1
|
Cavallaro A, Gabrielli M, Hammes F, Rhoads WJ. The impact of DNA extraction on the quantification of Legionella, with implications for ecological studies. Microbiol Spectr 2024; 12:e0071324. [PMID: 38953325 PMCID: PMC11302271 DOI: 10.1128/spectrum.00713-24] [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: 03/20/2024] [Accepted: 06/06/2024] [Indexed: 07/04/2024] Open
Abstract
Monitoring the levels of opportunistic pathogens in drinking water is important to plan interventions and understand the ecological niches that allow them to proliferate. Quantitative PCR is an established alternative to culture methods that can provide a faster, higher-throughput, and more precise enumeration of the bacteria in water samples. However, PCR-based methods are still not routinely applied for Legionella monitoring, and techniques, such as DNA extraction, differ notably between laboratories. Here, we quantify the impact that DNA extraction methods had on downstream PCR quantification and community sequencing. Through a community science campaign, we collected 50 water samples and corresponding shower hoses, and compared two commonly used DNA extraction methodologies to the same biofilm and water phase samples. The two methods showed clearly different extraction efficacies, which were reflected in both the quantity of DNA extracted and the concentrations of Legionella enumerated in both the matrices. Notably, one method resulted in higher enumeration in nearly all samples by about one order of magnitude and detected Legionella in 21 samples that remained undetected by the other method. 16S rRNA amplicon sequencing revealed that the relative abundance of individual taxa, including sequence variants of Legionella, significantly varied depending on the extraction method employed. Given the implications of these findings, we advocate for improvement in documentation of the performance of DNA extraction methods used in drinking water to detect and quantify Legionella, and characterize the associated microbial community.IMPORTANCEMonitoring for the presence of the waterborne opportunistic pathogen Legionella is important to assess the risk of infection and plan remediation actions. While monitoring is traditionally carried on through cultivation, there is an ever-increasing demand for rapid and high-throughput molecular-based approaches for Legionella detection. This paper provides valuable insights on how DNA extraction affects downstream molecular analysis such as the quantification of Legionella through droplet digital PCR and the characterization of natural microbial communities through sequencing analysis. We analyze the results from a risk-assessment, legislative, and ecological perspective, showing how initial DNA processing is an important step to take into account when shifting to molecular-based routine monitoring and discuss the central role of consistent and detailed reporting of the methods used.
Collapse
Affiliation(s)
- Alessio Cavallaro
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zürich, Switzerland
| | - Marco Gabrielli
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Frederik Hammes
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - William J. Rhoads
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| |
Collapse
|
2
|
Voolstra CR, Raina JB, Dörr M, Cárdenas A, Pogoreutz C, Silveira CB, Mohamed AR, Bourne DG, Luo H, Amin SA, Peixoto RS. The coral microbiome in sickness, in health and in a changing world. Nat Rev Microbiol 2024; 22:460-475. [PMID: 38438489 DOI: 10.1038/s41579-024-01015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 03/06/2024]
Abstract
Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.
Collapse
Affiliation(s)
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia.
| | - Melanie Dörr
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Anny Cárdenas
- Department of Biology, American University, Washington, DC, USA
| | - Claudia Pogoreutz
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | | | - Amin R Mohamed
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Haiwei Luo
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, State Key Laboratory of Agrobiotechnology and Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shady A Amin
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Raquel S Peixoto
- Red Sea Research Center (RSRC) and Computational Biology Research Center (CBRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| |
Collapse
|
3
|
Hu YY, Lo IH, Hsiao JT, Sheu F. Real-time PCR-based quantitative microbiome profiling elucidates the microbial dynamic succession in backslopping fermentation of Taiwanese pickled cabbage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38925544 DOI: 10.1002/jsfa.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Microbiota succession determines the flavor and quality of fermented foods. Quantitative PCR-based quantitative microbiome profiling (QMP) has been applied broadly for microbial analysis from absolute abundance perspectives, transforming microbiota ratios into counts by normalizing 16S ribosomal RNA (16S rRNA) gene sequencing data with gene copies quantified by quantitative PCR. However, the application of QMP in fermented foods is still limited. RESULTS QMP elucidated microbial succession of Taiwanese pickled cabbage. In the spontaneous first-round fermentation (FR), the 16S rRNA gene copies of total bacteria increased from 6.1 to 10 log copies mL-1. The dominant lactic acid bacteria genera were successively Lactococcus, Leuconostoc and Lactiplantibacillus. Despite the decrease in the proportion of Lactococcus during the succession, the absolute abundance of Lactococcus still increased. In the backslopping second-round fermentation (SR), the total bacteria 16S rRNA gene copies increased from 7.6 to 9.9 log copies mL-1. The addition of backslopping starter and vinegar rapidly led to a homogenous microbial community dominated by Lactiplantibacillus. The proportion of Lactiplantibacillus remained consistently around 90% during SR, whereas its absolute abundance exhibited a continuous increase. In SR without vinegar, Leuconostoc consistently dominated the fermentation. CONCLUSION The present study highlights that compositional analysis would misinterpret microbial dynamics, whereas QMP reflected the real succession profiles and unveiled the essential role of vinegar in promoting Lactiplantibacillus dominance in backslopping fermentation of Taiwanese pickled cabbage. Quantitative microbiome profiling (QMP) was found to be a more promising approach for the detailed observation of microbiome succession in food fermentation compared to compositional analysis. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- You-Yun Hu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - I-Hsuan Lo
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Jhih-Ting Hsiao
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Fuu Sheu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
4
|
Díez-Sánchez A, Lindholm HT, Vornewald PM, Ostrop J, Yao R, Single AB, Marstad A, Parmar N, Shaw TN, Martín-Alonso M, Oudhoff MJ. LSD1 drives intestinal epithelial maturation and controls small intestinal immune cell composition independent of microbiota in a murine model. Nat Commun 2024; 15:3412. [PMID: 38649356 PMCID: PMC11035651 DOI: 10.1038/s41467-024-47815-2] [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: 09/10/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Postnatal development of the gastrointestinal tract involves the establishment of the commensal microbiota, the acquisition of immune tolerance via a balanced immune cell composition, and maturation of the intestinal epithelium. While studies have uncovered an interplay between the first two, less is known about the role of the maturing epithelium. Here we show that intestinal-epithelial intrinsic expression of lysine-specific demethylase 1A (LSD1) is necessary for the postnatal maturation of intestinal epithelium and maintenance of this developed state during adulthood. Using microbiota-depleted mice, we find plasma cells, innate lymphoid cells (ILCs), and a specific myeloid population to depend on LSD1-controlled epithelial maturation. We propose that LSD1 controls the expression of epithelial-derived chemokines, such as Cxcl16, and that this is a mode of action for this epithelial-immune cell interplay in local ILC2s but not ILC3s. Together, our findings suggest that the maturing epithelium plays a dominant role in regulating the local immune cell composition, thereby contributing to gut homeostasis.
Collapse
Affiliation(s)
- Alberto Díez-Sánchez
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Håvard T Lindholm
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Pia M Vornewald
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jenny Ostrop
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rouan Yao
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Andrew B Single
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anne Marstad
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Naveen Parmar
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tovah N Shaw
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mara Martín-Alonso
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Menno J Oudhoff
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
- Department of Health Sciences, Carleton University, Ottawa, Ontario, ON, Canada.
| |
Collapse
|
5
|
Nixon MP, Gloor GB, Silverman JD. Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587602. [PMID: 38617212 PMCID: PMC11014594 DOI: 10.1101/2024.04.01.587602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Though statistical normalizations are often used in differential abundance or differential expression analysis to address sample-to-sample variation in sequencing depth, we offer a better alternative. These normalizations often make strong, implicit assumptions about the scale of biological systems (e.g., microbial load). Thus, analyses are susceptible to even slight errors in these assumptions, leading to elevated rates of false positives and false negatives. We introduce scale models as a generalization of normalizations so researchers can model potential errors in assumptions about scale. By incorporating scale models into the popular ALDEx2 software, we enhance the reproducibility of analyses while often drastically decreasing false positive and false negative rates. We design scale models that are guaranteed to reduce false positives compared to equivalent normalizations. At least in the context of ALDEx2, we recommend using scale models over normalizations in all practical situations.
Collapse
Affiliation(s)
- Michelle Pistner Nixon
- College of Information Science and Technology, Pennsylvania State University, University Park, PA, USA
| | - Gregory B. Gloor
- Department of Biochemistry, The University of Western Ontario, London, ON, CAN
| | - Justin D. Silverman
- College of Information Science and Technology, Pennsylvania State University, University Park, PA, USA
- Department of Statistics, Pennsylvania State University, University Park, PA, USA
- Department of Medicine, Pennsylvania State University, Hershey, PA, USA
| |
Collapse
|
6
|
Yi Z, Qiu M, Xiao X, Ma J, Yang H, Wang W. Quantitative characterization and dynamics of bacterial communities in ready-to-eat chicken using high-throughput sequencing combined with internal standard-based absolute quantification. Food Microbiol 2024; 118:104419. [PMID: 38049274 DOI: 10.1016/j.fm.2023.104419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/07/2023] [Accepted: 10/29/2023] [Indexed: 12/06/2023]
Abstract
Ready-to-eat (RTE) chicken products are prone to bacterial contamination, posing foodborne illness risks. High-throughput sequencing (HTS) has been widely used to study the distribution of pathogenic and spoilage bacteria in RTE chicken products but lacks quantitative data on taxa abundances. In this study, we employed a method combining HTS with absolute quantification, using Edwardsiella tarda as an internal standard strain, to achieve the relative and absolute abundances of microbiota in RTE chicken products stored at 4 and 25 °C. The results showed that the addition of appropriate concentration of internal standard strains exhibited no significant impact on the structure composition, relative abundance, and absolute abundance of bacterial communities in chicken meat, achieving comprehensive absolute quantification in RTE chicken products. Furthermore, the absolute abundance of bacterial genera at the end of storage followed a log-normal distribution, with most genera having an absolute abundance between 103 and 105 CFU/g. This study provides insights into the quantification of bacterial communities in RTE chicken products, laying a foundation for the development of strategies to extend the shelf life of RTE products.
Collapse
Affiliation(s)
- Zhengkai Yi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Mengjia Qiu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xingning Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiele Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
| |
Collapse
|
7
|
Sweeney CJ, Kaushik R, Bottoms M. Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2024; 20:337-358. [PMID: 37452668 DOI: 10.1002/ieam.4812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
There is increasing interest in further developing the plant protection product (PPP) environmental risk assessment, particularly within the European Union, to include the assessment of soil microbial community composition, as measured by metabarcoding approaches. However, to date, there has been little discussion as to how this could be implemented in a standardized, reliable, and robust manner suitable for regulatory decision-making. Introduction of metabarcoding-based assessments of the soil microbiome into the PPP risk assessment would represent a significant increase in the degree of complexity of the data that needs to be processed and analyzed in comparison to the existing risk assessment on in-soil organisms. The bioinformatics procedures to process DNA sequences into community compositional data sets currently lack standardization, while little information exists on how these data should be used to generate regulatory endpoints and the ways in which these endpoints should be interpreted. Through a thorough and critical review, we explore these challenges. We conclude that currently, we do not have a sufficient degree of standardization or understanding of the required bioinformatics and data analysis procedures to consider their use in an environmental risk assessment context. However, we highlight critical knowledge gaps and the further research required to understand whether metabarcoding-based assessments of the soil microbiome can be utilized in a statistically and ecologically relevant manner within a PPP risk assessment. Only once these challenges are addressed can we consider if and how we should use metabarcoding as a tool for regulatory decision-making to assess and monitor ecotoxicological effects on soil microorganisms within an environmental risk assessment of PPPs. Integr Environ Assess Manag 2024;20:337-358. © 2023 SETAC.
Collapse
Affiliation(s)
- Christopher J Sweeney
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
| | - Rishabh Kaushik
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
| | - Melanie Bottoms
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
| |
Collapse
|
8
|
Yunusbaeva M, Borodina L, Terentyeva D, Bogdanova A, Zakirova A, Bulatov S, Altinbaev R, Bilalov F, Yunusbayev B. Excess fermentation and lactic acidosis as detrimental functions of the gut microbes in treatment-naive TB patients. Front Cell Infect Microbiol 2024; 14:1331521. [PMID: 38440790 PMCID: PMC10910113 DOI: 10.3389/fcimb.2024.1331521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction The link between gut microbiota and host immunity motivated numerous studies of the gut microbiome in tuberculosis (TB) patients. However, these studies did not explore the metabolic capacity of the gut community, which is a key axis of impact on the host's immunity. Methods We used deep sequencing of fecal samples from 23 treatment-naive TB patients and 48 healthy donors to reconstruct the gut microbiome's metabolic capacity and strain/species-level content. Results We show that the systematic depletion of the commensal flora of the large intestine, Bacteroidetes, and an increase in Actinobacteria, Firmicutes, and Proteobacteria such as Streptococcaceae, Erysipelotrichaceae, Lachnospiraceae, and Enterobacteriaceae explains the strong taxonomic divergence of the gut community in TB patients. The cumulative expansion of diverse disease-associated pathobionts in patients reached 1/4 of the total gut microbiota, suggesting a heavy toll on host immunity along with MTB infection. Reconstruction of metabolic pathways showed that the microbial community in patients shifted toward rapid growth using glycolysis and excess fermentation to produce acetate and lactate. Higher glucose availability in the intestine likely drives fermentation to lactate and growth, causing acidosis and endotoxemia. Discussion Excessive fermentation and lactic acidosis likely characterize TB patients' disturbed gut microbiomes. Since lactic acidosis strongly suppresses the normal gut flora, directly interferes with macrophage function, and is linked to mortality in TB patients, our findings highlight gut lactate acidosis as a novel research focus. If confirmed, gut acidosis may be a novel potential host-directed treatment target to augment traditional TB treatment.
Collapse
Affiliation(s)
- Milyausha Yunusbaeva
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Liliya Borodina
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Darya Terentyeva
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, Saint Petersburg Pasteur Institute, Saint Petersburg, Russia
| | - Anna Bogdanova
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
| | - Aigul Zakirova
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Shamil Bulatov
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Radick Altinbaev
- Laboratory of Neurophysiology of Learning, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, Russia
| | - Fanil Bilalov
- Laboratory of Molecular Genetics, Republic Medical Genetic Centre, Ufa, Russia
- Department of Public Health and Health Organization with a course of ICPE, Bashkir State Medical University, Ufa, Russia
| | - Bayazit Yunusbayev
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| |
Collapse
|
9
|
Dungan AM, Geissler L, Williams AS, Gotze CR, Flynn EC, Blackall LL, van Oppen MJH. DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta. ENVIRONMENTAL MICROBIOME 2023; 18:86. [PMID: 38062479 PMCID: PMC10704692 DOI: 10.1186/s40793-023-00541-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/23/2023] [Indexed: 06/30/2024]
Abstract
BACKGROUND Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages. RESULTS By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A. loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, > 30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A. loripes and P. acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity. CONCLUSIONS Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.
Collapse
Affiliation(s)
- Ashley M Dungan
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia.
| | - Laura Geissler
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda S Williams
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Cecilie Ravn Gotze
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Emily C Flynn
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Linda L Blackall
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| |
Collapse
|
10
|
Prioux C, Tignat-Perrier R, Gervais O, Estaque T, Schull Q, Reynaud S, Béraud E, Mérigot B, Beauvieux A, Marcus MI, Richaume J, Bianchimani O, Cheminée A, Allemand D, Ferrier-Pagès C. Unveiling microbiome changes in Mediterranean octocorals during the 2022 marine heatwaves: quantifying key bacterial symbionts and potential pathogens. MICROBIOME 2023; 11:271. [PMID: 38053218 PMCID: PMC10696765 DOI: 10.1186/s40168-023-01711-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/27/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Climate change has accelerated the occurrence and severity of heatwaves in the Mediterranean Sea and poses a significant threat to the octocoral species that form the foundation of marine animal forests (MAFs). As coral health intricately relies on the symbiotic relationships established between corals and microbial communities, our goal was to gain a deeper understanding of the role of bacteria in the observed tissue loss of key octocoral species following the unprecedented heatwaves in 2022. RESULTS Using amplicon sequencing and taxon-specific qPCR analyses, we unexpectedly found that the absolute abundance of the major bacterial symbionts, Spirochaetaceae (C. rubrum) and Endozoicomonas (P. clavata), remained, in most cases, unchanged between colonies with 0% and 90% tissue loss. These results suggest that the impairment of coral health was not due to the loss of the main bacterial symbionts. However, we observed a significant increase in the total abundance of bacterial opportunists, including putative pathogens such as Vibrio, which was not evident when only their relative abundance was considered. In addition, there was no clear relation between bacterial symbiont loss and the intensity of thermal stress, suggesting that factors other than temperature may have influenced the differential response of octocoral microbiomes at different sampling sites. CONCLUSIONS Our results indicate that tissue loss in octocorals is not directly caused by the decline of the main bacterial symbionts but by the proliferation of opportunistic and pathogenic bacteria. Our findings thus underscore the significance of considering both relative and absolute quantification approaches when evaluating the impact of stressors on coral microbiome as the relative quantification does not accurately depict the actual changes in the microbiome. Consequently, this research enhances our comprehension of the intricate interplay between host organisms, their microbiomes, and environmental stressors, while offering valuable insights into the ecological implications of heatwaves on marine animal forests. Video Abstract.
Collapse
Affiliation(s)
- Camille Prioux
- Collège Doctoral, Sorbonne Université, Paris, France
- Unité de Recherche sur la Biologie des Coraux Précieux CSM - CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC-98000 Monaco, Principality of Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Romie Tignat-Perrier
- Unité de Recherche sur la Biologie des Coraux Précieux CSM - CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC-98000 Monaco, Principality of Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Ophélie Gervais
- Unité de Recherche sur la Biologie des Coraux Précieux CSM - CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC-98000 Monaco, Principality of Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Tristan Estaque
- Septentrion Environnement, Campus Nature Provence, Marseille, 13008, France
| | - Quentin Schull
- MARBEC, Univ. Montpellier, CNRS, IFREMER, IRD, Sète, France
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Eric Béraud
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | | | | | - Maria-Isabelle Marcus
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Justine Richaume
- Septentrion Environnement, Campus Nature Provence, Marseille, 13008, France
| | | | - Adrien Cheminée
- Septentrion Environnement, Campus Nature Provence, Marseille, 13008, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco
| | - Christine Ferrier-Pagès
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC 98000, Principality of Monaco.
| |
Collapse
|
11
|
Swarte JC, Knobbe TJ, Björk JR, Gacesa R, Nieuwenhuis LM, Zhang S, Vila AV, Kremer D, Douwes RM, Post A, Quint EE, Pol RA, Jansen BH, de Borst MH, de Meijer VE, Blokzijl H, Berger SP, Festen EAM, Zhernakova A, Fu J, Harmsen HJM, Bakker SJL, Weersma RK. Health-related quality of life is linked to the gut microbiome in kidney transplant recipients. Nat Commun 2023; 14:7968. [PMID: 38042820 PMCID: PMC10693618 DOI: 10.1038/s41467-023-43431-8] [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: 02/12/2023] [Accepted: 11/08/2023] [Indexed: 12/04/2023] Open
Abstract
Kidney transplant recipients (KTR) have impaired health-related quality of life (HRQoL) and suffer from intestinal dysbiosis. Increasing evidence shows that gut health and HRQoL are tightly related in the general population. Here, we investigate the association between the gut microbiome and HRQoL in KTR, using metagenomic sequencing data from fecal samples collected from 507 KTR. Multiple bacterial species are associated with lower HRQoL, many of which have previously been associated with adverse health conditions. Gut microbiome distance to the general population is highest among KTR with an impaired physical HRQoL (R = -0.20, P = 2.3 × 10-65) and mental HRQoL (R = -0.14, P = 1.3 × 10-3). Physical and mental HRQoL explain a significant part of variance in the gut microbiome (R2 = 0.58%, FDR = 5.43 × 10-4 and R2 = 0.37%, FDR = 1.38 × 10-3, respectively). Additionally, multiple metabolic and neuroactive pathways (gut brain modules) are associated with lower HRQoL. While the observational design of our study does not allow us to analyze causality, we provide a comprehensive overview of the associations between the gut microbiome and HRQoL while controlling for confounders.
Collapse
Affiliation(s)
- J Casper Swarte
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tim J Knobbe
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lianne M Nieuwenhuis
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shuyan Zhang
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Daan Kremer
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rianne M Douwes
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adrian Post
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Evelien E Quint
- Department of Surgery, division of Transplantation Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Robert A Pol
- Department of Surgery, division of Transplantation Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bernadien H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin H de Borst
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Vincent E de Meijer
- Department of Surgery, section of Hepatobiliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hans Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Stefan P Berger
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Stephan J L Bakker
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| |
Collapse
|
12
|
Hammad MI, Conrads G, Abdelbary MMH. Isolation, identification, and significance of salivary Veillonella spp., Prevotella spp., and Prevotella salivae in patients with inflammatory bowel disease. Front Cell Infect Microbiol 2023; 13:1278582. [PMID: 38053528 PMCID: PMC10694262 DOI: 10.3389/fcimb.2023.1278582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/30/2023] [Indexed: 12/07/2023] Open
Abstract
The global prevalence of inflammatory bowel disease (IBD) is on the rise, prompting significant attention from researchers worldwide. IBD entails chronic inflammatory disorders of the intestinal tract, characterized by alternating flares and remissions. Through high-throughput sequencing, numerous studies have unveiled a potential microbial signature for IBD patients showing intestinal enrichment of oral-associated bacteria. Simultaneously, the oral microbiome can be perturbed by intestinal inflammation. Our prior investigation, based on 16S rRNA amplicon sequencing, underscored elevated abundance of Veillonella spp. and Prevotella spp. in the salivary microbiomes of IBD patients. Noteworthy, Prevotella salivae emerged as a distinct species significantly associated with IBD. P. salivae is an under-recognized pathogen that was found to play a role in both oral and systemic diseases. In this study, we delve deeper into the salivary microbiomes of both IBD patients and healthy controls. Employing diverse cultivation techniques and real-time quantitative polymerase chain reactions (RT-qPCR), we gauged the prevalence and abundance of Veillonella spp., Prevotella spp., and P. salivae. Our isolation efforts yielded 407 and 168 strains of Veillonella spp., as well as 173 and 90 strains of Prevotella spp., from the saliva samples of IBD patients and healthy controls, respectively. Veillonella-vancomycin agar emerged as the discerning choice for optimal Veillonella spp. cultivation, while Schaedler kanamycin-vancomycin agar proved to be the most suitable medium for cultivating Prevotella spp. strains. Comparing our RT-qPCR findings to the previous 16S rRNA amplicon sequencing data, the results corroborated the higher abundance of Veillonella spp., Prevotella spp., and P. salivae in the saliva of IBD patients compared to healthy controls. However, it's worth noting that in contrast to RT-qPCR, the 16S rRNA amplicon sequencing data revealed greater absolute abundance of all three bacterial groups in both IBD patients and controls.
Collapse
Affiliation(s)
- Moshira I. Hammad
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule University Hospital, Aachen, Germany
| | - Georg Conrads
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule University Hospital, Aachen, Germany
| | - Mohamed M. H. Abdelbary
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule University Hospital, Aachen, Germany
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| |
Collapse
|
13
|
Davies LR, Barbero-López A, Lähteenmäki VM, Salonen A, Fedorik F, Haapala A, Watts PC. Microbes within the building envelope-a case study on the patterns of colonization and potential sampling bias. PeerJ 2023; 11:e16355. [PMID: 38025723 PMCID: PMC10658902 DOI: 10.7717/peerj.16355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
Humans are exposed to diverse communities of microbes every day. With more time spent indoors by humans, investigations into the communities of microbes inhabiting occupied spaces have become important to deduce the impacts of these microbes on human health and building health. Studies so far have given considerable insight into the communities of the indoor microbiota humans interact with, but mainly focus on sampling surfaces or indoor dust from filters. Beneath the surfaces though, building envelopes have the potential to contain environments that would support the growth of microbial communities. But due to design choices and distance from ground moisture, for example, the temperature and humidity across a building will vary and cause environmental gradients. These microenvironments could then influence the composition of the microbial communities within the walls. Here we present a case study designed to quantify any patterns in the compositions of fungal and bacterial communities existing in a building envelope and determine some of the key variables, such as cardinal direction, distance from floor or distance from wall joinings, that may influence any microbial community composition variation. By drilling small holes across walls of a house, we extracted microbes onto air filters and conducted amplicon sequencing. We found sampling height (distance from the floor) and cardinal direction the wall was facing caused differences in the diversity of the microbial communities, showing that patterns in the microbial composition will be dependent on sampling location within the building. By sampling beneath the surfaces, our approach provides a more complete picture of the microbial condition of a building environment, with the significant variation in community composition demonstrating a potential sampling bias if multiple sampling locations across a building are not considered. By identifying features of the built environment that promote/retard microbial growth, improvements to building designs can be made to achieve overall healthier occupied spaces.
Collapse
Affiliation(s)
- Lucy R. Davies
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | | | | | - Antti Salonen
- Civil Engineering, Faculty of Technology, University of Oulu, Oulu, Finland
| | - Filip Fedorik
- Civil Engineering, Faculty of Technology, University of Oulu, Oulu, Finland
| | - Antti Haapala
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Phillip C. Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| |
Collapse
|
14
|
Ziemons J, Aarnoutse R, Heuft A, Hillege L, Waelen J, de Vos-Geelen J, Valkenburg-van Iersel L, van Hellemond IEG, Creemers GJM, Baars A, Vestjens JHMJ, Penders J, Venema K, Smidt ML. Fecal levels of SCFA and BCFA during capecitabine in patients with metastatic or unresectable colorectal cancer. Clin Exp Med 2023; 23:3919-3933. [PMID: 37027066 PMCID: PMC10618330 DOI: 10.1007/s10238-023-01048-7] [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: 02/17/2023] [Accepted: 03/17/2023] [Indexed: 04/08/2023]
Abstract
BACKGROUND Gut bacteria-derived short-chain fatty acids (SCFA) and branched-chain fatty acids (BCFA) are considered to have beneficial metabolic, anti-inflammatory as well as anti-carcinogenic effects. Previous preclinical studies indicated bidirectional interactions between gut bacteria and the chemotherapeutic capecitabine or its metabolite 5-FU. This study investigated the effect of three cycles of capecitabine on fecal SCFA and BCFA levels and their associations with tumor response, nutritional status, physical performance, chemotherapy-induced toxicity, systemic inflammation and bacterial abundances in patients with colorectal cancer (CRC). METHODS Forty-four patients with metastatic or unresectable CRC, scheduled for treatment with capecitabine (± bevacizumab), were prospectively enrolled. Patients collected a fecal sample and completed a questionnaire before (T1), during (T2) and after (T3) three cycles of capecitabine. Tumor response (CT/MRI scans), nutritional status (MUST score), physical performance (Karnofsky Performance Score) and chemotherapy-induced toxicity (CTCAE) were recorded. Additional data on clinical characteristics, treatment regimen, medical history and blood inflammatory parameters were collected. Fecal SCFA and BCFA concentrations were determined by gas chromatography-mass spectrometry (GC-MS). Gut microbiota composition was assessed using 16S rRNA amplicon sequencing. RESULTS Fecal levels of the SCFA valerate and caproate decreased significantly during three cycles of capecitabine. Furthermore, baseline levels of the BCFA iso-butyrate were associated with tumor response. Nutritional status, physical performance and chemotherapy-induced toxicity were not significantly associated with SCFA or BCFA. Baseline SCFA correlated positively with blood neutrophil counts. At all time points, we identified associations between SCFA and BCFA and the relative abundance of bacterial taxa on family level. CONCLUSIONS The present study provided first indications for a potential role of SCFA and BCFA during capecitabine treatment as well as implications for further research. TRIAL REGISTRATION The current study was registered in the Dutch Trial Register (NTR6957) on 17/01/2018 and can be consulted via the International Clinical Trial Registry Platform (ICTRP).
Collapse
Affiliation(s)
- Janine Ziemons
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.
- Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands.
| | - Romy Aarnoutse
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Anne Heuft
- Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Lars Hillege
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Janneke Waelen
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Judith de Vos-Geelen
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Liselot Valkenburg-van Iersel
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | | | | | - Arnold Baars
- Department of Medical Oncology, Hospital Gelderse Vallei, Ede, The Netherlands
| | | | - John Penders
- NUTRIM - School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, Maastricht University Medical Centre, Maastricht, The Netherlands
- Euregional Microbiome Center, Maastricht, The Netherlands
| | - Koen Venema
- Euregional Microbiome Center, Maastricht, The Netherlands
- Centre for Healthy Eating and Food Innovation, Maastricht University - Campus Venlo, Venlo, The Netherlands
| | - Marjolein L Smidt
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| |
Collapse
|
15
|
Willmott T, Ormesher L, McBain AJ, Humphreys GJ, Myers JE, Singh G, Lundberg JO, Weitzberg E, Nihlen C, Cottrell EC. Altered Oral Nitrate Reduction and Bacterial Profiles in Hypertensive Women Predict Blood Pressure Lowering Following Acute Dietary Nitrate Supplementation. Hypertension 2023; 80:2397-2406. [PMID: 37702047 DOI: 10.1161/hypertensionaha.123.21263] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/26/2023] [Indexed: 09/14/2023]
Abstract
BACKGROUND The efficacy of dietary nitrate supplementation to lower blood pressure (BP) in pregnant women is highly variable. We aimed to investigate whether differences in oral microbiota profiles and oral nitrate-reducing capacity may explain interindividual differences in BP lowering following nitrate supplementation. METHODS Participants recruited for this study were both pregnant and nonpregnant women, with or without hypertension (n=55). Following an overnight fast, plasma, saliva, and tongue scraping samples were collected for measurement of nitrate/nitrite concentrations, oral NaR (nitrate reductase) activity, and microbiota profiling using 16S rRNA gene sequencing. Baseline BP was measured, followed by the administration of a single dose of dietary nitrate (400 mg nitrate in 70 mL beetroot juice). Post-nitrate intervention, plasma and salivary nitrate/nitrite concentrations and BP were determined 2.5 hours later. RESULTS Women with hypertension had significantly lower salivary nitrite concentrations (P=0.006) and reduced abundance of the nitrate-reducing taxa Veillonella(P=0.007) compared with normotensive women. Oral NaR activity was not significantly different in pregnant versus nonpregnant women (P=0.991) but tended to be lower in hypertensive compared with normotensive women (P=0.099). Oral NaR activity was associated with both baseline diastolic BP (P=0.050) and change in diastolic BP following acute nitrate intake (P=0.01, adjusted for baseline BP). CONCLUSIONS The abundance and activity of oral nitrate-reducing bacteria impact both baseline BP as well as the ability of dietary nitrate supplementation to lower BP. Strategies to increase oral nitrate-reducing capacity could lower BP and enhance the efficacy of dietary nitrate supplementation, in pregnancy as well as in nonpregnant adults. REGISTRATION URL: https://www. CLINICALTRIALS gov; Unique identifier: NCT03930693.
Collapse
Affiliation(s)
- Thomas Willmott
- Maternal and Fetal Health Research Centre, Division of Developmental Biology and Medicine, School of Medical Sciences (T.W., L.O., J.E.M., E.C.C.), Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
- Division of Pharmacy and Optometry, School of Health Sciences (T.W., A.J.M., G.J.H.), Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Laura Ormesher
- Maternal and Fetal Health Research Centre, Division of Developmental Biology and Medicine, School of Medical Sciences (T.W., L.O., J.E.M., E.C.C.), Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Andrew J McBain
- Division of Pharmacy and Optometry, School of Health Sciences (T.W., A.J.M., G.J.H.), Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Gavin J Humphreys
- Division of Pharmacy and Optometry, School of Health Sciences (T.W., A.J.M., G.J.H.), Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Jenny E Myers
- Maternal and Fetal Health Research Centre, Division of Developmental Biology and Medicine, School of Medical Sciences (T.W., L.O., J.E.M., E.C.C.), Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Gurdeep Singh
- Lydia Becker Institute of Immunology and Inflammation, Manchester Academic Health Science Centre (G.S.), Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Jon O Lundberg
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden (J.O.L., E.W., C.N.)
| | - Eddie Weitzberg
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden (J.O.L., E.W., C.N.)
| | - Carina Nihlen
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden (J.O.L., E.W., C.N.)
| | - Elizabeth C Cottrell
- Maternal and Fetal Health Research Centre, Division of Developmental Biology and Medicine, School of Medical Sciences (T.W., L.O., J.E.M., E.C.C.), Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| |
Collapse
|
16
|
Li X, Yu C, Zhang B, Shan X, Mao W, Zhang Z, Wang C, Jin X, Wang J, Zhao H. The recovery of the microbial community after plaque removal depends on periodontal health status. NPJ Biofilms Microbiomes 2023; 9:75. [PMID: 37805507 PMCID: PMC10560279 DOI: 10.1038/s41522-023-00441-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 09/25/2023] [Indexed: 10/09/2023] Open
Abstract
Plaque accumulation and microbial community changes are important causes of periodontal disease. Cleaned plaque microorganisms will reattach to form biofilms, but the recovery and outcome of plaque microbial communities in different periodontal health states remain unknown. In this study, we tracked the biofilm remodeling process in 206 dental plaque samples from 40 healthy periodontal, gingivitis and periodontitis volunteers at 6 time points before and after supragingival scaling. We found that microbial communities of different periodontal states changed asynchronously during the process, and the more severe the periodontal disease condition, the more lagged the recovery of plaque microorganisms to their original state after cleaning; this reflected a higher degree of plaque development in periodontitis samples. The plaque index and bleeding index were significantly correlated with plaque recovery, especially the recovery of bacteria such as Abiotrophia and Capnocytophaga. Meanwhile, we found that the microbial community structure of different periodontal health states was most similar at the Day 3 after plaque cleaning, and the communities gradually differentiated and developed in different directions. Abiotrophia and other bacteria might play an important role in determining the development trend of plaque biofilms. The discovery of specific time points and bacteria was of great value in clarifying the pathogenesis of periodontal disease and in seeking targets for prevention and treatment.
Collapse
Affiliation(s)
- Xiaoqing Li
- The Third Clinical Institute Affiliated to Wenzhou Medical University/Wenzhou People's Hospital/Wenzhou Maternal and Child Health Care Hospital/The Third Affiliated Hospital of Shanghai University, Wenzhou, Zhejiang, China
| | - Cheng Yu
- The Third Clinical Institute Affiliated to Wenzhou Medical University/Wenzhou People's Hospital/Wenzhou Maternal and Child Health Care Hospital/The Third Affiliated Hospital of Shanghai University, Wenzhou, Zhejiang, China
- Jiangyin Stomatological Hospital/Jiangyin Oral Disease Preventive Treatment, Jiangyin, Jiangsu, China
| | - Bing Zhang
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiaogang Shan
- The Third Clinical Institute Affiliated to Wenzhou Medical University/Wenzhou People's Hospital/Wenzhou Maternal and Child Health Care Hospital/The Third Affiliated Hospital of Shanghai University, Wenzhou, Zhejiang, China
| | - Wenjun Mao
- The Third Clinical Institute Affiliated to Wenzhou Medical University/Wenzhou People's Hospital/Wenzhou Maternal and Child Health Care Hospital/The Third Affiliated Hospital of Shanghai University, Wenzhou, Zhejiang, China
| | - Zicheng Zhang
- School of Biomedical Engineering, Hainan University, Haikou, Hainan, China
| | - Chunyan Wang
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, Henan, China
| | - Xiaoxia Jin
- The Third Clinical Institute Affiliated to Wenzhou Medical University/Wenzhou People's Hospital/Wenzhou Maternal and Child Health Care Hospital/The Third Affiliated Hospital of Shanghai University, Wenzhou, Zhejiang, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, China.
| | - Hui Zhao
- The Third Clinical Institute Affiliated to Wenzhou Medical University/Wenzhou People's Hospital/Wenzhou Maternal and Child Health Care Hospital/The Third Affiliated Hospital of Shanghai University, Wenzhou, Zhejiang, China.
| |
Collapse
|
17
|
Herzog EL, Kreuzer M, Zinkernagel MS, Zysset-Burri DC. Challenges and insights in the exploration of the low abundance human ocular surface microbiome. Front Cell Infect Microbiol 2023; 13:1232147. [PMID: 37727808 PMCID: PMC10505673 DOI: 10.3389/fcimb.2023.1232147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023] Open
Abstract
Purpose The low microbial abundance on the ocular surface results in challenges in the characterization of its microbiome. The purpose of this study was to reveal factors introducing bias in the pipeline from sample collection to data analysis of low-abundant microbiomes. Methods Lower conjunctiva and lower lid swabs were collected from six participants using either standard cotton or flocked nylon swabs. Microbial DNA was isolated with two different kits (with or without prior host DNA depletion and mechanical lysis), followed by whole-metagenome shotgun sequencing with a high sequencing depth set at 60 million reads per sample. The relative microbial compositions were generated using the two different tools MetaPhlan3 and Kraken2. Results The total amount of extracted DNA was increased by using nylon flocked swabs on the lower conjunctiva. In total, 269 microbial species were detected. The most abundant bacterial phyla were Actinobacteria, Firmicutes and Proteobacteria. Depending on the DNA extraction kit and tool used for profiling, the microbial composition and the relative abundance of viruses varied. Conclusion The microbial composition on the ocular surface is not dependent on the swab type, but on the DNA extraction method and profiling tool. These factors have to be considered in further studies about the ocular surface microbiome and other sparsely colonized microbiomes in order to improve data reproducibility. Understanding challenges and biases in the characterization of the ocular surface microbiome may set the basis for microbiome-altering interventions for treatment of ocular surface associated diseases.
Collapse
Affiliation(s)
- Elio L. Herzog
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marco Kreuzer
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Martin S. Zinkernagel
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Denise C. Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| |
Collapse
|
18
|
Vojtech L, Paktinat S, Luu T, Teichmann S, Soge OO, Suchland R, Barbee LA, Khosropour CM. Use of viability PCR for detection of live Chlamydia trachomatis in clinical specimens. FRONTIERS IN REPRODUCTIVE HEALTH 2023; 5:1199740. [PMID: 37601895 PMCID: PMC10436598 DOI: 10.3389/frph.2023.1199740] [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: 04/03/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Background The current testing approach to diagnose Chlamydia trachomatis (CT) infection relies on nucleic acid amplification tests (NAATs). These tests are highly sensitive, but do not distinguish between active infection and residual bacterial nucleic acid which may remain after resolution of infection, or via cross-contamination. Better methods to assess the viability of CT detected in clinical samples would be useful in determining the relevance of CT detection in a variety of clinical settings. The goal of this study was to test viability PCR (vPCR) as a method to distinguish viable bacteria from non-viable CT. Methods The vPCR relies on a propidium monoazide dye (PMAxx), which intercalates into accessible DNA from dead organisms and prevents their detection in a PCR assay for the CT ompA gene. We used digital PCR to quantify absolute genome copy numbers from samples. We validated the vPCR approach using laboratory stocks of CT with known viability. Then, we tested total DNA, viable CT DNA, and culture results from 18 clinical vaginal specimens and 25 rectal clinical specimens, all of which had tested positive by NAAT. Results In laboratory stocks of CT, vPCR using defined ratios of heat-killed to live bacteria tracked closely with expected results. In vaginal clinical specimens, vPCR and total DNA results were correlated, though total DNA genomes outnumbered viable genomes by 2.2-52.6-fold more copies. As expected, vPCR detected more total genomes than culture results. Both vPCR and total DNA correlated with culture results (Spearman correlation R = 0.8425 for total DNA and 0.8056 for vPCR). Ten rectal NAAT positive specimens were negative by total DNA PCR, vPCR, and were negative or inconclusive by culture. Of the 6 rectal specimens that were culture positive, all were total DNA and vPCR positive. vPCR additionally detected viable bacterial DNA in 8 specimens which were NAAT + and culture negative, though levels were very low (mean 1,357 copies/ml). Conclusions vPCR is a fast and easy method to assess viability in clinical specimens and is more correlated with culture results than total DNA PCR. Inconsistent ratios between total DNA and vPCR results suggest that the amount of dead bacteria varies considerably in clinical specimens. Results from rectal specimens suggest that many NAAT positive specimens do not in fact represent live replicating bacteria, and likely result in significant overuse of unnecessary antibiotics.
Collapse
Affiliation(s)
- Lucia Vojtech
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, United States
| | - Shahrokh Paktinat
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, United States
| | - Tiffany Luu
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, United States
| | - Stella Teichmann
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, United States
| | - Olusegun O. Soge
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Robert Suchland
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Lindley A. Barbee
- Department of Medicine, University of Washington, Seattle, WA, United States
- Public Health – Seattle and King County, HIV/STD Program, Seattle, WA, United States
| | | |
Collapse
|
19
|
Yang Y, Ma C, Li S, Cai W, Dai W, Zhang X, Yin L, Donge Tang, Liu F, Dai Y. Urinary microbiota and serum metabolite analysis in patients with diabetic kidney disease. Heliyon 2023; 9:e17040. [PMID: 37521000 PMCID: PMC10382294 DOI: 10.1016/j.heliyon.2023.e17040] [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: 07/13/2022] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 08/01/2023] Open
Abstract
Background Diabetic kidney disease (DKD) is a common and potentially fatal consequence of diabetes. Chronic renal failure or end-stage renal disease may result over time. Numerous studies have demonstrated the function of the microbiota in health and disease. The use of advanced urine culture techniques revealed the presence of resident microbiota in the urinary tract, undermining the idea of urine sterility. Studies have demonstrated that the urine microbiota is related with urological illnesses; nevertheless, the fundamental mechanisms by which the urinary microbiota influences the incidence and progression of DKD remain unclear. The purpose of this research was to describe key characteristics of the patients with DKD urinary microbiota in order to facilitate the development of diagnostic and therapeutic for DKD. Methods We evaluated the structure and composition of the microbiota extracted from urine samples taken from DKD patients (n = 19) and matched healthy controls (n = 15) using 16S rRNA gene sequencing. Meanwhile, serum metabolite profiles were compared using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Associations between clinical characteristics, urine microbiota, and serum metabolites were also examined. Finally, the interaction between urine microbiota and serum metabolites was clarified based on differential metabolite abundance analysis. Results The findings indicated that the DKD had a distinct urinary microbiota from the healthy controls (HC). Taxonomic investigations indicated that the DKD microbiome had less alpha diversity than a control group. Proteobacteria and Acidobacteria phyla increased in the DKD, while Firmicutes and Bacteroidetes decreased significantly (P < 0.05). Acidobacteria was the most prevalent microbiota in the DKD, as determined by the Linear discriminant analysis Effect Size (LEfSe) plot. Changes in the urinary microbiota of DKD also had an effect on the makeup of metabolites. Short-chain fatty acids (SCFAs) and protein-bound uremic toxins (PBUTs) were shown to be specific. Then we discovered that arginine and proline metabolism was the primary mechanism involved in the regulation of diabetic kidney disease. Conclusions This study placed the urinary microbiota and serum metabolite of DKD patients into a functional framework and identified the most abundant microbiota in DKD (Proteobacteria and Acidobacteria). Arginine metabolites may have a major effect on DKD patients, which correlated with the progression of DKD.
Collapse
Affiliation(s)
- Yan Yang
- Department of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, 510632, China
| | - Chiyu Ma
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, 518020, China
| | - Shishi Li
- Department of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, 510632, China
| | - Wanxia Cai
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, 518020, China
| | - Weier Dai
- College of Natural Science, The University of Texas at Austin, Austin, TX, 78712, United States
| | - Xinzhou Zhang
- Depart of Nephrology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, 518020, China
| | - Lianghong Yin
- Department of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, 510632, China
| | - Donge Tang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, 518020, China
| | - Fanna Liu
- Department of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, 510632, China
| | - Yong Dai
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, 518020, China
| |
Collapse
|
20
|
Elnaggar JH, Ardizzone CM, Cerca N, Toh E, Łaniewski P, Lillis RA, Herbst-Kralovetz MM, Quayle AJ, Muzny CA, Taylor CM. A novel Gardnerella, Prevotella, and Lactobacillus standard that improves accuracy in quantifying bacterial burden in vaginal microbial communities. Front Cell Infect Microbiol 2023; 13:1198113. [PMID: 37404722 PMCID: PMC10315654 DOI: 10.3389/fcimb.2023.1198113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
Bacterial vaginosis (BV) is the most common vaginal dysbiosis. In this condition, a polymicrobial biofilm develops on vaginal epithelial cells. Accurately quantifying the bacterial burden of the BV biofilm is necessary to further our understanding of BV pathogenesis. Historically, the standard for calculating total bacterial burden of the BV biofilm has been based on quantifying Escherichia coli 16S rRNA gene copy number. However, E. coli is improper for measuring the bacterial burden of this unique micro-environment. Here, we propose a novel qPCR standard to quantify bacterial burden in vaginal microbial communities, from an optimal state to a mature BV biofilm. These standards consist of different combinations of vaginal bacteria including three common BV-associated bacteria (BVAB) Gardnerella spp. (G), Prevotella spp. (P), and Fannyhessea spp. (F) and commensal Lactobacillus spp. (L) using the 16S rRNA gene (G:P:F:L, G:P:F, G:P:L and 1G:9L). We compared these standards to the traditional E. coli (E) reference standard using known quantities of mock vaginal communities and 16 vaginal samples from women. The E standard significantly underestimated the copy numbers of the mock communities, and this underestimation was significantly greater at lower copy numbers of these communities. The G:P:L standard was the most accurate across all mock communities and when compared to other mixed vaginal standards. Mixed vaginal standards were further validated with vaginal samples. This new G:P:L standard can be used in BV pathogenesis research to enhance reproducibility and reliability in quantitative measurements of BVAB, spanning from the optimal to non-optimal (including BV) vaginal microbiota.
Collapse
Affiliation(s)
- Jacob H. Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Caleb M. Ardizzone
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Nuno Cerca
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| | - Evelyn Toh
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Paweł Łaniewski
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, United States
| | - Rebecca A. Lillis
- Division of Infectious Diseases, Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Melissa M. Herbst-Kralovetz
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, United States
| | - Alison J. Quayle
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Christina A. Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| |
Collapse
|
21
|
Zhang C, McIntosh KD, Sienkiewicz N, Stelzer EA, Graham JL, Lu J. Using cyanobacteria and other phytoplankton to assess trophic conditions: A qPCR-based, multi-year study in twelve large rivers across the United States. WATER RESEARCH 2023; 235:119679. [PMID: 37011576 PMCID: PMC10123349 DOI: 10.1016/j.watres.2023.119679] [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: 10/26/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Phytoplankton is the essential primary producer in fresh surface water ecosystems. However, excessive phytoplankton growth due to eutrophication significantly threatens ecologic, economic, and public health. Therefore, phytoplankton identification and quantification are essential to understanding the productivity and health of freshwater ecosystems as well as the impacts of phytoplankton overgrowth (such as Cyanobacterial blooms) on public health. Microscopy is the gold standard for phytoplankton assessment but is time-consuming, has low throughput, and requires rich experience in phytoplankton morphology. Quantitative polymerase chain reaction (qPCR) is accurate and straightforward with high throughput. In addition, qPCR does not require expertise in phytoplankton morphology. Therefore, qPCR can be a useful alternative for molecular identification and enumeration of phytoplankton. Nonetheless, a comprehensive study is missing which evaluates and compares the feasibility of using qPCR and microscopy to assess phytoplankton in fresh water. This study 1) compared the performance of qPCR and microscopy in identifying and quantifying phytoplankton and 2) evaluated qPCR as a molecular tool to assess phytoplankton and indicate eutrophication. We assessed phytoplankton using both qPCR and microscopy in twelve large freshwater rivers across the United States from early summer to late fall in 2017, 2018, and 2019. qPCR- and microscope-based phytoplankton abundance had a significant positive linear correlation (adjusted R2 = 0.836, p-value < 0.001). Phytoplankton abundance had limited temporal variation within each sampling season and over the three years studied. The sampling sites in the midcontinent rivers had higher phytoplankton abundance than those in the eastern and western rivers. For instance, the concentration (geometric mean) of Bacillariophyta, Cyanobacteria, Chlorophyta, and Dinoflagellates at the sampling sites in the midcontinent rivers was approximately three times that at the sampling sites in the western rivers and approximately 18 times that at the sampling sites in the eastern rivers. Welch's analysis of variance indicates that phytoplankton abundance at the sampling sites in the midcontinent rivers was significantly higher than that at the sampling sites in the eastern rivers (p-value = 0.013) but was comparable to that at the sampling sites in the western rivers (p-value = 0.095). The higher phytoplankton abundance at the sampling sites in the midcontinent rivers was presumably because these rivers were more eutrophic. Indeed, low phytoplankton abundance occurred in oligotrophic or low trophic sites, whereas eutrophic sites had greater phytoplankton abundance. This study demonstrates that qPCR-based phytoplankton abundance can be a useful numerical indicator of the trophic conditions and water quality in freshwater rivers.
Collapse
Affiliation(s)
- Chiqian Zhang
- Department of Civil and Environmental Engineering, College of Sciences and Engineering, Southern University and A&M College, Baton Rouge, LA 70813, United States
| | - Kyle D McIntosh
- Oak Ridge Institute for Science and Education at the United States Environmental Protection Agency's Office of Research and Development, Oak Ridge, TN 37830, United States
| | - Nathan Sienkiewicz
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, United States
| | - Erin A Stelzer
- U.S. Geological Survey, Columbus, OH 43229, United States
| | | | - Jingrang Lu
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, United States.
| |
Collapse
|
22
|
Chen M, Cui Y, Liu C, Tong X, Wang M, Wu C, Liu Y, Zhao Y, Chen X. Characteristics of the microbiome in lung adenocarcinoma tissue from patients in Kunming city of southwestern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49992-50001. [PMID: 36787077 DOI: 10.1007/s11356-023-25528-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 01/19/2023] [Indexed: 04/16/2023]
Abstract
The purpose of this study is to identify the characteristics of microbial communities in the lung cancer tissues from patients in Kunming sity of southwestern China and to compare the microbial differences at different clinical stages of lung cancer to uncover potential microbial biomarkers. In total, 40 tissue samples of primary lung adenocarcinoma were collected and further performed by 16S rRNA gene sequencing. The subjects were grouped according to TNM stages (T and N group), clinical stage, and smoke status, and the microbial differences in each group were compared. Analysis of sequence data to determine beta diversity, the UniFrac distance was calculated by QIIME and visualized by principal coordinate analysis (PCoA) using R (version 2.15.3). Microbiome abundance and diversity between different groups were calculated by t test or Wilcoxon rank sum test and drawn by R. The linear discriminant analysis effect size (LEfSe) method was utilized to compare relative abundances of all bacterial taxa between groups. A total of 951 OTUs were identified in the cancer tissues. No significant difference has been found in the alpha diversity within all the groups. Beta diversity significantly differed in the N, T, and clinical stage groups. By LEfSe analysis, eight differential taxa including Bifidobacterium were identified in the N group. In the T1 and T2 group, the LEfSe result identified five phyla and ten genera. The differential genera were Moraxella, Dolosigranulum, unidentified_Corynebacteriaceae, and Citrobacter in the T2 group and Bifidobacterium, Alistipes, Akkermansia, Blautia, Lactobacillus, as well as Faecalibaculum in the T1 group. Differential bacterial composition and abundance were also observed in the clinical stage group. This study confirmed that by 16S rRNA sequencing, we identified the dominant microbe of lung cancer tissue in different groups. Bifidobacterium may play an essential role in lymph node metastasis and tumor progression, providing a specific potential microbial biomarker for lung adenocarcinoma. PCR products were subject to vertical electrophoresis on 2% agarose gels, and a colloid recovery kit (Qiagen, Valencia, CA) was applied to recover the target bands. Libraries were generated by the TruSeq DNA PCR-Free Sample Preparation Kit (Illumina, San Diego, USA), and the concentrations were quantitated with a Qubit fluorometer. Finally, the qualified libraries were sequenced by NovaSeq6000 (Illumina).
Collapse
Affiliation(s)
- Manjun Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, No.295 Xichang Road, Yunnan, 650032, Kunming, China
| | - Yue Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, No.295 Xichang Road, Yunnan, 650032, Kunming, China
| | - Chao Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, No.295 Xichang Road, Yunnan, 650032, Kunming, China
| | - Xinghe Tong
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, No.295 Xichang Road, Yunnan, 650032, Kunming, China
| | - Mengtian Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, No.295 Xichang Road, Yunnan, 650032, Kunming, China
| | - Chunman Wu
- Department of Medicine, Dinfectome Inc., Nanjing, Jiangsu, 210032, China
| | - Yong Liu
- Department of Medicine, Dinfectome Inc., Nanjing, Jiangsu, 210032, China
| | - Yunping Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, No.295 Xichang Road, Yunnan, 650032, Kunming, China
| | - Xiaobo Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, No.295 Xichang Road, Yunnan, 650032, Kunming, China.
| |
Collapse
|
23
|
Liu F, Lu H, Dong B, Huang X, Cheng H, Qu R, Hu Y, Zhong L, Guo Z, You Y, Xu ZZ. Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/– Bacteria. mSystems 2023; 8:e0073822. [PMID: 36971593 PMCID: PMC10134872 DOI: 10.1128/msystems.00738-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes.
Collapse
|
24
|
Broderick D, Marsh R, Waite D, Pillarisetti N, Chang AB, Taylor MW. Realising respiratory microbiomic meta-analyses: time for a standardised framework. MICROBIOME 2023; 11:57. [PMID: 36945040 PMCID: PMC10031919 DOI: 10.1186/s40168-023-01499-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
In microbiome fields of study, meta-analyses have proven to be a valuable tool for identifying the technical drivers of variation among studies and results of investigations in several diseases, such as those of the gut and sinuses. Meta-analyses also represent a powerful and efficient approach to leverage existing scientific data to both reaffirm existing findings and generate new hypotheses within the field. However, there are currently limited data in other fields, such as the paediatric respiratory tract, where extension of original data becomes even more critical due to samples often being difficult to obtain and process for a range of both technical and ethical reasons. Performing such analyses in an evolving field comes with challenges related to data accessibility and heterogeneity. This is particularly the case in paediatric respiratory microbiomics - a field in which best microbiome-related practices are not yet firmly established, clinical heterogeneity abounds and ethical challenges can complicate sharing of patient data. Having recently conducted a large-scale, individual participant data meta-analysis of the paediatric respiratory microbiota (n = 2624 children from 20 studies), we discuss here some of the unique barriers facing these studies and open and invite a dialogue towards future opportunities. Video Abstract.
Collapse
Affiliation(s)
- David Broderick
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Robyn Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - David Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, QLD, Australia
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| |
Collapse
|
25
|
Eco-evolutionary implications of helminth microbiomes. J Helminthol 2023; 97:e22. [PMID: 36790127 DOI: 10.1017/s0022149x23000056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The evolution of helminth parasites has long been seen as an interplay between host resistance to infection and the parasite's capacity to bypass such resistance. However, there has recently been an increasing appreciation of the role of symbiotic microbes in the interaction of helminth parasites and their hosts. It is now clear that helminths have a different microbiome from the organisms they parasitize, and sometimes amid large variability, components of the microbiome are shared among different life stages or among populations of the parasite. Helminths have been shown to acquire microbes from their parent generations (vertical transmission) and from their surroundings (horizontal transmission). In this latter case, natural selection has been strongly linked to the fact that helminth-associated microbiota is not simply a random assemblage of the pool of microbes available from their organismal hosts or environments. Indeed, some helminth parasites and specific microbial taxa have evolved complex ecological relationships, ranging from obligate mutualism to reproductive manipulation of the helminth by associated microbes. However, our understanding is still very elementary regarding the net effect of all microbiome components in the eco-evolution of helminths and their interaction with hosts. In this non-exhaustible review, we focus on the bacterial microbiome associated with helminths (as opposed to the microbiome of their hosts) and highlight relevant concepts and key findings in bacterial transmission, ecological associations, and taxonomic and functional diversity of the bacteriome. We integrate the microbiome dimension in a discussion of the evolution of helminth parasites and identify fundamental knowledge gaps, finally suggesting research avenues for understanding the eco-evolutionary impacts of the microbiome in host-parasite interactions in light of new technological developments.
Collapse
|
26
|
Peter VG, Morandi SC, Herzog EL, Zinkernagel MS, Zysset-Burri DC. Investigating the Ocular Surface Microbiome: What Can It Tell Us? Clin Ophthalmol 2023; 17:259-271. [PMID: 36698849 PMCID: PMC9870096 DOI: 10.2147/opth.s359304] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
While pathogens of the eye have been studied for a very long time, the existence of resident microbes on the surface of healthy eyes has gained interest only recently. It appears that commensal microbes are a normal feature of the healthy eye, whose role and properties are currently the subject of extensive research. This review provides an overview of studies that have used 16s rRNA gene sequencing and whole metagenome shotgun sequencing to characterize microbial communities associated with the healthy ocular surface from kingdom to genus level. Bacteria are the primary colonizers of the healthy ocular surface, with three predominant phyla: Proteobacteria, Actinobacteria, and Firmicutes, regardless of the host, environment, and method used. Refining the microbial classification to the genus level reveals a highly variable distribution from one individual and study to another. Factors accounting for this variability are intriguing - it is currently unknown to what extent this is attributable to the individuals and their environment and how much is artifactual. Clearly, it is technically challenging to accurately describe the microorganisms of the ocular surface because their abundance is relatively low, thus, permitting substantial contaminations. More research is needed, including better experimental standards to prevent biases, and the exploration of the ocular surface microbiome's role in a spectrum of healthy to pathological states. Outcomes from such research include the opportunity for therapeutic interventions targeting the microbiome.
Collapse
Affiliation(s)
- Virginie G Peter
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Correspondence: Virginie G Peter, Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Freiburgstrasse 15, Bern, 3010, Switzerland, Email
| | - Sophia C Morandi
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Elio L Herzog
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Martin S Zinkernagel
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Denise C Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland
| |
Collapse
|
27
|
Kallastu A, Malv E, Aro V, Meikas A, Vendelin M, Kattel A, Nahku R, Kazantseva J. Absolute quantification of viable bacteria abundances in food by next-generation sequencing: Quantitative NGS of viable microbes. Curr Res Food Sci 2023; 6:100443. [PMID: 36691592 PMCID: PMC9860258 DOI: 10.1016/j.crfs.2023.100443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/15/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Next-generation sequencing (NGS) is an important tool for taxonomical bacteria identification. Recent technological developments have led to its improvement and availability. Despite the undeniable advantages of this approach, it has several limitations and shortcomings. The usual outcome of microbiota sequencing is a relative abundance of bacterial taxa. The information about bacteria viability or enumeration is missing. However, this knowledge is crucial for many applications. In the current study, we elaborated the complete workflow for the absolute quantification of living bacteria based on 16S rRNA gene amplicon sequencing. A fluorescent PMAxx reagent penetrating a damaged cell membrane was used to discriminate between the total and viable bacterial population. Bacteria enumeration was estimated by the spike-in technique or qPCR quantification. For method optimization, twenty bacterial species were taken, and the results of the workflow were validated by widely accepted methodologies: flow cytometry, microbiological plating, and viability-qPCR. Despite the minor discrepancy between all methods used, they all showed compatible results. Finally, we tested the workflow with actual food samples and received a good correlation between the methods regarding the estimation of the number of viable bacteria. Overall, the elaborated and integrated NGS approach could be the next step in perceiving a holistic picture of a sample microbiota.
Collapse
Affiliation(s)
- Aili Kallastu
- Center of Food and Fermentation Technologies, Mäealuse 2/4, Tallinn, 12618, Estonia
| | - Esther Malv
- Center of Food and Fermentation Technologies, Mäealuse 2/4, Tallinn, 12618, Estonia
| | - Valter Aro
- Center of Food and Fermentation Technologies, Mäealuse 2/4, Tallinn, 12618, Estonia,Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn, 12618, Estonia
| | - Anne Meikas
- Center of Food and Fermentation Technologies, Mäealuse 2/4, Tallinn, 12618, Estonia
| | - Mariann Vendelin
- Center of Food and Fermentation Technologies, Mäealuse 2/4, Tallinn, 12618, Estonia
| | - Anna Kattel
- Center of Food and Fermentation Technologies, Mäealuse 2/4, Tallinn, 12618, Estonia,Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn, 12618, Estonia
| | - Ranno Nahku
- Center of Food and Fermentation Technologies, Mäealuse 2/4, Tallinn, 12618, Estonia
| | - Jekaterina Kazantseva
- Center of Food and Fermentation Technologies, Mäealuse 2/4, Tallinn, 12618, Estonia,Corresponding autho.
| |
Collapse
|
28
|
Panah FM, Nielsen KD, Simpson GL, Schönherz A, Schramm A, Lauridsen C, Nielsen TS, Højberg O, Fredborg M, Purup S, Canibe N. A westernized diet changed the colonic bacterial composition and metabolite concentration in a dextran sulfate sodium pig model for ulcerative colitis. Front Microbiol 2023; 14:1018242. [PMID: 37138607 PMCID: PMC10150118 DOI: 10.3389/fmicb.2023.1018242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction Ulcerative colitis (UC) is characterized by chronic inflammation in the colonic epithelium and has a blurred etiology. A western diet and microbial dysbiosis in the colon were reported to play a role in UC development. In this study, we investigated the effect of a westernized diet, i.e., increasing fat and protein content by including ground beef, on the colonic bacterial composition in a dextran sulfate sodium (DexSS) challenged pig study. Methods The experiment was carried out in three complete blocks following a 2×2 factorial design including 24 six-week old pigs, fed either a standard diet (CT) or the standard diet substituted with 15% ground beef to simulate a typical westernized diet (WD). Colitis was induced in half of the pigs on each dietary treatment by oral administration of DexSS (DSS and WD+DSS, respectively). Samples from proximal and distal colon and feces were collected. Results and discussion Bacterial alpha diversity was unaffected by experimental block, and sample type. In proximal colon, WD group had similar alpha diversity to CT group and the WD+DSS group showed the lowest alpha diversity compared to the other treatment groups. There was a significant interaction between western diet and DexSS for beta diversity, based on Bray-Curtis dissimilarly. The westernized diet and DexSS resulted in three and seven differentially abundant phyla, 21 and 65 species, respectively, mainly associated with the Firmicutes and Bacteroidota phyla followed by Spirochaetota, Desulfobacterota, and Proteobacteria. The concentration of short-chain fatty acids (SCFA) was lowest in the distal colon. Treatment had a slight effect on the estimates for microbial metabolites that might have valuable biological relevance for future studies. The concentration of putrescine in the colon and feces and that of total biogenic amines was highest in the WD+DSS group. We conclude that a westernized diet could be a potential risk factor and an exacerbating agent for UC by reducing the abundance of SCFA-producing bacteria, increasing the abundance of pathogens such as Helicobacter trogontum, and by increasing the concentration of microbial proteolytic-derived metabolites in the colon.
Collapse
Affiliation(s)
- Farhad M. Panah
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
- *Correspondence: Farhad M. Panah,
| | - Katrine D. Nielsen
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Gavin L. Simpson
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Anna Schönherz
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | | | - Charlotte Lauridsen
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Tina S. Nielsen
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Ole Højberg
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Marlene Fredborg
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Stig Purup
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Nuria Canibe
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| |
Collapse
|
29
|
Simon MC, Sina C, Ferrario PG, Daniel H. Gut Microbiome Analysis for Personalized Nutrition: The State of Science. Mol Nutr Food Res 2023; 67:e2200476. [PMID: 36424179 DOI: 10.1002/mnfr.202200476] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/17/2022] [Indexed: 11/27/2022]
Abstract
Whereas most concepts of personalized nutrition (PN) in the past, included genotyping, recent years have brought new approaches that include microbiome analysis to optimize recommendations for diet and lifestyle changes. The new approach, offered by companies, that microbiome analysis provides a real benefit to either more concise recommendations or for increased compliance to PN, is largely lacking scientific validation. Although the microbiome field shows enormous proliferation, it has some major flaws that make its use in the public health domain currently critical. Starting with the quality and representative character of the stool samples, its processing and analysis as well as assembly of metagenome data and the interpretation. Moreover, there is still no consensus of what constitutes a "normal/healthy" microbiome, nor what features characterize a dysbiotic microbiome. And, based on hundreds of individual parameters and environmental factors, the intestinal microbiome shows a huge variability and consequently changing one factor-such as food intake-is likely to have a limited impact in achieving optimized health. The present review intends to summarize the state of consolidated knowledge on human gut microbiome in the context of diet and disease, its key features, and its influencing factors as well as its "add-on" quality for PN offers.
Collapse
Affiliation(s)
- Marie-Christine Simon
- Department of Nutrition and Food Science, Nutrition and Microbiome, University of Bonn, 53115, Bonn, Germany
| | - Christian Sina
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, 23538, Campus Lübeck, Germany
| | - Paola G Ferrario
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, 76131, Karlsruhe, Germany
| | | | -
- Department of Nutrition and Food Science, Nutrition and Microbiome, University of Bonn, 53115, Bonn, Germany
| |
Collapse
|
30
|
Gruneck L, Marriott LK, Gentekaki E, Kespechara K, Sharpton TJ, Denny J, Shannon J, Popluechai S. A Non-Randomized Trial Investigating the Impact of Brown Rice Consumption on Gut Microbiota, Attention, and Short-Term Working Memory in Thai School-Aged Children. Nutrients 2022; 14:nu14235176. [PMID: 36501207 PMCID: PMC9738792 DOI: 10.3390/nu14235176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
While dietary fiber has been shown to influence the composition of gut microbiota and cognitive function in adults, much less is known about the fiber-microbiome-cognition association in children. We profiled gut microbiota using quantitative PCR (qPCR) and evaluated cognitive function using the Corsi block-tapping test (CBT) and the psychomotor vigilance test (PVT) before, during, and after the dietary intervention of 127 school-aged children in northern Thailand. While we found that Sinlek rice (SLR) consumption did not significantly alter the abundance of gut microbiota or the cognitive performance of school-aged children, we did find age to be associated with variations in both the gut microbiota profiles and cognitive outcomes. Gammaproteobacteria was significantly lower in the control and SLR groups during the middle time points of both phases (Weeks 4 and 61), and its abundance was associated with age. Cognitive performance using CBT and PVT were also found to be age-sensitive, as older children outperformed younger children on both of these cognitive assessments. Finally, a multiple factor analysis (MFA) revealed that age and cognitive performance best explain individual variation in this study. Collectively, these findings further describe the influence of host variables on the microbial profiles and cognitive outcomes of school-aged children consuming Sinlek rice in Thailand.
Collapse
Affiliation(s)
- Lucsame Gruneck
- Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
| | - Lisa K. Marriott
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR 97201, USA
| | - Eleni Gentekaki
- Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
| | | | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
- Department of Statistics, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Denny
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR 97201, USA
| | - Jackilen Shannon
- Division of Oncologic Sciences, Oregon Health & Science University, Portland, OR 97331, USA
- Correspondence: (J.S.); (S.P.)
| | - Siam Popluechai
- Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
- Correspondence: (J.S.); (S.P.)
| |
Collapse
|
31
|
McChalicher CW, Auniņš JG. Drugging the microbiome and bacterial live biotherapeutic consortium production. Curr Opin Biotechnol 2022; 78:102801. [PMID: 36228531 DOI: 10.1016/j.copbio.2022.102801] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 12/14/2022]
Abstract
Research leading to characterization, quantification, and functional attribution of the microbes throughout the human body has led to many drug-development programs. These programs aim to manipulate a patient's microbiome through the addition of new strains or functions, the subtraction of deleterious microbes, or the rebalancing of the existing population through various drug modalities. Here, we present a general overview of those modalities with a specific focus on bacterial live biotherapeutic products (LBPs). The bacterial LBP modality has unique concerns to ensure product quality, thus, topics related to manufacturing, quality control, and regulation are addressed.
Collapse
Affiliation(s)
| | - John G Auniņš
- Seres Therapeutics Inc, 200 Sidney St, Cambridge, MA 02139, United States.
| |
Collapse
|
32
|
Moderate and transient impact of antibiotic use on the gut microbiota in a rural Vietnamese cohort. Sci Rep 2022; 12:20189. [PMID: 36424459 PMCID: PMC9691687 DOI: 10.1038/s41598-022-24488-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022] Open
Abstract
The human gut microbiota has been shown to be significantly perturbed by antibiotic use, while recovering to the pre-treatment state several weeks after short antibiotic exposure. The effects of antibiotics on the gut microbiota have however been mainly documented in high-income settings with lower levels of antibiotic resistance as compared to lower and middle income countries (LMIC). This study aimed to examine the long-term consequences of repeated exposure to commonly use antibiotics on the fecal microbiota of residents living in a low income setting with high prevalence of antibiotic resistance. Fecal samples from household individuals (n = 63) participating in a rural cohort in northern Vietnam were collected monthly for a period of 6 months. Using 16S V4 rRNA gene region amplicon sequencing and linear mixed-effects models analysis, we observed only a minor and transient effect of antibiotics on the microbial richness (ß = - 31.3, 95%CI = - 55.3, - 7.3, p = 0.011), while the microbial diversity was even less affected (ß = - 0.298, 95%CI - 0.686, 0.090, p = 0.132). Principal Component Analyses (PCA) did not reveal separation of samples into distinct microbiota-based clusters by antibiotics use, suggesting the microbiota composition was not affected by the antibiotics commonly used in this population. Additionally, the fecal microbial diversity of the subjects in our study cohort was lower when compared to that of healthy Dutch adults (median 3.95 (IQR 3.72-4.13) vs median 3.69 (IQR3.31-4.11), p = 0.028, despite the higher dietary fiber content in the Vietnamese as compared to western diet. Our findings support the hypothesis that frequent antibiotic exposure may push the microbiota to a different steady state that is less diverse but more resilient to disruption by subsequent antibiotic use.
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Armbruster CR, Li K, Kiedrowski MR, Zemke AC, Melvin JA, Moore J, Atteih S, Fitch AC, DuPont M, Manko CD, Weaver ML, Gaston JR, Alcorn JF, Morris A, Methé BA, Lee SE, Bomberger JM. Low Diversity and Instability of the Sinus Microbiota over Time in Adults with Cystic Fibrosis. Microbiol Spectr 2022; 10:e0125122. [PMID: 36094193 PMCID: PMC9603634 DOI: 10.1128/spectrum.01251-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/10/2022] [Indexed: 12/30/2022] Open
Abstract
Chronic rhinosinusitis (CRS) is a common, yet underreported and understudied manifestation of upper respiratory disease in people with cystic fibrosis (CF). Recently developed standard of care guidelines for the management of CF CRS suggest treatment of upper airway disease may ameliorate lower airway disease. We sought to determine whether changes to sinus microbial community diversity and specific taxa known to cause CF lung disease are associated with increased respiratory disease and inflammation. We performed 16S rRNA gene sequencing, supplemented with cytokine analyses, microscopy, and bacterial culturing, on samples from the sinuses of 27 adults with CF CRS. At each study visit, participants underwent endoscopic paranasal sinus sampling and clinical evaluation. We identified key drivers of microbial community composition and evaluated relationships between diversity and taxa with disease outcomes and inflammation. Sinus community diversity was low, and the composition was unstable, with many participants exhibiting alternating dominance between Pseudomonas aeruginosa and staphylococci over time. Despite a tendency for dominance by these two taxa, communities were highly individualized and shifted composition during exacerbation of sinus disease symptoms. Exacerbations were also associated with communities dominated by Staphylococcus spp. Reduced microbial community diversity was linked to worse sinus disease and the inflammatory status of the sinuses (including increased interleukin-1β [IL-1β]). Increased IL-1β was also linked to worse sinus endoscopic appearance, and other cytokines were linked to microbial community dynamics. Our work revealed previously unknown instability of sinus microbial communities and a link between inflammation, lack of microbial community diversity, and worse sinus disease. IMPORTANCE Together with prior sinus microbiota studies of adults with CF chronic rhinosinusitis, our study underscores similarities between sinus and lower respiratory tract microbial community structures in CF. We show how community structure tracks with inflammation and several disease measures. This work strongly suggests that clinical management of CRS could be leveraged to improve overall respiratory health in CF. Our work implicates elevated IL-1β in reduced microbiota diversity and worse sinus disease in CF CRS, suggesting applications for existing therapies targeting IL-1β. Finally, the widespread use of highly effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy has led to less frequent availability of spontaneous expectorated sputum for microbiological surveillance of lung infections. A better understanding of CF sinus microbiology could provide a much-needed alternative site for monitoring respiratory infection status by important CF pathogens.
Collapse
Affiliation(s)
- Catherine R. Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Megan R. Kiedrowski
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anna C. Zemke
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jeffrey A. Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John Moore
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Samar Atteih
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Adam C. Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Matthew DuPont
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christopher D. Manko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Madison L. Weaver
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jordon R. Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John F. Alcorn
- Department of Pediatrics, Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Barbara A. Methé
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Stella E. Lee
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
35
|
Proctor A, Parvinroo S, Richie T, Jia X, Lee STM, Karp PD, Paley S, Kostic AD, Pierre JF, Wannemuehler MJ, Phillips GJ. Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function. mSystems 2022; 7:e0029322. [PMID: 35968975 PMCID: PMC9600240 DOI: 10.1128/msystems.00293-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/20/2022] [Indexed: 12/24/2022] Open
Abstract
Animals colonized with a defined microbiota represent useful experimental systems to investigate microbiome function. The altered Schaedler flora (ASF) represents a consortium of eight murine bacterial species that have been used for more than 4 decades where the study of mice with a reduced microbiota is desired. In contrast to germ-free mice, or mice colonized with only one or two species, ASF mice show the normal gut structure and immune system development. To further expand the utility of the ASF, we have developed technical and bioinformatic resources to enable a systems-based analysis of microbiome function using this model. Here, we highlighted four distinct applications of these resources that enable and improve (i) measurements of the abundance of each ASF member by quantitative PCR; (ii) exploration and comparative analysis of ASF genomes and the metabolic pathways they encode that comprise the entire gut microbiome; (iii) global transcriptional profiling to identify genes whose expression responds to environmental changes within the gut; and (iv) discovery of genetic changes resulting from the evolutionary adaptation of the microbiota. These resources were designed to be accessible to a broad community of researchers that, in combination with conventionally-reared mice (i.e., with complex microbiome), should contribute to our understanding of microbiome structure and function. IMPORTANCE Improved experimental systems are needed to advance our understanding of how the gut microbiome influences processes of the mammalian host as well as microbial community structure and function. An approach that is receiving considerable attention is the use of animal models that harbor a stable microbiota of known composition, i.e., defined microbiota, which enables control over an otherwise highly complex and variable feature of mammalian biology. The altered Schaedler flora (ASF) consortium is a well-established defined microbiota model, where mice are stably colonized with 8 distinct murine bacterial species. To take better advantage of the ASF, we established new experimental and bioinformatics resources for researchers to make better use of this model as an experimental system to study microbiome function.
Collapse
Affiliation(s)
- Alexandra Proctor
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Shadi Parvinroo
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Tanner Richie
- Division of Biology, Kansas State University, Manhattan Kansas, USA
| | - Xinglin Jia
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan Kansas, USA
| | - Peter D. Karp
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Suzanne Paley
- Bioinformatics Research Group, SRI International, Menlo Park, California, USA
| | - Aleksandar D. Kostic
- Department of Microbiology and Immunology, Joslin Diabetes Center, Harvard University, Cambridge Massachusetts, USA
| | - Joseph F. Pierre
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison Wisconsin, USA
| | | | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| |
Collapse
|
36
|
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: 4] [Impact Index Per Article: 2.0] [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.
Collapse
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
| |
Collapse
|
37
|
Morgan EW, Perdew GH, Patterson AD. Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research. Toxicol Sci 2022; 187:189-213. [PMID: 35285497 PMCID: PMC9154275 DOI: 10.1093/toxsci/kfac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microbial communities on and within the host contact environmental pollutants, toxic compounds, and other xenobiotic compounds. These communities of bacteria, fungi, viruses, and archaea possess diverse metabolic potential to catabolize compounds and produce new metabolites. Microbes alter chemical disposition thus making the microbiome a natural subject of interest for toxicology. Sequencing and metabolomics technologies permit the study of microbiomes altered by acute or long-term exposure to xenobiotics. These investigations have already contributed to and are helping to re-interpret traditional understandings of toxicology. The purpose of this review is to provide a survey of the current methods used to characterize microbes within the context of toxicology. This will include discussion of commonly used techniques for conducting omic-based experiments, their respective strengths and deficiencies, and how forward-looking techniques may address present shortcomings. Finally, a perspective will be provided regarding common assumptions that currently impede microbiome studies from producing causal explanations of toxicologic mechanisms.
Collapse
Affiliation(s)
- Ethan W Morgan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Gary H Perdew
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew D Patterson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
38
|
Lau HC, Shen Y, Huang H, Yuan X, Ji M, Gong H, Hsueh CY, Zhou L. Cross-comparison of microbiota in the oropharynx, hypopharyngeal squamous cell carcinoma and their adjacent tissues through quantitative microbiome profiling. J Oral Microbiol 2022; 14:2073860. [PMID: 35573640 PMCID: PMC9103590 DOI: 10.1080/20002297.2022.2073860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Aims To clarify the absolute abundance of microbial communities on hypopharyngeal squamous cell carcinoma and their correlation to those in the oropharynx. Methods Clinical data, swabs, and tissue samples from 27 HPSCC patients were collected in this study and divided into three sampling groups: 19 oropharyngeal mucosa (OPM), 27 hypopharyngeal carcinomas tissues (HC), and 26 corresponding adjacent tissues (AT). Relative microbiome profiling (RMP), and quantitative microbiome profiling (QMP) of 16S rRNA amplicon sequencing were used for analysis. Results Beta-diversity showed that abundance and phylogenetic tree in OPM group were less when compared to either HC and AT. Although HC and AT were found to have similar microbiota, Bray-Curtis based beta-diversity still highlighted differences. Fusobacterium, Porphyromonas, Haemophilus, and Peptostreptococcus at the genus level in OPM were positively correlated with HC. After categorizing HC through TNM staging, the abundance of genera Fusobacterium, Parvimonas, and Dialister were found to be enhanced in higher T classifications (T3-4) and advanced stages (Ⅳ). Conclusions QMP yielded more comprehensive results than RMP. Dysbiosis was found in OPM groups and could be used to narrow down differential microbiome for the HC group. Genera of Parvimonas, Fusobacterium, and Dialister were deemed asrisk factors of advanced HPSCC.
Collapse
Affiliation(s)
- Hui-Ching Lau
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, PR, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR, China
| | - Yujie Shen
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, PR, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR, China
| | - Huiying Huang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, PR, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR, China
| | - Xiaohui Yuan
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, PR, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR, China
| | - Mengyou Ji
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, PR, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR, China
| | - Hongli Gong
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, PR, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR, China
| | - Chi-Yao Hsueh
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, PR, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR, China
| | - Liang Zhou
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, PR, China
- Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, PR, China
| |
Collapse
|
39
|
Chuang JY. Stressor-Specific Microbiota Intervention. Front Nutr 2022; 9:870665. [PMID: 35520283 PMCID: PMC9063858 DOI: 10.3389/fnut.2022.870665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
To date, mental disorders are diagnosed and treated by the subjective judgment of psychiatrists based on diagnostic criteria and treatment guidelines, respectively. Mental disorders are heterogeneous illnesses with a substantial treatment-refractory rate. Thus, there is a great need for novel treatment approaches. This article proposes a treatment approach centered on the concept of the gut–brain axis. There is mounting evidence indicating an association between stressors, microbiota, microglia, and mental disorders. Stressors might facilitate dysbiosis, inflammation, and the occurrence of mental disorders. This novel treatment approach is based on the idea that stressor types instead of the heterogeneous psychiatric diagnosis might be closer to the neurobiological underpinnings of mental disorders. First of all, patients with treatment-resistant mental disorders will be asked to describe their major stressors. Then, clinicians will calculate the total threat score and the total deprivation score. Subsequently, treatment tailored to the major stressor type will be administered to restore a healthy gut microbiome. Presumably, treatment will be aimed at increasing microbiota diversity in those who mainly have deprivation stressors and boosting Actinobacteria in those who have mainly threat stressors. Large-scale clinical trials are warranted to test this hypothetical approach.
Collapse
Affiliation(s)
- Jie-Yu Chuang
- Department of Psychiatry, Cardinal Tien Hospital, New Taipei City, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
- *Correspondence: Jie-Yu Chuang
| |
Collapse
|
40
|
Celis AI, Aranda-Díaz A, Culver R, Xue K, Relman D, Shi H, Huang KC. Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals. iScience 2022; 25:103907. [PMID: 35340431 PMCID: PMC8941205 DOI: 10.1016/j.isci.2022.103907] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/24/2021] [Accepted: 02/08/2022] [Indexed: 01/04/2023] Open
Abstract
While microbial communities inhabit a wide variety of complex natural environments, in vitro culturing enables highly controlled conditions and high-throughput interrogation for generating mechanistic insights. In vitro assemblies of gut commensals have recently been introduced as models for the intestinal microbiota, which plays fundamental roles in host health. However, a protocol for 16S rRNA sequencing and analysis of in vitro samples that optimizes financial cost, time/effort, and accuracy/reproducibility has yet to be established. Here, we systematically identify protocol elements that have significant impact, introduce bias, and/or can be simplified. Our results indicate that community diversity and composition are generally unaffected by substantial protocol streamlining. Additionally, we demonstrate that a strictly aerobic halophile is an effective spike-in for estimating absolute abundances in communities of anaerobic gut commensals. This time- and money-saving protocol should accelerate discovery by increasing 16S rRNA data reliability and comparability and through the incorporation of absolute abundance estimates.
Collapse
Affiliation(s)
- Arianna I. Celis
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrés Aranda-Díaz
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Rebecca Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katherine Xue
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| |
Collapse
|
41
|
Bodnar TS, Lee C, Wong A, Rubin I, Parfrey LW, Weinberg J. Evidence for long-lasting alterations in the fecal microbiota following prenatal alcohol exposure. Alcohol Clin Exp Res 2022; 46:542-555. [PMID: 35102585 PMCID: PMC9238389 DOI: 10.1111/acer.14784] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND There is growing evidence that the gut microbiota can be shaped by early-life experiences/exposures, with long-term consequences for brain, behavior, and health. Changes in the gut microbiota have also been identified in neurodevelopmental disorders including Autism Spectrum Disorder and schizophrenia. In contrast, no studies to date have investigated whether the gut microbiota is altered in individuals with Fetal Alcohol Spectrum Disorder (FASD), the neurodevelopmental disorder that results from prenatal alcohol exposure (PAE). The current study was designed to assess the impact of PAE on the fecal microbiota. METHODS We used a rodent model in which pregnant Sprague-Dawley rats were provided with an EtOH-containing diet or a control diet throughout gestation. Fecal samples were collected from adult male and female animals and 16s rRNA sequencing was performed. RESULTS Overall, PAE rats showed greater richness of bacterial species, with community structure investigations demonstrating distinct clustering by prenatal treatment. In addition, prenatal treatment and sex-specific alterations were observed for many specific microbes. For example, in males, Bacteroides and Bifidobacterium, and in females, Faecalitalea and Proteus, differed in abundance between PAE and control rats. CONCLUSIONS Taken together, these results show for the first time that PAE has a long-lasting and sex-specific impact on the fecal microbiota. Further research is needed that considers fetal microbiota in the development of new interventions in FASD.
Collapse
Affiliation(s)
- Tamara S. Bodnar
- Department of Cellular and Physiological Sciences, 2350 Health Sciences Mall, University of British Columbia, Vancouver, BC, Canada, V6T 1Z3
| | - Christopher Lee
- Department of Microbiology and Immunology, 2185 E Mall, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Athena Wong
- Department of Biology, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Ilan Rubin
- Department of Zoology, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Laura Wegener Parfrey
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 109 – 2212 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Joanne Weinberg
- Department of Cellular and Physiological Sciences, 2350 Health Sciences Mall, University of British Columbia, Vancouver, BC, Canada, V6T 1Z3
| |
Collapse
|
42
|
|
43
|
Berkhout M, Zoetendal E, Plugge C, Belzer C. Use of synthetic communities to study microbial ecology of the gut. MICROBIOME RESEARCH REPORTS 2022; 1:4. [PMID: 38089065 PMCID: PMC10714298 DOI: 10.20517/mrr.2021.11] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 01/06/2024]
Abstract
The application of in vitro synthetic microbial communities is an excellent approach to model the ecological interactions between microbes in the human gastrointestinal tract. Although DNA-based studies have provided a wealth of information, they do not consider the ecological properties of the human gut microbiota. Ecological interactions between gut microbes of interest can be studied by applying synthetic communities. This review describes the considerations that should be taken into account when constructing a synthetic community by discussing example research questions that can be answered by using a synthetic microbial community, the choice of microbial species, the growth conditions, possible reactor setups, and the parameters to analyze.
Collapse
Affiliation(s)
| | | | | | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Wageningen 6708 WE, Gelderland, The Netherland
| |
Collapse
|
44
|
Aarnoutse R, Hillege LE, Ziemons J, De Vos-Geelen J, de Boer M, Aerts EMER, Vriens BEPJ, van Riet Y, Vincent J, van de Wouw AJ, Le GN, Venema K, Rensen SS, Penders J, Smidt ML. Intestinal Microbiota in Postmenopausal Breast Cancer Patients and Controls. Cancers (Basel) 2021; 13:cancers13246200. [PMID: 34944820 PMCID: PMC8699039 DOI: 10.3390/cancers13246200] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/24/2021] [Accepted: 12/03/2021] [Indexed: 12/29/2022] Open
Abstract
Simple Summary Besides the already known factors that increase the risk of breast cancer, like hormonal treatment, heredity, and obesity, growing evidence exists that intestinal microbiota can influence breast cancer carcinogenesis. Current clinical information into the role of the intestinal microbiota in breast cancer patients is limited. This study aimed to see whether there are differences in intestinal microbiota richness, diversity, and composition between oestrogen receptor positive breast cancer patients and controls. We concluded that the intestinal microbiota richness, diversity, and composition were not different between breast cancer patients and postmenopausal controls. An increased relative abundance of Dialister and Veillonellaceae was observed in breast cancer patients scheduled for adjuvant treatment, which might be caused by a relative decrease in other bacteria due to surgery associated factors rather than an absolute increase. For future studies, we strongly advise a more homogeneous group of breast cancer patients of preferably treatment-naive patients. Abstract Background: Previous preclinical and clinical research has investigated the role of intestinal microbiota in carcinogenesis. Growing evidence exists that intestinal microbiota can influence breast cancer carcinogenesis. However, the role of intestinal microbiota in breast cancer needs to be further investigated. This study aimed to identify the microbiota differences between postmenopausal breast cancer patients and controls. Patients and methods: This prospective cohort study compared the intestinal microbiota richness, diversity, and composition in postmenopausal histologically proven ER+/HER2- breast cancer patients and postmenopausal controls. Patients scheduled for (neo)adjuvant adriamycin, cyclophosphamide (AC), and docetaxel (D), or endocrine therapy (tamoxifen) were prospectively enrolled in a multicentre cohort study in the Netherlands. Patients collected a faecal sample and completed a questionnaire before starting systemic cancer treatment. Controls, enrolled from the National Dutch Breast Cancer Screening Programme, also collected a faecal sample and completed a questionnaire. Intestinal microbiota was analysed by amplicon sequencing of the 16S rRNA V4 gene region. Results: In total, 81 postmenopausal ER+/HER2- breast cancer patients and 67 postmenopausal controls were included, resulting in 148 faecal samples. Observed species richness, Shannon index, and overall microbial community structure were not significantly different between breast cancer patients and controls. There was a significant difference in overall microbial community structure between breast cancer patients scheduled for adjuvant treatment, neoadjuvant treatment, and controls at the phylum (p = 0.042) and genus levels (p = 0.015). Dialister (p = 0.001) and its corresponding family Veillonellaceae (p = 0.001) were higher in patients scheduled for adjuvant treatment, compared to patients scheduled for neoadjuvant treatment. Additional sensitivity analysis to correct for the potential confounding effect of prophylactic antibiotic use, indicated no differences in microbial community structure between patients scheduled for neoadjuvant systemic treatment, adjuvant systemic treatment, and controls at the phylum (p = 0.471) and genus levels (p = 0.124). Conclusions: Intestinal microbiota richness, diversity, and composition are not different between postmenopausal breast cancer patients and controls. The increased relative abundance of Dialister and Veillonellaceae was observed in breast cancer patients scheduled for adjuvant treatment, which might be caused by a relative decrease in other bacteria due to prophylactic antibiotic administration rather than an absolute increase.
Collapse
Affiliation(s)
- Romy Aarnoutse
- GROW—School for Oncology and Developmental Biology, Maastricht University Medical Centre, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (R.A.); (J.Z.); (J.D.V.-G.); (M.d.B.)
- Department of Surgery, Maastricht University Medical Centre, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands;
| | - Lars E. Hillege
- GROW—School for Oncology and Developmental Biology, Maastricht University Medical Centre, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (R.A.); (J.Z.); (J.D.V.-G.); (M.d.B.)
- Department of Surgery, Maastricht University Medical Centre, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands;
- Correspondence: (L.E.H.); (M.L.S.); Tel.: +31-(0)43-3877477 (M.L.S.)
| | - Janine Ziemons
- GROW—School for Oncology and Developmental Biology, Maastricht University Medical Centre, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (R.A.); (J.Z.); (J.D.V.-G.); (M.d.B.)
- Department of Surgery, Maastricht University Medical Centre, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands;
| | - Judith De Vos-Geelen
- GROW—School for Oncology and Developmental Biology, Maastricht University Medical Centre, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (R.A.); (J.Z.); (J.D.V.-G.); (M.d.B.)
- Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Centre, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Maaike de Boer
- GROW—School for Oncology and Developmental Biology, Maastricht University Medical Centre, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (R.A.); (J.Z.); (J.D.V.-G.); (M.d.B.)
- Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Centre, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Elvira M. E. R. Aerts
- Department of Surgery, Maastricht University Medical Centre, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands;
| | - Birgit E. P. J. Vriens
- Department of Medical Oncology, Catharina Hospital, P.O. Box 1350, 5602 ZA Eindhoven, The Netherlands;
| | - Yvonne van Riet
- Department of Surgery, Catharina Hospital, P.O. Box 1350, 5602 ZA Eindhoven, The Netherlands;
| | - Jeroen Vincent
- Department of Medical Oncology, Elkerliek Hospital, P.O. Box 98, 5700 AB Helmond, The Netherlands;
| | - Agnes J. van de Wouw
- Department of Medical Oncology, VieCuri Medical Centre, P.O. Box 1926, 5900 BX Venlo, The Netherlands;
| | - Giang N. Le
- Department of Medical Microbiology, Maastricht University Medical Centre, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands; (G.N.L.); (J.P.)
| | - Koen Venema
- NUTRIM—School of Nutrition and Translational Research In Metabolism, Maastricht University Medical Centre, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (K.V.); (S.S.R.)
- Euregional Microbiome Center, Maastricht University, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
- Centre for Healthy Eating & Food Innovation, Maastricht University-Campus Venlo, P.O. Box 8, 5900 AA Venlo, The Netherlands
| | - Sander S. Rensen
- NUTRIM—School of Nutrition and Translational Research In Metabolism, Maastricht University Medical Centre, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (K.V.); (S.S.R.)
| | - John Penders
- Department of Medical Microbiology, Maastricht University Medical Centre, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands; (G.N.L.); (J.P.)
- NUTRIM—School of Nutrition and Translational Research In Metabolism, Maastricht University Medical Centre, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (K.V.); (S.S.R.)
| | - Marjolein L. Smidt
- GROW—School for Oncology and Developmental Biology, Maastricht University Medical Centre, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (R.A.); (J.Z.); (J.D.V.-G.); (M.d.B.)
- Department of Surgery, Maastricht University Medical Centre, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands;
- Correspondence: (L.E.H.); (M.L.S.); Tel.: +31-(0)43-3877477 (M.L.S.)
| |
Collapse
|
45
|
Yap M, Ercolini D, Álvarez-Ordóñez A, O'Toole PW, O'Sullivan O, Cotter PD. Next-Generation Food Research: Use of Meta-Omic Approaches for Characterizing Microbial Communities Along the Food Chain. Annu Rev Food Sci Technol 2021; 13:361-384. [PMID: 34678075 DOI: 10.1146/annurev-food-052720-010751] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread of antimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Min Yap
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; .,School of Microbiology, University College Cork, County Cork, Ireland
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain.,Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul W O'Toole
- School of Microbiology, University College Cork, County Cork, Ireland.,APC Microbiome Ireland, University College Cork, County Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; .,APC Microbiome Ireland, University College Cork, County Cork, Ireland.,VistaMilk SFI Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; .,APC Microbiome Ireland, University College Cork, County Cork, Ireland.,VistaMilk SFI Research Centre, Moorepark, Fermoy, County Cork, Ireland
| |
Collapse
|
46
|
Aarnoutse R, Ziemons J, de Vos-Geelen J, Valkenburg-van Iersel L, Wildeboer ACL, Vievermans A, Creemers GJM, Baars A, Vestjens HJHMJ, Le GN, Barnett DJM, Rensen SS, Penders J, Smidt ML. The Role of Intestinal Microbiota in Metastatic Colorectal Cancer Patients Treated With Capecitabine. Clin Colorectal Cancer 2021; 21:e87-e97. [PMID: 34801414 DOI: 10.1016/j.clcc.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/29/2021] [Accepted: 10/13/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Previous pre-clinical research has indicated that the intestinal microbiota can potentiate anti-tumour efficacy of capecitabine and that capecitabine treatment impacts intestinal microbiota composition and diversity. Using a longitudinal design, this study explores the associations between the intestinal microbiota and treatment response in patients with metastatic colorectal cancer (mCRC) during capecitabine treatment. PATIENTS AND METHODS Patients with mCRC treated with capecitabine were prospectively enrolled in a multicentre cohort study. Patients collected a faecal sample and completed a questionnaire before, during, and after three cycles of capecitabine. Several clinical characteristics, including tumour response, toxicity and antibiotic use were recorded. Intestinal microbiota were analysed by amplicon sequencing of the 16S rRNA V4 gene-region. RESULTS Thirty-three patients were included. After three cycles of capecitabine, six patients (18%) achieved a partial response, 25 (76%) showed stable disease, and one (3%) experienced progressive disease. Of the 90 faecal samples were collected. Microbial diversity (α-diversity), community structure (β-diversity), and bacterial abundance on phylum and genus level were not significantly different between responders and non-responders and were not significantly affected by three cycles of capecitabine. CONCLUSION This is the first clinical study with longitudinal intestinal microbiota sampling in mCRC patients that explores the role of the intestinal microbiota during treatment with capecitabine. Intestinal microbiota composition and diversity before, during, and after three cycles of capecitabine were not associated with response in this study population. Capecitabine did not induce significant changes in the microbiota composition and diversity during the treatment period. Individual effects of antibiotics during capecitabine treatment were observed.
Collapse
Affiliation(s)
- Romy Aarnoutse
- GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands; Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Janine Ziemons
- GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands; Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Judith de Vos-Geelen
- GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands; Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Liselot Valkenburg-van Iersel
- GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands; Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Aurelia C L Wildeboer
- GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands; Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Anne Vievermans
- GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands; Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands
| | | | - Arnold Baars
- Department of Medical Oncology, Hospital Gelderse Vallei, Ede, The Netherlands
| | | | - Giang N Le
- Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - David J M Barnett
- Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
| | - Sander S Rensen
- Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands; NUTRIM - School of Nutrition and Translational research In Metabolism, Maastricht University, Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands; NUTRIM - School of Nutrition and Translational research In Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Marjolein L Smidt
- GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands; Department of Surgery, Maastricht University Medical Centre, Maastricht, The Netherlands.
| |
Collapse
|
47
|
Cross-Sectional Analysis of the Microbiota of Human Gut and Its Direct Environment in a Household Cohort with High Background of Antibiotic Use. Microorganisms 2021; 9:microorganisms9102115. [PMID: 34683436 PMCID: PMC8539590 DOI: 10.3390/microorganisms9102115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/31/2021] [Accepted: 09/29/2021] [Indexed: 01/01/2023] Open
Abstract
Comprehensive insight into the microbiota of the gut of humans and animals, as well as their living environment, in communities with a high background of antibiotic use and antibiotic resistance genes is scarce. Here, we used 16S rRNA gene sequencing to describe the (dis)similarities in the microbiota of feces from humans (n = 107), domestic animals (n = 36), water (n = 89), and processed food (n = 74) in a cohort with individual history of antibiotic use in northern Vietnam. A significantly lower microbial diversity was observed among individuals who used antibiotics in the past 4 months (n = 44) compared to those who did not (n = 63). Fecal microbiota of humans was more diverse than nonhuman samples and shared a small part of its amplicon sequence variants (ASVs) with feces from animals (7.4% (3.2–9.9)), water (2.2% (1.2–2.8)), and food (3.1% (1.5–3.1)). Sharing of ASVs between humans and companion animals was not associated with the household. However, we did observe a correlation between an Enterobacteriaceae ASV and the presence of extended-spectrum beta-lactamase CTX-M-group-2 encoding genes in feces from humans and animals (p = 1.6 × 10−3 and p = 2.6 × 10−2, respectively), hinting toward an exchange of antimicrobial-resistant strains between reservoirs.
Collapse
|
48
|
Inter-microbial relations shape the preterm gut. Nat Microbiol 2021; 6:423-424. [PMID: 33753920 DOI: 10.1038/s41564-021-00883-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
49
|
Lewe N, Hermans S, Lear G, Kelly LT, Thomson-Laing G, Weisbrod B, Wood SA, Keyzers RA, Deslippe JR. Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data. J Microbiol Methods 2021; 188:106271. [PMID: 34146605 DOI: 10.1016/j.mimet.2021.106271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023]
Abstract
Microbial biodiversity monitoring through the analysis of DNA extracted from environmental samples is increasingly popular because it is perceived as being rapid, cost-effective, and flexible concerning the sample types studied. DNA can be extracted from diverse media before high-throughput sequencing of the prokaryotic 16S rRNA gene is used to characterize the taxonomic diversity and composition of the sample (known as metabarcoding). While sources of bias in metabarcoding methodologies are widely acknowledged, previous studies have focused mainly on the effects of these biases within a single substrate type, and relatively little is known of how these vary across substrates. We investigated the effect of substrate type (water, microbial mats, lake sediments, stream sediments, soil and a mock microbial community) on the relative performance of DNA metabarcoding in parallel with phospholipid fatty acid (PLFA) analysis. Quantitative estimates of the biomass of different taxonomic groups in samples were made through the analysis of PLFAs, and these were compared to the relative abundances of microbial taxa estimated from metabarcoding. Furthermore, we used the PLFA-based quantitative estimates of the biomass to adjust relative abundances of microbial groups determined by metabarcoding to provide insight into how the biomass of microbial taxa from PLFA analysis can improve understanding of microbial communities from environmental DNA samples. We used two sets of PLFA biomarkers that differed in their number of PLFAs to evaluate how PLFA biomarker selection influences biomass estimates. Metabarcoding and PLFA analysis provided significantly different views of bacterial composition, and these differences varied among substrates. We observed the most notable differences for the Gram-negative bacteria, which were overrepresented by metabarcoding in comparison to PLFA analysis. In contrast, the relative biomass and relative sequence abundances aligned reasonably well for Cyanobacteria across the tested freshwater substrates. Adjusting relative abundances of microbial taxa estimated by metabarcoding with PLFA-based quantification estimates of the microbial biomass led to significant changes in the microbial community compositions in all substrates. We recommend including independent estimates of the biomass of microbial groups to increase comparability among metabarcoding libraries from environmental samples, especially when comparing communities associated with different substrates.
Collapse
Affiliation(s)
- Natascha Lewe
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiversity and Restoration Ecology, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Syrie Hermans
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Laura T Kelly
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Georgia Thomson-Laing
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Barbara Weisbrod
- Human and Environmental Toxicology, Department of Biology, Universität Konstanz, 78457 Konstanz, Germany
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Robert A Keyzers
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Julie R Deslippe
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiversity and Restoration Ecology, Victoria University of Wellington, Wellington 6012, New Zealand.
| |
Collapse
|
50
|
Jian C, Salonen A, Korpela K. Commentary: How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches. Front Cell Infect Microbiol 2021; 11:627910. [PMID: 33763385 PMCID: PMC7982878 DOI: 10.3389/fcimb.2021.627910] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ching Jian
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Katri Korpela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| |
Collapse
|