opin Microbiol 2021; 62:84-92. [PMID: 34098512 PMCID: PMC8286325 DOI: 10.1016/j.mib.2021.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022]
Abstract
Microbial communities and their functions are shaped by complex networks of interactions among microbes and with their environment. While the critical roles microbial communities play in numerous environments have become increasingly appreciated, we have a very limited understanding of their interactions and how these interactions combine to generate community-level behaviors. This knowledge gap hinders our ability to predict community responses to perturbations and to design interventions that manipulate these communities to our benefit. Dynamic models are promising tools to address these questions. We review existing modeling techniques to construct dynamic models of microbial communities at different scales and suggest ways to leverage multiple types of models and data to facilitate our understanding and engineering of microbial communities.
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Affiliation(s)
- Yili Qian
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Freeman Lan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States.
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46
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Lundberg DS, Pramoj Na Ayutthaya P, Strauß A, Shirsekar G, Lo WS, Lahaye T, Weigel D. Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition. eLife 2021; 10:e66186. [PMID: 34292157 PMCID: PMC8387020 DOI: 10.7554/elife.66186] [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] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.
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Affiliation(s)
- Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | | | - Annett Strauß
- Department of Evolutionary Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Wen-Sui Lo
- ZMBP-General Genetics, University of TübingenTübingenGermany
| | - Thomas Lahaye
- ZMBP-General Genetics, University of TübingenTübingenGermany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
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47
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Leggieri PA, Liu Y, Hayes M, Connors B, Seppälä S, O'Malley MA, Venturelli OS. Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annu Rev Biomed Eng 2021; 23:169-201. [PMID: 33781078 PMCID: PMC8277735 DOI: 10.1146/annurev-bioeng-082120-022836] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review, we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.
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Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Yiyi Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Madeline Hayes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Bryce Connors
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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48
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Wu WL, Adame MD, Liou CW, Barlow JT, Lai TT, Sharon G, Schretter CE, Needham BD, Wang MI, Tang W, Ousey J, Lin YY, Yao TH, Abdel-Haq R, Beadle K, Gradinaru V, Ismagilov RF, Mazmanian SK. Microbiota regulate social behaviour via stress response neurons in the brain. Nature 2021; 595:409-414. [PMID: 34194038 DOI: 10.1038/s41586-021-03669-y] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 05/25/2021] [Indexed: 02/07/2023]
Abstract
Social interactions among animals mediate essential behaviours, including mating, nurturing, and defence1,2. The gut microbiota contribute to social activity in mice3,4, but the gut-brain connections that regulate this complex behaviour and its underlying neural basis are unclear5,6. Here we show that the microbiome modulates neuronal activity in specific brain regions of male mice to regulate canonical stress responses and social behaviours. Social deviation in germ-free and antibiotic-treated mice is associated with elevated levels of the stress hormone corticosterone, which is primarily produced by activation of the hypothalamus-pituitary-adrenal (HPA) axis. Adrenalectomy, antagonism of glucocorticoid receptors, or pharmacological inhibition of corticosterone synthesis effectively corrects social deficits following microbiome depletion. Genetic ablation of glucocorticoid receptors in specific brain regions or chemogenetic inactivation of neurons in the paraventricular nucleus of the hypothalamus that produce corticotrophin-releasing hormone (CRH) reverse social impairments in antibiotic-treated mice. Conversely, specific activation of CRH-expressing neurons in the paraventricular nucleus induces social deficits in mice with a normal microbiome. Via microbiome profiling and in vivo selection, we identify a bacterial species, Enterococcus faecalis, that promotes social activity and reduces corticosterone levels in mice following social stress. These studies suggest that specific gut bacteria can restrain the activation of the HPA axis, and show that the microbiome can affect social behaviours through discrete neuronal circuits that mediate stress responses in the brain.
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Affiliation(s)
- Wei-Li Wu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. .,Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Mark D Adame
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chia-Wei Liou
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jacob T Barlow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tzu-Ting Lai
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Gil Sharon
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Catherine E Schretter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brittany D Needham
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Madelyn I Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Weiyi Tang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - James Ousey
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yuan-Yuan Lin
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tzu-Hsuan Yao
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Reem Abdel-Haq
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Keith Beadle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rustem F Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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49
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Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases. Nat Commun 2021; 12:3562. [PMID: 34117246 PMCID: PMC8196019 DOI: 10.1038/s41467-021-23821-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible. Here, the authors use simulated quantitative gut microbial communities to benchmark the performance of 13 common data transformations in determining diversity as well as microbe-microbe and microbe-metadata associations, finding that quantitative approaches incorporating microbial load variation outperform computational strategies in downstream analyses, urging for a widespread adoption of quantitative approaches, or recommending specific computational transformations whenever determination of microbial load of samples is not feasible.
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50
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Liu W, Zhang X, Xu H, Li S, Lau HCH, Chen Q, Zhang B, Zhao L, Chen H, Sung JJY, Yu J. Microbial Community Heterogeneity Within Colorectal Neoplasia and its Correlation With Colorectal Carcinogenesis. Gastroenterology 2021; 160:2395-2408. [PMID: 33581124 DOI: 10.1053/j.gastro.2021.02.020] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 02/02/2021] [Accepted: 02/09/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Gut microbial dysbiosis has pivotal involvement in colorectal cancer (CRC). However, the intratumoral microbiota and its association with CRC progression remain elusive. We aimed to determine the microbial community architecture within a neoplasia (CRC or adenoma) and its contribution to colorectal carcinogenesis. METHODS We collected 436 tissue biopsies from patients with CRC (n = 36) or adenoma (n = 32) (2-6 biopsies from a neoplasia plus 2-5 biopsies from adjacent normal tissues per individual). Microbial profiling was performed using 16S ribosomal RNA gene sequencing with subsequent investigation of microbiota diversities and heterogeneity. The correlation between microbial dysbiosis and host genetic alterations (KRAS mutation and microsatellite instability) in all neoplasia biopsies was also analyzed. RESULTS We discovered that intra-neoplasia microbial communities are heterogeneous. Abundances of some CRC-associated pathobionts (eg, Fusobacterium, Bacteroides, Parvimonas, and Prevotella) were found to be highly varied within a single neoplasia. Correlation of such heterogeneity with CRC development revealed alterations in microbial communities involving microbes with high intra-neoplasia variation in abundance. Moreover, we found that the intra-neoplasia variation in abundance of individual microbes changed along the adenoma-carcinoma sequence. We further determined that there was a significant difference in intra-neoplasia microbiota between biopsies with and without KRAS mutation (P < .001) or microsatellite instability (P < .001), and illustrated the association of intratumoral microbial heterogeneity with genetic alteration. CONCLUSIONS We demonstrated that intra-neoplasia microbiota is heterogeneous and correlated with colorectal carcinogenesis. Our findings provide new insights on the contribution of gut microbiota heterogeneity to CRC progression.
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Affiliation(s)
- Weixin Liu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Xiang Zhang
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Hongzhi Xu
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Shengmian Li
- Department of Gastroenterology, the Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
| | - Harry Cheuk-Hay Lau
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Qiongyun Chen
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Bin Zhang
- Department of Gastroenterology, the Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
| | - Liuyang Zhao
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Huarong Chen
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Joseph Jao-Yiu Sung
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Jun Yu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong.
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