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Beck KL, Haiminen N, Agarwal A, Carrieri AP, Madgwick M, Kelly J, Pylro V, Kawas B, Wiedmann M, Ganda E. Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production. mSystems 2024:e0084024. [PMID: 39387577 DOI: 10.1128/msystems.00840-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 07/26/2024] [Indexed: 10/15/2024] Open
Abstract
The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection could be a valuable approach to be used in food systems. These methods could be used to identify ingredients that deviate from their typical microbial composition, which could indicate food fraud or safety issues. The objective of this study was to assess the feasibility of using shotgun sequencing data as input into anomaly detection algorithms using fluid milk as a model system. Contrastive principal component analysis (PCA), cluster-based methods, and explainable artificial intelligence (AI) were evaluated for the detection of two anomalous sample classes using longitudinal metagenomic profiling of fluid milk compared to baseline (BL) samples collected under comparable circumstances. Traditional methods (alpha and beta diversity, clustering-based contrastive PCA, multidimensional scaling, and dendrograms) failed to differentiate anomalous sample classes; however, explainable AI was able to classify anomalous vs baseline samples and indicate microbial drivers in association with antibiotic use. We validated the potential for explainable AI to classify different milk sources using larger publicly available fluid milk 16S rDNA sequencing data sets and demonstrated that explainable AI is able to differentiate between milk storage methods, processing stages, and seasons. Our results indicate that the application of artificial intelligence continues to hold promise in the realm of microbiome data analysis and could present further opportunities for downstream analytic automation to aid in food safety and quality. IMPORTANCE We evaluated the feasibility of using untargeted metagenomic sequencing of raw milk for detecting anomalous food ingredient content with artificial intelligence methods in a study specifically designed to test this hypothesis. We also show through analysis of publicly available fluid milk microbial data that our artificial intelligence approach is able to successfully predict milk in different stages of processing. The approach could potentially be applied in the food industry for safety and quality control.
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Affiliation(s)
| | - Niina Haiminen
- IBM T.J. Watson Research Center, New York, New York, USA
| | | | | | | | - Jennifer Kelly
- IBM Research Europe-Daresbury, Warrington, United Kingdom
| | - Victor Pylro
- Department of Biology, Federal University of Lavras, Lavras, Minas Gerais, Brazil
| | - Ban Kawas
- IBM Almaden Research Center, San Jose, California, USA
| | - Martin Wiedmann
- Cornell University, College of Agriculture and Life Sciences, Ithaca, New York, USA
| | - Erika Ganda
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, USA
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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2
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Haverkamp THA, Spilsberg B, Johannessen GS, Torp M, Sekse C. Detection and characterization of Campylobacter in air samples from poultry houses using shot-gun metagenomics - a pilot study. BMC Microbiol 2024; 24:399. [PMID: 39385092 PMCID: PMC11462905 DOI: 10.1186/s12866-024-03563-3] [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: 05/03/2024] [Accepted: 10/03/2024] [Indexed: 10/11/2024] Open
Abstract
BACKGROUND Foodborne pathogens such as Campylobacter jejuni are responsible for a large proportion of the gastrointestinal infections worldwide associated with poultry meat. Campylobacter spp. can be found in the chicken fecal microbiome and can contaminate poultry meat during the slaughter process. Commonly used sampling methods to detect Campylobacter spp. at poultry farms use fecal droppings or boot swabs in combination with conventional culture techniques or PCR. In this pilot study, we have used air filtering and filters spiked with mock communities in combination with shotgun metagenomics to detect Campylobacter and test the applicability of this approach for the detection and characterization of foodborne pathogens. To the best of our knowledge is this the first study that combines air filtering with shotgun metagenomic sequencing for detection and characterization of Campylobacter. RESULTS Analysis of air filters spiked with different levels of Campylobacter, into a background of mock or poultry house communities, indicated that we could detect as little as 200 colony forming units (CFU) Campylobacter per sample using our protocols. The results indicate that even with limited sequencing effort we could detect Campylobacter in the samples analysed in this study. We observed significant amounts of Campylobacter in real-life samples from poultry houses using both real-time PCR as well as shotgun metagenomics, suggesting that the flocks in both houses were infected with Campylobacter spp. Interestingly, in both houses we find diverse microbial communities present in the indoor air which reflect the fecal microbiome of poultry. Some of the identified genera such as Staphylococcus, Escherichia and Pseudomonas are known to contain opportunistic pathogenic species. CONCLUSIONS These results show that air sampling of poultry houses in combination with shotgun metagenomics can detect and identify Campylobacter spp. present at low levels. This is important since early detection of Campylobacter enables measures to be put in place to ensure the safety of broiler products, animal health and public health. This approach has the potential to detect any pathogen present in poultry house air.
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Affiliation(s)
| | | | | | - Mona Torp
- Norwegian Veterinary Institute, Oslo, Norway
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3
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Shigematsu Y, Saito R, Amori G, Kanda H, Takahashi Y, Takeuchi K, Takahashi S, Inamura K. Fusobacterium nucleatum, immune responses, and metastatic organ diversity in colorectal cancer liver metastasis. Cancer Sci 2024; 115:3248-3255. [PMID: 39140431 PMCID: PMC11447885 DOI: 10.1111/cas.16315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/19/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024] Open
Abstract
The presence of Fusobacterium nucleatum is associated with an immunosuppressive tumor immune microenvironment (TIM) in primary colorectal cancer (CRC), contributing to tumor progression. Its persistence in CRC liver metastasis tissues raises questions about its role in modulating local and systemic immune responses and influencing recurrence patterns. This retrospective cohort study of 218 patients with CRC liver metastasis investigated the association of F. nucleatum in CRC liver metastasis tissues with systemic inflammation, TIM alterations, and the number of metastatic organs involved in recurrence. Two-step polymerase chain reaction (PCR), including digital PCR, detected F. nucleatum in 42% (92/218) of fresh-frozen specimens of CRC liver metastases. Compared with the F. nucleatum-none group, the F. nucleatum-high group showed higher C-reactive protein levels (0.82 vs. 0.22 mg/dL; Ptrend = 0.02), lower numbers of CD8+ cells (33.2 vs. 65.3 cells/mm2; Ptrend = 0.04) and FOXP3+ cells (11.3 vs. 21.7 cells/mm2; Ptrend = 0.01) in the TIM, and a greater number of metastatic organs involved in recurrence (1.6 vs. 1.1; p < 0.001). The presence of F. nucleatum in CRC liver metastasis tissues was associated with increased systemic inflammation, TIM alterations, and a greater number of metastatic organs involved in recurrence. These findings suggest a potential contribution of F. nucleatum to the metastatic propensity of CRC cells and could inform future research to enhance understanding of the interaction between tumor, host, and microbes in the metastatic process.
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Affiliation(s)
- Yasuyuki Shigematsu
- Department of Pathology, Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
- Division of Pathology, Cancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
| | - Rumiko Saito
- Department of Medical Oncology, Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
- Department of Clinical Chemotherapy, Cancer Chemotherapy CenterJapanese Foundation for Cancer ResearchTokyoJapan
- Graduate School of EngineeringChiba Institute of TechnologyChibaJapan
| | - Gulanbar Amori
- Department of Pathology, Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
- Division of Pathology, Cancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
- Division of Tumor PathologyJichi Medical UniversityTochigiJapan
| | - Hiroaki Kanda
- Department of PathologySaitama Cancer CenterSaitamaJapan
| | - Yu Takahashi
- Division of Hepatobiliary and Pancreatic Surgery, Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Kengo Takeuchi
- Department of Pathology, Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
- Division of Pathology, Cancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
- Pathology Project for Molecular Targets, Cancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
| | - Shunji Takahashi
- Department of Medical Oncology, Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
- Department of Clinical Chemotherapy, Cancer Chemotherapy CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Kentaro Inamura
- Department of Pathology, Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
- Division of Pathology, Cancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
- Division of Tumor PathologyJichi Medical UniversityTochigiJapan
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Martin S, Smith C, Stewart K, Barr W, Cheslett D, O'Connor I, Swords F, Ijaz UZ, O'Dwyer K. The hepatopancreas microbiome of velvet crab, Necora puber. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70014. [PMID: 39354672 PMCID: PMC11445078 DOI: 10.1111/1758-2229.70014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 09/03/2024] [Indexed: 10/03/2024]
Abstract
Crustaceans are a valuable resource globally, both ecologically and economically, and investigations into their health are becoming increasingly important as exploitation rises. The microbiome plays a crucial role in crustacean immunity, and understanding its composition and structure can provide insights into the health of an organism and its interactions with various factors. In this study, we investigated the hepatopancreas microbiome of the velvet swimming crab, Necora puber, and compared its composition and structure with several study factors, including two different sampling points and infection with a paramyxid parasite, Paramarteilia canceri. To our knowledge, we provide the first description of a velvet crab microbiome, highlighting the dominance of a single microorganism, Candidatus hepatoplasma. We identified variations in microbiome composition between sampling points and discussed the possible processes affecting microbiome assembly. We also outline a core microbiome for the velvet crab hepatopancreas, consisting of 12 core phyla. Our study adds to the growing literature on crustacean microbiomes and provides a baseline for future investigations into the velvet crab microbiome and the health of this crustacean species.
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Affiliation(s)
- Signe Martin
- Marine and Freshwater Research Centre, Atlantic Technological University, Galway, Ireland
| | - Cindy Smith
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | - Kelly Stewart
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | - William Barr
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | | | - Ian O'Connor
- Marine and Freshwater Research Centre, Atlantic Technological University, Galway, Ireland
| | | | - Umer Zeeshan Ijaz
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | - Katie O'Dwyer
- Marine and Freshwater Research Centre, Atlantic Technological University, Galway, Ireland
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Mancin L, Paoli A, Berry S, Gonzalez JT, Collins AJ, Lizarraga MA, Mota JF, Nicola S, Rollo I. Standardization of gut microbiome analysis in sports. Cell Rep Med 2024:101759. [PMID: 39368478 DOI: 10.1016/j.xcrm.2024.101759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 08/09/2024] [Accepted: 09/10/2024] [Indexed: 10/07/2024]
Abstract
The gut microbiome plays a significant role in physiological functions such as nutrient processing, vitamin production, inflammatory response, and immune modulation, which, in turn, are important contributors to athlete health and performance. To date, the interpretation, discussion, and visualization of microbiome results of athletes are challenging, due to a lack of standard parameters and reference data for collection and comparison. The purpose of this perspective piece is to provide researchers with an easy-to-understand framework for the collection, analysis, and data management related to the gut microbiome with a specific focus on athletic populations. In the absence of a consensus on microbiome research in the sports field, we hope that these considerations serve as foundational "best practice." Adherence to these standard operating procedures will accelerate the path toward improving the quality of data and ultimately our understanding of the influence of the gut microbiome in sport settings.
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Affiliation(s)
- Laura Mancin
- Department of Biomedical Sciences, University of Padua, Padua, Italy; Human Inspired Technology Research Center HIT, University of Padua, Padua, Italy.
| | - Antonio Paoli
- Department of Biomedical Sciences, University of Padua, Padua, Italy; Human Inspired Technology Research Center HIT, University of Padua, Padua, Italy
| | - Sara Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | | | - Adam J Collins
- Department for Health, University of Bath, BA2 7AY Bath, UK
| | | | - Joao Felipe Mota
- APC Microbiome Ireland, Department of Medicine, School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
| | - Segata Nicola
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Ian Rollo
- Gatorade Sports Science Institute, PepsiCo Life Sciences, Global R&D, Leicestershire, UK; School of Sports Exercise and Health Sciences, Loughborough University, Leicestershire, UK
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6
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Andriienko V, Buczek M, Meier R, Srivathsan A, Łukasik P, Kolasa MR. Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction. PeerJ 2024; 12:e18025. [PMID: 39329134 PMCID: PMC11426317 DOI: 10.7717/peerj.18025] [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: 05/03/2024] [Accepted: 08/10/2024] [Indexed: 09/28/2024] Open
Abstract
Background Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens. Methods High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals. Results We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species. Conclusion Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.
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Affiliation(s)
- Veronika Andriienko
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
- Institute of Zoology and Biomedical Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Rudolf Meier
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Amrita Srivathsan
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Michał R. Kolasa
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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7
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Bozzi D, Neuenschwander S, Cruz Dávalos DI, Sousa da Mota B, Schroeder H, Moreno-Mayar JV, Allentoft ME, Malaspinas AS. Towards predicting the geographical origin of ancient samples with metagenomic data. Sci Rep 2024; 14:21794. [PMID: 39294129 PMCID: PMC11411106 DOI: 10.1038/s41598-023-40246-x] [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: 03/10/2023] [Accepted: 08/07/2023] [Indexed: 09/20/2024] Open
Abstract
Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples.
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Affiliation(s)
- Davide Bozzi
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
| | - Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Diana Ivette Cruz Dávalos
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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8
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Thomas-White K, Hilt EE, Olmschenk G, Gong M, Phillips CD, Jarvis C, Sanford N, White J, Navarro P. A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples. Diagnostics (Basel) 2024; 14:2039. [PMID: 39335716 PMCID: PMC11431210 DOI: 10.3390/diagnostics14182039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 08/27/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
Vaginitis is a widespread issue for women worldwide, yet current diagnostic tools are lacking. Bacterial vaginosis (BV) is the most prevalent type of vaginitis, found in 10-50% of reproductive-aged women. Current diagnostic methods for BV rely on clinical criteria, microscopy, or the detection of a few microbes by qPCR. However, many vaginal infections lack a single etiological agent and are characterized by changes in the vaginal microbiome community structure (e.g., BV is defined as a loss of protective lactobacilli resulting in an overgrowth of anaerobic bacteria). Shotgun metagenomic sequencing provides a comprehensive view of all the organisms present in the vaginal microbiome (VMB), allowing for a better understanding of all potential etiologies. Here, we describe a robust VMB metagenomics sequencing test with a sensitivity of 93.1%, a specificity of 90%, a negative predictive value of 93.4%, and a positive predictive value of 89.6% certified by Clinical Laboratory Improvement Amendments (CLIA), the College of American Pathologist (CAP), and the Clinical Laboratory Evaluation Program (CLEP). We sequenced over 7000 human vaginal samples with this pipeline and described general findings and comparisons to US census data.
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Affiliation(s)
| | - Evann E Hilt
- Department of Pathology and Laboratory Medicine, University of Minnesota Medical Center, Minneapolis, MN 55455, USA
| | | | | | - Caleb D Phillips
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
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9
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Stuij TM, Cleary DFR, Rocha RJM, Polonia ARM, Machado E Silva DA, Frommlet JC, Louvado A, Huang YM, De Voogd NJ, Gomes NCM. Development and validation of an experimental life support system to study coral reef microbial communities. Sci Rep 2024; 14:21260. [PMID: 39261551 PMCID: PMC11391067 DOI: 10.1038/s41598-024-69514-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/06/2024] [Indexed: 09/13/2024] Open
Abstract
In the present study, we developed and validated an experimental life support system (ELSS) designed to investigate coral reef associated bacterial communities. The microcosms in the ELSS consisted of coral reef sediment, synthetic seawater, and specimens of five benthic reef species. These included two hard corals Montipora digitata and Montipora capricornis, a soft coral Sarcophyton glaucum, a zoanthid Zoanthus sp., and a sponge Chondrilla sp.. Physicochemical parameters and bacterial communities in the ELSS were similar to those observed at shallow coral reef sites. Sediment bacterial evenness and higher taxonomic composition were more similar to natural-type communities at days 29 and 34 than at day 8 after transfer to the microcosms, suggesting microbial stabilization after an initial recovery period. Biotopes were compositionally distinct but shared a number of ASVs. At day 34, sediment specific ASVs were found in hosts and visa versa. Transplantation significantly altered the bacterial community composition of M. digitata and Chondrilla sp., suggesting microbial adaptation to altered environmental conditions. Altogether, our results support the suitability of the ELSS developed in this study as a model system to investigate coral reef associated bacterial communities using multi-factorial experiments.
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Affiliation(s)
- T M Stuij
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal.
| | - D F R Cleary
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - R J M Rocha
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - A R M Polonia
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - D A Machado E Silva
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - J C Frommlet
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - A Louvado
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Y M Huang
- National Penghu University of Science and Technology, Magong, Taiwan
| | - N J De Voogd
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology (IBL), Leiden University, Leiden, the Netherlands
| | - N C M Gomes
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal.
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10
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Dalvi H, De Nisco NJ. The evolving world of the urinary microbiome. Curr Opin Urol 2024:00042307-990000000-00185. [PMID: 39224916 DOI: 10.1097/mou.0000000000001222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
PURPOSE OF REVIEW The existence of urinary microbiome in healthy individuals is now widely accepted as the longstanding belief in urinary tract sterility was disproved over a decade ago. The urinary microbiome has since been implicated in multiple urologic conditions including urinary tract infection (UTI), urinary incontinence, and bladder cancer. This review relays new findings of urinary microbiome compositional changes associated with aging and UTI susceptibility. RECENT FINDINGS Recent advancements have established how the urinary microbiome changes over the lifespan. Studies finding distinct urinary microbiomes in prepubescent, reproductive age, and postmenopausal females have identified sex hormones as potential modulators of urinary microbiome composition and have identified prevalent species that may be markers of dysbiosis. Research in male children finds a cultivable urinary microbiota that varies with age or urologic history but not delivery mode. Emerging research also addresses the function of the urinary microbiota, including genetic factors associated with urinary tract colonization and interactions with uropathogens. SUMMARY The urinary microbiome is a promising therapeutic target for urologic disease. However, a more functional understanding is necessary for the development of microbiome-based therapies. Future research should develop accurate animal models and explore functional relationships between the urinary microbiome and the host environment.
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Affiliation(s)
- Hrishikesh Dalvi
- Department of Biological Sciences, The University of Texas at Dallas, Richardson
| | - Nicole J De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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11
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Cornish AJ, Gruber AJ, Kinnersley B, Chubb D, Frangou A, Caravagna G, Noyvert B, Lakatos E, Wood HM, Thorn S, Culliford R, Arnedo-Pac C, Househam J, Cross W, Sud A, Law P, Leathlobhair MN, Hawari A, Woolley C, Sherwood K, Feeley N, Gül G, Fernandez-Tajes J, Zapata L, Alexandrov LB, Murugaesu N, Sosinsky A, Mitchell J, Lopez-Bigas N, Quirke P, Church DN, Tomlinson IPM, Sottoriva A, Graham TA, Wedge DC, Houlston RS. The genomic landscape of 2,023 colorectal cancers. Nature 2024; 633:127-136. [PMID: 39112709 PMCID: PMC11374690 DOI: 10.1038/s41586-024-07747-9] [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: 11/14/2022] [Accepted: 06/24/2024] [Indexed: 08/17/2024]
Abstract
Colorectal carcinoma (CRC) is a common cause of mortality1, but a comprehensive description of its genomic landscape is lacking2-9. Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichia colipks+ colibactin in rectal cancers10 and the importance of the SBS93 signature11-13, which suggests that diet or smoking is a risk factor. Immune-escape driver mutations14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care.
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Affiliation(s)
- Alex J Cornish
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Andreas J Gruber
- Department of Biology, University of Konstanz, Konstanz, Germany
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- University College London Cancer Institute, London, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Frangou
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Boris Noyvert
- Cancer Research UK Centre and Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Henry M Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Steve Thorn
- Department of Oncology, University of Oxford, Oxford, UK
| | - Richard Culliford
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Jacob Househam
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - William Cross
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Research Department of Pathology, University College London, UCL Cancer Institute, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Philip Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | | | - Aliah Hawari
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Connor Woolley
- Department of Oncology, University of Oxford, Oxford, UK
| | - Kitty Sherwood
- Department of Oncology, University of Oxford, Oxford, UK
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Nathalie Feeley
- Department of Oncology, University of Oxford, Oxford, UK
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Güler Gül
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Luis Zapata
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Nirupa Murugaesu
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alona Sosinsky
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Jonathan Mitchell
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Philip Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - David N Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Andrea Sottoriva
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A Graham
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - David C Wedge
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
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12
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Yuan C, Xie K, Feng L, Gao S, Cai L. The role and challenges of regulating endometrial microbiome in uterine health and diseases. Crit Rev Microbiol 2024; 50:937-954. [PMID: 38488586 DOI: 10.1080/1040841x.2024.2320247] [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: 10/25/2023] [Accepted: 02/10/2024] [Indexed: 10/09/2024]
Abstract
The uterine environment provides necessary conditions for the existence of endometrial microbiota, which in turn plays an important role in maintaining the homeostasis of the uterine environment. The endometrial microbiome is highly susceptible to external factors such as age, hormones, menstrual, pregnancy, etc. When the microbiota is imbalanced, it will further promote the occurrence of uterine diseases such as endometritis and endometrial cancer. Regulating the microbiome of the endometrium is of positive significance for promoting uterine health. Among them, antibiotics, probiotics, prebiotics, and microbial transplantation may be important pathways for regulating endometrial microbiota in the future. However, there is currently no unified plan for evaluating the endometrial microbiota. In addition, due to the small sample size, it is easy to be contaminated by exogenous bacterial DNA, which poses great challenges for studying the mechanism of microbial community regulating uterine health. Therefore, there are still many areas worth exploring for the future of endometrial microbiome.
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Affiliation(s)
- Chongshan Yuan
- Department of Obstetrics, China-Japan Union hospital of Jilin University, Changchun, Jilin, China
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Kunyu Xie
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Lianjun Feng
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
| | - Shouyang Gao
- Department of Obstetrics, China-Japan Union hospital of Jilin University, Changchun, Jilin, China
| | - Lifu Cai
- Department of Obstetrics, China-Japan Union hospital of Jilin University, Changchun, Jilin, China
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13
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Chen VS, James C, Khemmani M, Desai S, Doshi C, Rac G, Ellis JL, Patel HD, Barkan GA, Gupta GN, Flanigan RC, Wolfe AJ. A prospective evaluation of the prostate microbiome in malignant and benign tissue using transperineal biopsy. Prostate 2024; 84:1251-1261. [PMID: 38946139 DOI: 10.1002/pros.24763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/08/2024] [Accepted: 06/18/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND The link between the prostate microbiome and prostate cancer remains unclear. Few studies have analyzed the microbiota of prostate tissue, and these have been limited by potential contamination by transrectal biopsy. Transperineal prostate biopsy offers an alternative and avoids fecal cross-contamination. We aim to characterize the prostate microbiome using transperineal biopsy. METHODS Patients with clinical suspicion for prostate cancer who were to undergo transperineal prostate biopsy with magnetic resonance imaging (MRI) fusion guidance were prospectively enrolled from 2022 to 2023. Patients were excluded if they had Prostate Imaging Reporting and Data System lesions with scores ≤ 3, a history of prostate biopsy within 1 year, a history of prostate cancer, or antibiotic use within 30 days of biopsy. Tissue was collected from the MRI target lesions and nonneoplastic transitional zone. Bacteria were identified using 16S ribosomal RNA gene sequencing. RESULTS Across the 42 patients, 76% were found to have prostate cancer. Beta diversity indices differed significantly between the perineum, voided urine, and prostate tissue. There were no beta diversity differences between cancerous or benign tissue, or between pre- and postbiopsy urines. There appear to be unique genera more abundant in cancerous versus benign tissue. There were no differences in alpha diversity indices relative to clinical findings including cancer status, grade, and risk group. CONCLUSIONS We demonstrate a rigorous method to better characterize the prostate microbiome using transperineal biopsy and to limit contamination. These findings provide a framework for future large-scale studies of the microbiome of prostate cancer.
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Affiliation(s)
- Victor S Chen
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Christopher James
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Mark Khemmani
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Shalin Desai
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Chirag Doshi
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Goran Rac
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Jeffrey L Ellis
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Hiten D Patel
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Guliz A Barkan
- Department of Pathology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Gopal N Gupta
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Robert C Flanigan
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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14
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Reynolds MC, Cadillo-Quiroz H. Microbial DNA sample preservation and possible artifacts for field-based research in remote tropical peatlands. J Microbiol Methods 2024; 224:106997. [PMID: 39009285 DOI: 10.1016/j.mimet.2024.106997] [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: 08/27/2023] [Revised: 07/07/2024] [Accepted: 07/12/2024] [Indexed: 07/17/2024]
Abstract
Surveying bacterial and archaeal microbial communities in host and environmental studies requires the collection and storage of samples. Many studies are conducted in distant locations challenging these prerequisites. The use of preserving buffers is an important alternative when lacking access to cryopreservation, however, its effectivity for samples with challenging chemistry or samples that provide opportunities for fast bacterial or archaeal growth upon exposure to an aerobic environment, like peat samples, requires methodological assessment. Here, in combination with an identified optimal DNA extraction kit for peat soil samples, we test the application of several commercial and a homemade preservation buffer and make recommendations on the method that can most effectively preserve a microbiome reflective of the original state. In treatments with a non-optimal buffer or in the absence, we observed notable community shifts beginning as early as three days post-preservation lowering diversity and community evenness, with growth-driven artifacts from a few specific phyla. However other buffers retain a very close composition relative to the original state, and we described several metrics to understand some variation across them. Due to the chemical effects of preservation buffers, it is critical to test their compatibility and reliability to preserve the original bacterial and archaeal community in different environments.
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Affiliation(s)
- Mark C Reynolds
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States; Biodesign Institute, Arizona State University, Tempe, AZ 85287, United States
| | - Hinsby Cadillo-Quiroz
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States; Biodesign Institute, Arizona State University, Tempe, AZ 85287, United States.
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15
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Gerasimova Y, Ali H, Nadeem U. Challenges for pathologists in implementing clinical microbiome diagnostic testing. J Pathol Clin Res 2024; 10:e70002. [PMID: 39289163 PMCID: PMC11407905 DOI: 10.1002/2056-4538.70002] [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: 12/21/2023] [Revised: 08/11/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024]
Abstract
Recent research has established that the microbiome plays potential roles in the pathogenesis of numerous chronic diseases, including carcinomas. This discovery has led to significant interest in clinical microbiome testing among physicians, translational investigators, and the lay public. As novel, inexpensive methodologies to interrogate the microbiota become available, research labs and commercial vendors have offered microbial assays. However, these tests still have not infiltrated the clinical laboratory space. Here, we provide an overview of the challenges of implementing microbiome testing in clinical pathology. We discuss challenges associated with preanalytical and analytic sample handling and collection that can influence results, choosing the appropriate testing methodology for the clinical context, establishing reference ranges, interpreting the data generated by testing and its value in making patient care decisions, regulation, and cost considerations of testing. Additionally, we suggest potential solutions for these problems to expedite the establishment of microbiome testing in the clinical laboratory.
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Affiliation(s)
- Yulia Gerasimova
- Department of Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Haroon Ali
- Department of Medicine, Woodland Heights Medical Center, Lufkin, TX, USA
| | - Urooba Nadeem
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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16
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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17
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Shigematsu Y, Saito R, Kanda H, Takahashi Y, Takeuchi K, Takahashi S, Inamura K. Inverse Correlation between pks-Carrying Escherichia coli Abundance in Colorectal Cancer Liver Metastases and the Number of Organs Involved in Recurrence. Cancers (Basel) 2024; 16:3003. [PMID: 39272861 PMCID: PMC11394077 DOI: 10.3390/cancers16173003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/26/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
Colibactin, a genotoxin produced by Escherichia coli strains harboring the polyketide synthetase (pks) gene cluster, causes DNA damage and somatic mutations. pks+E. coli is enriched in primary colorectal cancer (CRC) and is associated with clonal driver mutations, but its role in CRC liver metastasis is unclear. We assessed the association of pks+ E. coli in CRC liver metastasis tissues with systemic and local immune responses and the number of organs involved in recurrence using specimens and clinicopathological data from 239 patients with CRC liver metastasis who underwent metastasectomy. The levels of pks+E. coli in fresh-frozen specimens were quantified as "very low" (<50th percentile), "low" (50th to 75th percentiles), and "high" (>75th percentile) using a digital PCR. Immunohistochemical analysis of tumor-infiltrating immune cells was performed using tissue microarrays. Systemic inflammation was evaluated using serum C-reactive protein (CRP) levels. pks+E. coli was detected in 66.7% (157 of 239) liver metastasis tissues. Higher levels of pks+E. coli were associated with decreased serum CRP levels and reduced densities of CD4+ cells and CD163+ cells in the tumor-immune microenvironment. The "high" pks+ E. coli group had fewer metastatic organs involved than the "very low" pks+ E. coli group (mean number of organs: 1.00 vs. 1.23). These findings suggest that pks+E. coli play a modulating role in CRC metastasis.
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Affiliation(s)
- Yasuyuki Shigematsu
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
- Division of Pathology, Cancer Institute, JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Rumiko Saito
- Department of Medical Oncology, Cancer Institute Hospital, JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
- Department of Clinical Chemotherapy, Cancer Chemotherapy Center, JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
- Graduate School of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Hiroaki Kanda
- Department of Pathology, Saitama Cancer Center, 780 Komuro, Ina, Kita-adachi-gun, Saitama 362-0806, Japan
| | - Yu Takahashi
- Division of Hepatobiliary and Pancreatic Surgery, Cancer Institute Hospital, JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Kengo Takeuchi
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
- Division of Pathology, Cancer Institute, JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
- Pathology Project for Molecular Targets, Cancer Institute, JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Shunji Takahashi
- Department of Medical Oncology, Cancer Institute Hospital, JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
- Department of Clinical Chemotherapy, Cancer Chemotherapy Center, JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Kentaro Inamura
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
- Division of Pathology, Cancer Institute, JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
- Division of Tumor Pathology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0431, Japan
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18
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Austin GI, Korem T. Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective. J Infect Dis 2024:jiae378. [PMID: 39189314 DOI: 10.1093/infdis/jiae378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Indexed: 08/28/2024] Open
Abstract
As investigations of low-biomass microbial communities have become more common, so too has the recognition of major challenges affecting these analyses. These challenges have been shown to compromise biological conclusions and have contributed to several controversies. Here, we review some of the most common and influential challenges in low-biomass microbiome research. We highlight key approaches to alleviate these potential pitfalls, combining experimental planning strategies and data analysis methods.
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Affiliation(s)
- George I Austin
- Department of Biomedical Informatics
- Program for Mathematical Genomics, Department of Systems Biology
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York
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19
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Geyer JK, Grunberg RL, Wang J, Mitchell CE. Leaf age structures phyllosphere microbial communities in the field and greenhouse. Front Microbiol 2024; 15:1429166. [PMID: 39206365 PMCID: PMC11349622 DOI: 10.3389/fmicb.2024.1429166] [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: 05/07/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
The structure of the leaf microbiome can alter host fitness and change in response to abiotic and biotic factors, like seasonality, climate, and leaf age. However, relatively few studies consider the influence of host age on microbial communities at a time scale of a few days, a short time scale relevant to microbes. To understand how host age modulates changes in the fungal and bacterial leaf microbiome on a short time scale, we ran independent field and greenhouse-based studies and characterized phyllosphere communities using next-generation sequencing approaches. Our field study characterized changes in the fungal and bacterial phyllosphere by examining leaves of different relative ages across individuals, whereas the greenhouse study examined changes in the fungal microbiome by absolute leaf age across individuals. Together, these results indicate that fungal communities are susceptible to change as a leaf ages as evidenced by shifts in the diversity of fungal taxa both in the field and the greenhouse. Similarly, there were increases in the diversity of fungal taxa by leaf age in the greenhouse. In bacterial communities in the field, we observed changes in the diversity, composition, and relative abundance of common taxa. These findings build upon previous literature characterizing host-associated communities at longer time scales and provide a foundation for targeted work examining how specific microbial taxa might interact with each other, such as fine-scale interactions between pathogenic and non-pathogenic species.
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Affiliation(s)
- Julie K. Geyer
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Rita L. Grunberg
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Wilson Center for Science and Justice at Duke Law, Durham, NC, United States
| | - Jeremy Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Charles E. Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Environment, Ecology, and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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20
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Kubosawa Y, Sujino T, Miyamoto K, Kayashima A, Minezaki D, Morioka K, Iwata K, Miyazaki K, Masunaga T, Mizutani M, Akimoto T, Takatori Y, Matsuura N, Nakayama A, Takabayashi K, Nakamoto N, Honda A, Kato M, Yahagi N, Kanai T. Distinctive duodenal microbiomes and bile acid profiles in duodenal tumor patients revealed by prospective observational study. Sci Rep 2024; 14:18705. [PMID: 39134638 PMCID: PMC11319767 DOI: 10.1038/s41598-024-69820-7] [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: 11/18/2023] [Accepted: 08/08/2024] [Indexed: 08/15/2024] Open
Abstract
The incidence of duodenal tumors (DTs) is increasing. However, the mechanisms underlying its development remain unclear. Environmental factors, including the microbiome and bile acids (BAs), are believed to influence tumor development. Therefore, we conducted a single-center, prospective, observational study to investigate the potential differences between patients with DTs and healthy controls (HCs) based on these factors. In addition, the BAs in the duodenal fluid were measured using liquid chromatography-tandem mass spectrometry. We recruited 41 patients and performed 16S rRNA-seq. There was no difference in the observed ASVs or PCoA plot of Bray-Curtis dissimilarity between the DTs and HCs. The lithocholic acid concentration was significantly lower in the DT group than in the control group. The ratio of CDCA to LCA was significantly higher in patients with DTs. No significant differences in microbiota were observed between DTs and HCs. In patients with DTs, the lithocholic acid concentration in duodenal was significantly lower than in HCs.
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Affiliation(s)
- Yoko Kubosawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Tomohisa Sujino
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
- Keio Global Research Institute, Keio Univerisy, Mita, Tokyo, 108-0073, Japan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.
| | - Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Central Research Institute, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Torocho, Kita-ku, Saitama-shi, Saitama, 331-0804, Japan
| | - Atsuto Kayashima
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Daisuke Minezaki
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kohei Morioka
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kentaro Iwata
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kurato Miyazaki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Teppei Masunaga
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Mari Mizutani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Teppei Akimoto
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yusaku Takatori
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Noriko Matsuura
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Atsushi Nakayama
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kaoru Takabayashi
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Akira Honda
- Division of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, 3-20-1 chuo, Ami-machi, Inashiki-gun, Ibaraki, 300-0395, Japan
| | - Motohiko Kato
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Naohisa Yahagi
- Division of Research and Development for Minimally Invasive Treatment Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.
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Lewis ZJ, Scott A, Madden C, Vik D, Zayed AA, Smith GJ, Justice SS, Rudinsky A, Hokamp J, Hale VL. Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome. RESEARCH SQUARE 2024:rs.3.rs-4688526. [PMID: 39149494 PMCID: PMC11326377 DOI: 10.21203/rs.3.rs-4688526/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Background The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml - 5 mL), and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and Propidium Monoazide. Results In relation to urine sample volume, 3 3.0 mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data, and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for core metabolic functions and environmental chemical metabolism. We identified long chain alkane utilization in two of the urine MAGs. Long chain alkanes are common pollutants that result from industrial combustion processes and end up in urine. Conclusions This is the first study, to our knowledge, to demonstrate environmental chemical degradation potential in urine microbes through genome-resolved metagenomics. These findings provide guidelines for studying the urobiome in relation to sample volume and host depletion, and lay the foundation for future evaluation of urobiome function in relation to health and disease.
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Affiliation(s)
- Zachary J Lewis
- Department of Veterinary Preventive Medicine, The Ohio State University
| | - Angela Scott
- Department of Veterinary Preventive Medicine, The Ohio State University
| | | | - Dean Vik
- Center of Microbiome Science, The Ohio State University
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University
| | | | | | - Adam Rudinsky
- Department of Veterinary Clinical Sciences, The Ohio State University
| | - Jessica Hokamp
- Department of Veterinary Biosciences, The Ohio State University
| | - Vanessa L Hale
- Department of Veterinary Preventive Medicine, The Ohio State University
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22
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Seixas MH, Munroe JS, Eggleston EM. Bacterial diversity and geomicrobiology of Winter Wonderland ice cave, Utah, USA. Microbiologyopen 2024; 13:e1426. [PMID: 38995161 PMCID: PMC11241547 DOI: 10.1002/mbo3.1426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 06/19/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
The Winter Wonderland ice cave, located at an elevation of 3140 m above sea level in the Uinta Mountains of northern Utah, USA, maintains a constant sub-zero temperature. Seasonal snowmelt and rain enter the cave, freeze on the surface of the existing ice, and contribute to a 3-m-thick layered ice mass. This ice mass contains organic matter and cryogenic cave carbonates (CCCs) that date back centuries. In this study, samples of ice, liquid water, and exposed CCCs were collected to examine the bacterial communities within the cave and to determine if these communities vary spatially and between sample types. Flow cytometry showed that cell counts are an order of magnitude higher in liquid water samples than in ice. Epifluorescence microscopy and scanning electron microscopy imaging revealed potential coccoid and bacillus microbial morphologies in water samples and putative cells or calcite spherules in the CCCs. The diversity of bacteria associated with soil, identified through sequence-based analysis, supports the hypothesis that water enters the cave by filtering through soil and bedrock. A differential abundance of bacterial taxa was observed between sample types, with the greatest diversity found in CCCs. This supports a geomicrobiological framework where microbes aggregate in the water, sink into a concentrated layer, and precipitate out of the ice with the CCCs, thereby reducing the cell counts in the ice. These CCCs may provide essential nutrients for the bacteria or could themselves be products of biomineralization.
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Affiliation(s)
- Miranda Herschel Seixas
- Department of Earth and Climate SciencesMiddlebury CollegeMiddleburyVermontUSA
- Biology DepartmentMiddlebury CollegeMiddleburyVermontUSA
| | - Jeffrey S. Munroe
- Department of Earth and Climate SciencesMiddlebury CollegeMiddleburyVermontUSA
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23
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Wang F, Chen Y, Zhou S, Li H, Wan C, Yan K, Zhang H, Xu Z. Aerosol sources and transport paths co-control the atmospheric bacterial diversity over the coastal East China Sea. MARINE POLLUTION BULLETIN 2024; 205:116589. [PMID: 38875970 DOI: 10.1016/j.marpolbul.2024.116589] [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: 03/16/2024] [Revised: 05/07/2024] [Accepted: 06/09/2024] [Indexed: 06/16/2024]
Abstract
Airborne bacteria along with chemical composition of aerosols were investigated during five sampling seasons at an offshore island of the East China Sea. Bacterial diversity was the lowest in spring, the highest in winter, and similar between the autumns of 2019 and 2020, suggesting remarkably seasonal variation but little interannual change. Geodermatophilus (Actinobacteria) was the indicator genus of mineral dust (MD) showed higher proportion in spring than in other seasons. Mastigocladopsis_PCC-10914 (Cyanobacteria) as the indicator of sea salt (SS) demonstrated the highest percentages in both autumns, when the air masses mainly passed over the ocean prior to the sampling site. The higher proportions of soil-derived genera Rubellimicrobium and Craurococcus (both Proteobacteria) and extremophile Chroococcidiopsis_SAG_2023 (Cyanobacteria) were found in summer and winter, respectively. Our study explores the linkage between aerosol source and transport path and bacterial composition, which has implication to understanding of land-sea transmission of bacterial taxa.
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Affiliation(s)
- Fanghui Wang
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Ying Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China; State Environmental Protection Key Laboratory of Land and Sea Ecological Governance and Systematic Regulation, Jinan, Shandong 250101, China; Institute of Eco-Chongming (IEC), National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Shanghai 200062, China.
| | - Shengqian Zhou
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Haowen Li
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Chunli Wan
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Ke Yan
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Hongliang Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China; State Environmental Protection Key Laboratory of Land and Sea Ecological Governance and Systematic Regulation, Jinan, Shandong 250101, China
| | - Zongjun Xu
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
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24
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Zhang E, Wong SY, Czechowski P, Terauds A, Ray AE, Benaud N, Chelliah DS, Wilkins D, Montgomery K, Ferrari BC. Effects of increasing soil moisture on Antarctic desert microbial ecosystems. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14268. [PMID: 38622950 DOI: 10.1111/cobi.14268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 04/17/2024]
Abstract
Overgeneralization and a lack of baseline data for microorganisms in high-latitude environments have restricted the understanding of the microbial response to climate change, which is needed to establish Antarctic conservation frameworks. To bridge this gap, we examined over 17,000 sequence variants of bacteria and microeukarya across the hyperarid Vestfold Hills and Windmill Islands regions of eastern Antarctica. Using an extended gradient forest model, we quantified multispecies response to variations along 79 edaphic gradients to explore the effects of change and wind-driven dispersal on community dynamics under projected warming trends. We also analyzed a second set of soil community data from the Windmill Islands to test our predictions of major environmental tipping points. Soil moisture was the most robust predictor for shaping the regional soil microbiome; the highest rates of compositional turnover occurred at 10-12% soil moisture threshold for photoautotrophs, such as Cyanobacteria, Chlorophyta, and Ochrophyta. Dust profiles revealed a high dispersal propensity for Chlamydomonas, a microalga, and higher biomass was detected at trafficked research stations. This could signal the potential for algal blooms and increased nonendemic species dispersal as human activities increase in the region. Predicted increases in moisture availability on the Windmill Islands were accompanied by high photoautotroph abundances. Abundances of rare oligotrophic taxa, such as Eremiobacterota and Candidatus Dormibacterota, which play a crucial role in atmospheric chemosynthesis, declined over time. That photosynthetic taxa increased as soil moisture increased under a warming scenario suggests the potential for competition between primary production strategies and thus a more biotically driven ecosystem should the climate become milder. Better understanding of environmental triggers will aid conservation efforts, and it is crucial that long-term monitoring of our study sites be established for the protection of Antarctic desert ecosystems. Furthermore, the successful implementation of an improved gradient forest model presents an exciting opportunity to broaden its use on microbial systems globally.
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Affiliation(s)
- Eden Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Sin Yin Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Paul Czechowski
- Helmholtz Institute for Metabolic, Obesity and Vascular Research, Leipzig, Germany
| | - Aleks Terauds
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
| | - Angelique E Ray
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Devan S Chelliah
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Wilkins
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
| | - Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
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25
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Beneke V, Grieger KM, Hartwig C, Müller J, Sohn K, Blaudszun AR, Hilger N, Schaudien D, Fricke S, Braun A, Sewald K, Hesse C. Homeostatic T helper 17 cell responses triggered by complex microbiota are maintained in ex vivo intestinal tissue slices. Eur J Immunol 2024; 54:e2350946. [PMID: 38763899 DOI: 10.1002/eji.202350946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024]
Abstract
Segmented filamentous bacteria (SFB) are members of the commensal intestinal microbiome. They are known to contribute to the postnatal maturation of the gut immune system, but also to augment inflammatory conditions in chronic diseases such as Crohn's disease. Living primary tissue slices are ultrathin multicellular sections of the intestine and provide a unique opportunity to analyze tissue-specific immune responses ex vivo. This study aimed to investigate whether supplementation of the gut flora with SFB promotes T helper 17 (Th17) cell responses in primary intestinal tissue slices ex vivo. Primary tissue slices were prepared from the small intestine of healthy Taconic mice with SFB-positive and SFB-negative microbiomes and stimulated with anti-CD3/CD28 or Concanavalin A. SFB-positive and -negative mice exhibited distinct microbiome compositions and Th17 cell frequencies in the intestine and complex microbiota including SFB induced up to 15-fold increase in Th17 cell-associated mediators, serum amyloid A (SAA), and immunoglobulin A (IgA) responses ex vivo. This phenotype could be transmitted by co-housing of mice. Our findings highlight that changes in the gut microbiome can be observed in primary intestinal tissue slices ex vivo. This makes the system very attractive for disease modeling and assessment of new therapies.
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Affiliation(s)
- Valerie Beneke
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
| | - Klaudia M Grieger
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
| | - Christina Hartwig
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Jan Müller
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
- Center of Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- Member of the Vienna Biocenter PhD Program, University of Vienna and the Medical University of Vienna, Vienna, Austria
| | - Kai Sohn
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - André-René Blaudszun
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Nadja Hilger
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Dirk Schaudien
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Stephan Fricke
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Department of Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Armin Braun
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
- Institute for Immunology, Hannover Medical School, Hannover, Germany
| | - Katherina Sewald
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
| | - Christina Hesse
- Division of Preclinical Pharmacology and Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network, Hannover, Germany
- Member of the Fraunhofer Excellence Cluster of Immune Mediated Diseases (CIMD), Germany
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26
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Ribère M, Lemieux-Labonté V, Pincez T, Azria E, Lapointe FJ. Duration of rupture of membranes and microbiome transmission to the newborn: A prospective study. BJOG 2024; 131:1249-1258. [PMID: 38311451 DOI: 10.1111/1471-0528.17774] [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: 09/21/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 02/06/2024]
Abstract
OBJECTIVE To assess whether labour variables (i.e. individuals characteristics, labour characteristics and medical interventions) impact maternal and newborn microbiomes. DESIGN Prospective monocentric study. SETTING Saint-Joseph Hospital tertiary maternity unit, in Paris, France. POPULATION All consecutive primiparous women with a physiological pregnancy and term labour from 15 April to 1 June 2017. METHODS 16S ribosomal RNA gene sequencing of the maternal vaginal, newborn skin and newborn oral microbiomes from 58 mother-baby dyads. MAIN OUTCOME MEASURES Analysis of the effects of 19 labour variables on the composition and diversity of these microbiomes. RESULTS The 19 labour variables explained a significant part of the variability in the vaginal, newborn oral and skin microbiomes (44%-67%). Strikingly, duration of rupture of membranes was the single factor that explained the greatest variability (adjusted R2: 7.7%-8.4%, p ≤ 0.002) and conditioned, by itself, the compositions of the three microbiomes under study. Long duration of rupture of membranes was specifically associated with a lower relative abundance of the Lactobacillus genus (1.7-fold to 68-fold reduction, p < 0.0001) as well as an increase in microbiome diversity, including genera implicated in nosocomial infections. The effects of duration of rupture of membranes were also present in newborns delivered by non-elective caesarean section. CONCLUSIONS Maternal and newborn microbiomes were greatly affected by labour variables. Duration of rupture of membranes, even in non-elective caesarean sections, should be considered in epidemiological and microbiological studies, as well as in vaginal seeding practices.
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Affiliation(s)
- Maïté Ribère
- Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | | | - Thomas Pincez
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
| | - Elie Azria
- Maternité Notre Dame de Bon Secours, Groupe Hospitalier Paris Saint-Joseph, Université Paris Cité, Paris, France
- UMR1153 - Obstetrical, Perinatal and Pediatric Epidemiology (EPOPé Research Team), FHU Prema, Université Paris Cité - INSERM, Paris, France
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27
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Older CE, Rodrigues Hoffmann A. Considerations for performing companion animal skin microbiome studies. Vet Dermatol 2024; 35:367-374. [PMID: 38654617 DOI: 10.1111/vde.13250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/16/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
The microbiome field has grown significantly in the past decade, and published studies have provided an overview of the microorganisms inhabiting the skin of companion animals. With the continued growth and interest in this field, concerns have been raised regarding sample collection methods, reagent contamination, data processing and environmental factors that may impair data interpretation (especially as related to low-biomass skin samples). In order to assure transparency, it is important to report all steps from sample collection to data analysis, including use of proper controls, and to make sequence data and sample metadata publicly available. Whilst interstudy variation will continue to exist, efforts to standardise methods will reduce confounding variables, and allow for reproducibility and comparability of results between studies. Companion animal microbiome studies often include clinical cases, and small sample sizes may result in lack of statistical significance within small datasets. The ability to combine results from standardised studies through meta-analyses would mitigate the limitations of these smaller studies, providing for more robust interpretation of results which could then inform clinical decisions. In this narrative review, we aim to present considerations for designing a study to evaluate the skin microbiome of companion animals, from conception to data analysis.
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Affiliation(s)
- Caitlin E Older
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Aline Rodrigues Hoffmann
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
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28
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Salgado JFM, Premkrishnan BNV, Oliveira EL, Vettath VK, Goh FG, Hou X, Drautz-Moses DI, Cai Y, Schuster SC, Junqueira ACM. The dynamics of the midgut microbiome in Aedes aegypti during digestion reveal putative symbionts. PNAS NEXUS 2024; 3:pgae317. [PMID: 39157462 PMCID: PMC11327924 DOI: 10.1093/pnasnexus/pgae317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 07/02/2024] [Indexed: 08/20/2024]
Abstract
Blood-feeding is crucial for the reproductive cycle of the mosquito Aedes aegypti, as well as for the transmission of arboviruses to hosts. It is postulated that blood meals may influence the mosquito microbiome but shifts in microbial diversity and function during digestion remain elusive. We used whole-genome shotgun metagenomics to monitor the midgut microbiome in 60 individual females of A. aegypti throughout digestion, after 12, 24, and 48 h following blood or sugar meals. Additionally, ten individual larvae were sequenced, showing microbiomes dominated by Microbacterium sp. The high metagenomic coverage allowed for microbial assignments at the species taxonomic level, also providing functional profiling. Females in the post-digestive period and larvae displayed low microbiome diversities. A striking proliferation of Enterobacterales was observed during digestion in blood-fed mosquitoes. The compositional shift was concomitant with enrichment in genes associated with carbohydrate and protein metabolism, as well as virulence factors for antimicrobial resistance and scavenging. The bacterium Elizabethkingia anophelis (Flavobacteriales), a known human pathogen, was the dominant species at the end of blood digestion. Phylogenomics suggests that its association with hematophagous mosquitoes occurred several times. We consider evidence of mutually beneficial host-microbe interactions raised from this association, potentially pivotal for the mosquito's resistance to arbovirus infection. After digestion, the observed shifts in blood-fed females' midguts shifted to a sugar-fed-like microbial profile. This study provides insights into how the microbiome of A. aegypti is modulated to fulfil digestive roles following blood meals, emphasizing proliferation of potential symbionts in response to the dynamic midgut environment.
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Affiliation(s)
- João Felipe M Salgado
- RG Insect Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch str. 10, Marburg 35043, Germany
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, 373 Avenida Carlos Chagas Filho, Rio de Janeiro, RJ 21941-902, Brazil
| | - Balakrishnan N V Premkrishnan
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Elaine L Oliveira
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Vineeth Kodengil Vettath
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Feng Guang Goh
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Block S3, #05-01, Singapore 117558, Singapore
| | - Xinjun Hou
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Block S3, #05-01, Singapore 117558, Singapore
| | - Daniela I Drautz-Moses
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yu Cai
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Block S3, #05-01, Singapore 117558, Singapore
| | - Stephan C Schuster
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Ana Carolina M Junqueira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, 373 Avenida Carlos Chagas Filho, Rio de Janeiro, RJ 21941-902, Brazil
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Sokou R, Moschari E, Palioura AE, Palioura AP, Mpakosi A, Adamakidou T, Vlachou E, Theodoraki M, Iacovidou N, Tsartsalis AN. The Impact of Gestational Diabetes Mellitus (GDM) on the Development and Composition of the Neonatal Gut Microbiota: A Systematic Review. Microorganisms 2024; 12:1564. [PMID: 39203408 PMCID: PMC11356352 DOI: 10.3390/microorganisms12081564] [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: 07/01/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 09/03/2024] Open
Abstract
Gestational diabetes mellitus (GDM) is an important health issue, as it is connected with adverse effects to the mother as well as the fetus. A factor of essence for the pathology of this disorder is the gut microbiota, which seems to have an impact on the development and course of GDM. The role of the gut microbiota on maternal reproductive health and all the changes that happen during pregnancy as well as during the neonatal period is of high interest. The correct establishment and maturation of the gut microbiota is of high importance for the development of basic biological systems. The aim of this study is to provide a systematic review of the literature on the effect of GDM on the gut microbiota of neonates, as well as possible links to morbidity and mortality of neonates born to mothers with GDM. Systematic research took place in databases including PubMed and Scopus until June 2024. Data that involved demographics, methodology, and changes to the microbiota were derived and divided based on patients with exposure to or with GDM. The research conducted on online databases revealed 316 studies, of which only 16 met all the criteria and were included in this review. Research from the studies showed great heterogeneity and varying findings at the level of changes in α and β diversity and enrichment or depletion in phylum, gene, species, and operational taxonomic units in the neonatal gut microbiota of infants born to mothers with GDM. The ways in which the microbiota of neonates and infants are altered due to GDM remain largely unclear and require further investigation. Future studies are needed to explore and clarify these mechanisms.
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Affiliation(s)
- Rozeta Sokou
- Neonatal Intensive Care Unit, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece; (E.M.); (A.E.P.); (A.-P.P.); (M.T.)
- Neonatal Department, National and Kapodistrian University of Athens, Aretaieio Hospital, 11528 Athens, Greece;
| | - Eirini Moschari
- Neonatal Intensive Care Unit, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece; (E.M.); (A.E.P.); (A.-P.P.); (M.T.)
| | - Alexia Eleftheria Palioura
- Neonatal Intensive Care Unit, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece; (E.M.); (A.E.P.); (A.-P.P.); (M.T.)
| | - Aikaterini-Pothiti Palioura
- Neonatal Intensive Care Unit, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece; (E.M.); (A.E.P.); (A.-P.P.); (M.T.)
| | - Alexandra Mpakosi
- Department of Microbiology, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece;
| | - Theodoula Adamakidou
- Department of Nursing, School of Health Sciences, University of West Attica, Ag. Spydironos 28, 12243 Athens, Greece; (T.A.); (E.V.)
| | - Eugenia Vlachou
- Department of Nursing, School of Health Sciences, University of West Attica, Ag. Spydironos 28, 12243 Athens, Greece; (T.A.); (E.V.)
| | - Martha Theodoraki
- Neonatal Intensive Care Unit, General Hospital of Nikea “Agios Panteleimon”, 18454 Piraeus, Greece; (E.M.); (A.E.P.); (A.-P.P.); (M.T.)
| | - Nicoletta Iacovidou
- Neonatal Department, National and Kapodistrian University of Athens, Aretaieio Hospital, 11528 Athens, Greece;
| | - Athanasios N. Tsartsalis
- Department of Endocrinology Diabetes and Metabolism, Naval Hospital of Athens, Dinokratous 70, 11521 Athens, Greece;
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Haslbauer JD, Wiegand C, Hamelin B, Ivanova VS, Menter T, Savic Prince S, Tzankov A, Mertz KD. Two cases demonstrate an association between Tropheryma whipplei and pulmonary marginal zone lymphoma. Infect Agent Cancer 2024; 19:33. [PMID: 39068468 PMCID: PMC11282790 DOI: 10.1186/s13027-024-00597-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Marginal zone lymphomas of mucosa-associated lymphatic tissues (MZL of MALT) are a group of indolent B-cell neoplasms, which are thought to arise from chronic antigenic stimulation of B-cells either due to underlying chronic infection or autoimmune disease. Little is known about potential causative pathogens in pulmonary MZL (PMZL), although some data suggests a potential role of Achromobacter (A.) xylosoxidans. METHODS An index case of chronic pulmonary colonisation with Tropheryma (T.) whipplei and subsequent development of PMZL was identified by T. whipplei specific PCR and metagenomic next genome sequencing (mNGS). This case prompted a retrospectively conducted analysis of T. whipplei-specific PCRs in lung tissue from PMZL patients (n = 22), other pulmonary lymphomas, and normal controls. Positive results were confirmed by mNGS. A systematic search for T. whipplei and A. xylosoxidans in our in-house mNGS dataset comprising autopsy lungs, lung biopsies and lung resection specimens (n = 181) was subsequently performed. RESULTS A 69-year-old patient presented with weight loss and persistent pulmonary consolidation. Subsequent mNGS analysis detected T. whipplei in the resected lung specimen. An antibiotic regimen eventually eliminated the bacterium. However, the consolidation persisted, and the diagnosis of PMZL was made in a second lung resection specimen. A second case of T. whipplei-associated PMZL was subsequently detected in the retrospectively analysed PMZL cohort. Both cases showed comparatively few mutations and no mutations in genes encoding for NF-κB pathway components, suggesting that T. whipplei infection may substitute for mutations in these PMZL. None of the samples in our in-house dataset tested positive for T. whipplei. In contrast, A. xylosoxidans was frequently found in both autopsy lungs and lung biopsy / resection specimens that were not affected by PMZL (> 50%). CONCLUSIONS Our data suggests that T. whipplei colonisation of lungs may trigger PMZL as a potential driver. Systematic analyses with larger cohorts should be conducted to further support this hypothesis. The frequent detection of A. xylosoxidans in lung tissue suggests that it is a common component of the pulmonary microbiome and therefore less likely to trigger lymphomas.
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Affiliation(s)
- J D Haslbauer
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - C Wiegand
- Institute of Pathology, Cantonal Hospital Baselland, Mühlemattstrasse 11, CH-4410, Liestal, Switzerland
| | - B Hamelin
- Institute of Pathology, Cantonal Hospital Baselland, Mühlemattstrasse 11, CH-4410, Liestal, Switzerland
| | - V S Ivanova
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - T Menter
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - S Savic Prince
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - A Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - K D Mertz
- Institute of Pathology, Cantonal Hospital Baselland, Mühlemattstrasse 11, CH-4410, Liestal, Switzerland.
- University of Basel, Basel, Switzerland.
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Kunath BJ, De Rudder C, Laczny CC, Letellier E, Wilmes P. The oral-gut microbiome axis in health and disease. Nat Rev Microbiol 2024:10.1038/s41579-024-01075-5. [PMID: 39039286 DOI: 10.1038/s41579-024-01075-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2024] [Indexed: 07/24/2024]
Abstract
The human body hosts trillions of microorganisms throughout many diverse habitats with different physico-chemical characteristics. Among them, the oral cavity and the gut harbour some of the most dense and diverse microbial communities. Although these two sites are physiologically distinct, they are directly connected and can influence each other in several ways. For example, oral microorganisms can reach and colonize the gastrointestinal tract, particularly in the context of gut dysbiosis. However, the mechanisms of colonization and the role that the oral microbiome plays in causing or exacerbating diseases in other organs have not yet been fully elucidated. Here, we describe recent advances in our understanding of how the oral and intestinal microbiota interplay in relation to their impact on human health and disease.
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Affiliation(s)
- Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Charlotte De Rudder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Elisabeth Letellier
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Belvaux, Luxembourg.
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32
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Sun M, Lu F, Yu D, Wang Y, Chen P, Liu S. Respiratory diseases and gut microbiota: relevance, pathogenesis, and treatment. Front Microbiol 2024; 15:1358597. [PMID: 39081882 PMCID: PMC11286581 DOI: 10.3389/fmicb.2024.1358597] [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: 01/04/2024] [Accepted: 06/26/2024] [Indexed: 08/02/2024] Open
Abstract
Preclinical evidence has firmly established a bidirectional interaction among the lung, gut, and gut microbiome. There are many complex communication pathways between the lung and intestine, which affect each other's balance. Some metabolites produced by intestinal microorganisms, intestinal immune cells, and immune factors enter lung tissue through blood circulation and participate in lung immune function. Altered gut-lung-microbiome interactions have been identified in rodent models and humans of several lung diseases such as pulmonary fibrosis, chronic obstructive pulmonary disease, lung cancer, asthma, etc. Emerging evidence suggests that microbial therapies can prevent and treat respiratory diseases, but it is unclear whether this association is a simple correlation with the pathological mechanisms of the disease or the result of causation. In this review, we summarize the complex and critical link between the gut microbiota and the lung, as well as the influence and mechanism of the gut microbiota on respiratory diseases, and discuss the role of interventions such as prebiotics and fecal bacteria transplantation on respiratory diseases. To provide a reference for the rational design of large-scale clinical studies, the direct application of microbial therapy to respiratory-related diseases can reduce the incidence and severity of diseases and accompanying complications.
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Affiliation(s)
- Mengdi Sun
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Fang Lu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Donghua Yu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yu Wang
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Pingping Chen
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Shumin Liu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
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Darabi A, Sobhani S, Aghdam R, Eslahchi C. AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides. BMC Bioinformatics 2024; 25:241. [PMID: 39014300 PMCID: PMC11253361 DOI: 10.1186/s12859-024-05859-7] [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: 08/27/2023] [Accepted: 07/09/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU. RESULTS In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector. CONCLUSION The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function. AVAILABILITY A python package is available at: https://github.com/SayehSobhani/AFITBin .
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Affiliation(s)
- Amin Darabi
- Department of Computer and Data Sciences, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran
| | - Sayeh Sobhani
- Department of Computer and Data Sciences, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Rosa Aghdam
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Changiz Eslahchi
- Department of Computer and Data Sciences, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran.
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
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Chen P, Hu T, Jiang H, Li B, Li G, Ran P, Zhou Y. The effects of different lung parts, age, and batches on the lung microbiota of healthy rats. Ann Med 2024; 56:2381085. [PMID: 39099020 PMCID: PMC11299442 DOI: 10.1080/07853890.2024.2381085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/21/2023] [Accepted: 05/16/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Rat models are valuable tools to study the lung microbiota in diseases. Yet the impacts of different lung parts, young and mature adult stages, and the different batches of the same conditions on the healthy rat lung microbiome have not been investigated. METHODS The rat lung microbiome was analyzed to clarify the lung part-dependent and age-dependent differences and to evaluate the effects of several 'batch environmental factors' on normal rats, after eliminating potential contamination. RESULTS The results showed that the contamination could be identified and excluded. The lung microbiome from left and right lung parts was very similar so one representative part could be used in the microbiome study. There were significantly different lung microbial communities between the young and mature adult groups, and also between the different feeding batches groups of the same repetitive feeding conditions, but a common lung microbiota characterized by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria as the most dominant phyla were present in all adult rats. It indicated that the experiment under the same condition of the same rats batch was needed to compare the difference in the lung microbiota and repeated experiments were necessary to confirm the results. CONCLUSION These data represented that the lung bacterial communities were dynamic and rapidly susceptible to environmental influence, clustered strongly by age or different feeding batches but similar in the different lung tissue parts. This study improved the basic understanding of the potential effects on the lung microbiome of healthy rats.
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Affiliation(s)
- Ping Chen
- GMU-GIBH Joint School of Life Sciences, the Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China
- Department of Gastroenterology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Tingting Hu
- GMU-GIBH Joint School of Life Sciences, the Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China
| | - Haonan Jiang
- GMU-GIBH Joint School of Life Sciences, the Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China
| | - Bing Li
- GMU-GIBH Joint School of Life Sciences, the Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China
| | - Guiying Li
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, China
| | - Pixin Ran
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bioland, Guangzhou, China
| | - Yumin Zhou
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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Hale B, Watts C, Conatser M, Brown E, Wijeratne AJ. Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing. ENVIRONMENTAL MICROBIOME 2024; 19:46. [PMID: 38997772 PMCID: PMC11241880 DOI: 10.1186/s40793-024-00590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions. RESULTS Synthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi - a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties. CONCLUSIONS This study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research.
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Affiliation(s)
- Brett Hale
- AgriGro Incorporated, Doniphan, MO, USA
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA
- College of Science and Mathematics, Arkansas State University, State University, AR, USA
| | - Caitlin Watts
- College of Agriculture, Arkansas State University, State University, AR, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew Conatser
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Edward Brown
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Asela J Wijeratne
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA.
- College of Science and Mathematics, Arkansas State University, State University, AR, USA.
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Tian Q, Jin S, Zhang G, Liu Y, Liu J, Tang X, Li Y, Liu J, Liu Y, Wang Z. Assessing vaginal microbiome through Vaginal Microecology Evaluation System as a predictor for in vitro fertilization outcomes: a retrospective study. Front Endocrinol (Lausanne) 2024; 15:1380187. [PMID: 39045277 PMCID: PMC11263289 DOI: 10.3389/fendo.2024.1380187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 06/25/2024] [Indexed: 07/25/2024] Open
Abstract
Objective This study aims to evaluate the effectiveness of the Vaginal Microecology Evaluation System (VMES) in assessing the dynamics of the vaginal microbiome (VM) throughout the process of in vitro fertilization and embryo transfer (IVF-ET). Furthermore, it seeks to explore the potential correlation between distinct types of VM ecology and the success rate of IVF-ET. Methods This study employed VMES to ascertain the composition of the VM. Data were collected from infertile women who underwent their initial IVF-ET treatment for tubal factor between January 2018 and December 2021. A retrospective analysis of pregnancy outcomes resulting from their fresh embryo transfer was conducted to determine the predictive significance of the vaginal microenvironment. Results We demonstrate that VMES is able to predict IVF-ET outcomes in patients diagnosed with Bacterial Vaginosis (BV). Notably, a discernible shift in the VM was observed in a decent subset of patients following Controlled Ovarian Stimulation (COS), though this phenomenon was not universal across all participants. Specifically, there was a noteworthy increase in the proportion of patients exhibiting BV and uncharacterized dysbiosis subsequent to COS. Furthermore, our investigation revealed a significant correlation between VM and both the live birth rate and early miscarriage rate. Employing a multivariable logistic regression model, we identified that VM status pre-COS, VM status post-COS, patient age, and the number of embryos transferred emerged as independent predictors of the live birth rate. Conclusion Our study suggests that, during IVF-ET treatment, the VMES can effectively detect changes in the VM, which are strongly correlated with the pregnancy outcome of IVF-ET procedures.
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Affiliation(s)
- Quan Tian
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong, China
- Department of Reproductive Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Shengxi Jin
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong, China
| | - Guangmin Zhang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong, China
| | - Yujie Liu
- Department of Reproductive Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jianxin Liu
- Department of Reproductive Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiuming Tang
- Department of Reproductive Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yufeng Li
- Department of Reproductive Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jiane Liu
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong, China
- Department of Reproductive Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yifei Liu
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Pennsylvania State Hershey Medical Center, Hershey, PA, United States
| | - Zheng Wang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong, China
- Department of Reproductive Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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Klimov PB, Hubert J, Erban T, Alejandra Perotti M, Braig HR, Flynt A, He Q, Cui Y. Genomic and metagenomic analyses of the domestic mite Tyrophagus putrescentiae identify it as a widespread environmental contaminant and a host of a basal, mite-specific Wolbachia lineage (supergroup Q). Int J Parasitol 2024:S0020-7519(24)00138-3. [PMID: 38992783 DOI: 10.1016/j.ijpara.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024]
Abstract
Tyrophagus putrescentiae (mould mite) is a global, microscopic trophic generalist that commonly occurs in various human-created habitats, causing allergies and damaging stored food. Its ubiquity and extraordinary ability to penetrate research samples or cultures through air currents or by active walking through tights spaces (such as treads of screw caps) may lead to sample contamination and introduction of its DNA to research materials in the laboratory. This prompts a thorough investigation into potential sequence contamination in public genomic databases. The trophic success of T. putrescentiae is primarily attributed to the symbiotic bacteria housed in specialized internal mite structures, facilitating adaptation to varied nutritional niches. However, recent work suggests that horizontal transfer of bacterial/fungal genes related to nutritional functionality may also contribute to the mite's trophic versatility. This aspect requires independent confirmation. Additionally, T. putrescentiae harbors an uncharacterized and genetically divergent bacterium, Wolbachia, displaying blocking and microbiome-modifying effects. The phylogenomic position and supergroup assignment of this bacterium are unknown. Here, we sequenced and assembled the T. putrescentiae genome, analyzed its microbiome, and performed detailed phylogenomic analyses of the mite-specific Wolbachia. We show that T. putrescentiae DNA is a substantial source of contamination of research samples. Its DNA may inadvertently be co-extracted with the DNA of the target organism, eventually leading to sequence contamination in public databases. We identified a diversity of bacterial species associated with T. putrescentiae, including those capable of rapidly developing antibiotic resistance, such as Escherichia coli. Despite the presence of diverse bacterial communities in T. putrescentiae, we did not detect any recent horizontal gene transfers in this mite species and/or in astigmatid (domestic) mites in general. Our phylogenomic analysis of Wolbachia recovered a basal, mite-specific lineage (supergroup Q) represented by two Wolbachia spp. from the mould mite and a gall-inducing plant mite. Fluorescence in situ hybridization confirmed the presence of Wolbachia inside the mould mite. The discovery of an early derivative Wolbachia lineage (supergroup Q) in two phylogenetically unrelated and ecologically dissimilar mites suggests that this endosymbiotic bacterial lineage formed a long-term association with mites. This finding provides a unique insight into the early evolution and host associations of Wolbachia. Further discoveries of Wolbachia diversity in acariform mites are anticipated.
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Affiliation(s)
- Pavel B Klimov
- Purdue University, Department of Biological Sciences, 915 W State St, West Lafayette, IN, USA; Tyumen State University, Institute of Environmental and Agricultural Biology (X-BIO), Tyumen, Russia.
| | - Jan Hubert
- Crop Research Institute, Department of Stored Product and Food Safety, Prague, Czechia; Czech University of Life Science, Faculty of Microbiology Nutrient and Dietics, Prague, Czechia
| | - Tomas Erban
- Crop Research Institute, Department of Stored Product and Food Safety, Prague, Czechia
| | - M Alejandra Perotti
- University of Reading, Ecology and Evolutionary Biology Section, School of Biological Sciences, Reading RG6 6AS, United Kingdom
| | - Henk R Braig
- Institute and Museum of Natural Sciences, Faculty of Natural and Exact Sciences, National University of San Juan, San Juan, J5400 DNQ, Argentina
| | - Alex Flynt
- University of Southern Mississippi, School of Biological, Environmental, and Earth Sciences, Hattiesburg, MS, USA
| | - Qixin He
- Purdue University, Department of Biological Sciences, 915 W State St, West Lafayette, IN, USA.
| | - Yubao Cui
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University.Wuxi, PR Chin.
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Senthakumaran T, Tannæs TM, Moen AEF, Brackmann SA, Jahanlu D, Rounge TB, Bemanian V, Tunsjø HS. Detection of colorectal-cancer-associated bacterial taxa in fecal samples using next-generation sequencing and 19 newly established qPCR assays. Mol Oncol 2024. [PMID: 38970464 DOI: 10.1002/1878-0261.13700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/15/2024] [Accepted: 06/28/2024] [Indexed: 07/08/2024] Open
Abstract
We have previously identified increased levels of distinct bacterial taxa within mucosal biopsies from colorectal cancer (CRC) patients. Following prior research, the aim of this study was to investigate the detection of the same CRC-associated bacteria in fecal samples and to evaluate the suitability of fecal samples as a non-invasive material for the detection of CRC-associated bacteria. Next-generation sequencing (NGS) of the 16S ribosomal RNA (rRNA) V4 region was performed to evaluate the detection of the CRC-associated bacteria in the fecal microbiota of cancer patients, patients with adenomatous polyp and healthy controls. Furthermore, 19 novel species-specific quantitative PCR (qPCR) assays were established to detect the CRC-associated bacteria. Approximately, 75% of the bacterial taxa identified in biopsies were reflected in fecal samples. NGS failed to detect low-abundance CRC-associated taxa in fecal samples, whereas qPCR exhibited high sensitivity and specificity in identifying all targeted taxa. Comparison of fecal microbial composition between the different patient groups showed enrichment of Fusobacterium nucleatum, Parvimonas micra, and Gemella morbillorum in cancer patients. Our findings suggest that low-abundance mucosa-associated bacteria can be detected in fecal samples using sensitive qPCR assays.
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Affiliation(s)
| | - Tone M Tannæs
- Section for Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Norway
| | - Aina E F Moen
- Section for Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Norway
- Department of Methods Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephan A Brackmann
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway
- Institute for Clinical Medicine, University of Oslo, Norway
| | - David Jahanlu
- Department of Life Sciences and Health, Oslo Metropolitan University, Norway
| | - Trine B Rounge
- Department of Pharmacy, Centre for Bioinformatics, University of Oslo, Norway
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Vahid Bemanian
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway
| | - Hege S Tunsjø
- Department of Life Sciences and Health, Oslo Metropolitan University, Norway
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39
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Ockert LE, McLennan EA, Fox S, Belov K, Hogg CJ. Characterising the Tasmanian devil (Sarcophilus harrisii) pouch microbiome in lactating and non-lactating females. Sci Rep 2024; 14:15188. [PMID: 38956276 PMCID: PMC11220038 DOI: 10.1038/s41598-024-66097-8] [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: 01/11/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
Wildlife harbour a diverse range of microorganisms that affect their health and development. Marsupials are born immunologically naïve and physiologically underdeveloped, with primary development occurring inside a pouch. Secretion of immunological compounds and antimicrobial peptides in the epithelial lining of the female's pouch, pouch young skin, and through the milk, are thought to boost the neonate's immune system and potentially alter the pouch skin microbiome. Here, using 16S rRNA amplicon sequencing, we characterised the Tasmanian devil pouch skin microbiome from 25 lactating and 30 non-lactating wild females to describe and compare across these reproductive stages. We found that the lactating pouch skin microbiome had significantly lower amplicon sequence variant richness and diversity than non-lactating pouches, however there was no overall dissimilarity in community structure between lactating and non-lactating pouches. The top five phyla were found to be consistent between both reproductive stages, with over 85% of the microbiome being comprised of Firmicutes, Proteobacteria, Fusobacteriota, Actinobacteriota, and Bacteroidota. The most abundant taxa remained consistent across all taxonomic ranks between lactating and non-lactating pouch types. This suggests that any potential immunological compounds or antimicrobial peptide secretions did not significantly influence the main community members. Of the more than 16,000 total identified amplicon sequence variants, 25 were recognised as differentially abundant between lactating and non-lactating pouches. It is proposed that the secretion of antimicrobial peptides in the pouch act to modulate these microbial communities. This study identifies candidate bacterial clades on which to test the activity of Tasmanian devil antimicrobial peptides and their role in pouch young protection, which in turn may lead to future therapeutic development for human diseases.
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Affiliation(s)
- Lucy E Ockert
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Elspeth A McLennan
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Samantha Fox
- Save the Tasmanian Devil Program, NRE Tasmania, Hobart, TAS, 7001, Australia
- Toledo Zoo, 2605 Broadway, Toledo, OH, 43609, USA
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia.
- San Diego Zoo Wildlife Alliance, PO BOX 120551, San Diego, CA, 92112, USA.
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40
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Williams SE, Varliero G, Lurgi M, Stach JEM, Race PR, Curnow P. Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39073401 DOI: 10.1099/mic.0.001478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.
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Affiliation(s)
- Sam E Williams
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs., Lyngby, Denmark
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Miguel Lurgi
- Department of Biosciences, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul R Race
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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41
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Massier L, Musat N, Stumvoll M, Tremaroli V, Chakaroun R, Kovacs P. Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges. Nat Metab 2024; 6:1209-1224. [PMID: 38898236 DOI: 10.1038/s42255-024-01065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Although the impact of the gut microbiome on health and disease is well established, there is controversy regarding the presence of microorganisms such as bacteria and their products in organs and tissues. However, recent contamination-aware findings of tissue-resident microbial signatures provide accumulating evidence in support of bacterial translocation in cardiometabolic disease. The latter provides a distinct paradigm for the link between microbial colonizers of mucosal surfaces and host metabolism. In this Perspective, we re-evaluate the concept of tissue-resident bacteria including their role in metabolic low-grade tissue and systemic inflammation. We examine the limitations and challenges associated with studying low bacterial biomass samples and propose experimental and analytical strategies to overcome these issues. Our Perspective aims to encourage further investigation of the mechanisms linking tissue-resident bacteria to host metabolism and their potentially actionable health implications for prevention and treatment.
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Affiliation(s)
- Lucas Massier
- Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
| | - Niculina Musat
- Aarhus University, Department of Biology, Section for Microbiology, Århus, Denmark
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
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42
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Quesada S, Rosso AD, Mascardi F, Soler-Rivero V, Aguilera P, Mascuka SN, Boiro A, Arenielo E, Vijoditz G, Ferreyra-Mufarregue LR, Caputo MF, Cimolai MC, Coluccio Leskow F, Penas-Steinhardt A, Belforte FS. Integrative analysis of systemic lupus erythematosus biomarkers: Role of fecal hsa-mir-223-3p and gut microbiota in transkingdom dynamics. Mol Immunol 2024; 171:77-92. [PMID: 38795687 DOI: 10.1016/j.molimm.2024.05.004] [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: 01/26/2024] [Revised: 04/20/2024] [Accepted: 05/10/2024] [Indexed: 05/28/2024]
Abstract
Systemic lupus erythematosus (SLE) involves a florid set of clinical manifestations whose autoreactive origin is characterized by an overactivation of the immune system and the production of a large number of autoantibodies. Because it is a complex pathology with an inflammatory component, its pathogenesis is not yet fully understood, assuming both genetic and environmental predisposing factors. Currently, it is known that the role of the human microbiome is crucial in maintaining the transkingdom balance between commensal microorganisms and the immune system. In the present work we study the intestinal microbiota of Argentine patients with different stages of SLE receiving or not different treatments. Microbiota composition and fecal miRNAs were assessed by 16 S sequencing and qPCR. hsa-miR-223-3p, a miRNA involved in several inflammation regulation pathways, was found underexpressed in SLE patients without immunosuppressive treatment. In terms of microbiota there were clear differences in population structure (Weighted and Unweighted Unifrac distances, p-value <0.05) and core microbiome between cases and controls. In addition, Collinsella, Bifidobacterium, Streptococcus genera and aromatics degradation metabolisms were overrepresented in the SLE group. Medical treatment was also determinant as several microbial metabolic pathways were influenced by immunosuppressive therapy. Particularly, allantoin degradation metabolism was differentially expressed in the group of patients receiving immunosuppressants. Finally, we performed a logistic regression model (LASSO: least absolute shrinkage and selection operator) considering the expression levels of the fecal hsa-miR223-3p; the core microbiota; the differentially abundant bacterial taxa and the differentially abundant metabolic pathways (p<0.05). The model predicted that SLE patients could be associated with greater relative abundance of the formaldehyde oxidation pathway (RUMP_PWY). On the contrary, the preponderance of the ketodeoxyoctonate (Kdo) biosynthesis and activation route (PWY_1269) and the genera Lachnospiraceae_UCG_004, Lachnospira, Victivallis and UCG_003 (genus belonging to the family Oscillospiraceae of the class Clostridia) were associated with a control phenotype. Overall, the present work could contribute to the development of integral diagnostic tools for the comprehensive phenotyping of patients with SLE. In this sense, studying the commensal microbial profile and possible pathobionts associated with SLE in our population proposes more effective and precise strategies to explore possible treatments based on the microbiota of SLE patients.
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Affiliation(s)
- Sofía Quesada
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Ayelén Daiana Rosso
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Florencia Mascardi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
| | - Valeria Soler-Rivero
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Pablo Aguilera
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Sebastian Nicolas Mascuka
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Andrea Boiro
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Evangelina Arenielo
- Sección Inmunología, Hospital Nacional Profesor Alejandro Posadas, Buenos Aires, Argentina
| | - Gustavo Vijoditz
- Sección Inmunología, Hospital Nacional Profesor Alejandro Posadas, Buenos Aires, Argentina
| | | | - Marina Flavia Caputo
- Sección Inmunología, Hospital Nacional Profesor Alejandro Posadas, Buenos Aires, Argentina
| | - María Cecilia Cimolai
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Federico Coluccio Leskow
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Alberto Penas-Steinhardt
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Instituto Universitario de Ciencias de la Salud, Fundación H.A. Barceló, Ciudad Autónoma de Buenos Aires, Argentina
| | - Fiorella Sabrina Belforte
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina.
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43
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Maurer ML, Goyco-Blas JF, Kohl KD. Dietary tannins alter growth, behavior, and the gut microbiome of larval amphibians. Integr Zool 2024; 19:585-595. [PMID: 37551631 DOI: 10.1111/1749-4877.12758] [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: 08/09/2023]
Abstract
Research has shown that leached plant toxins negatively impact the growth and development of larval amphibians. However, tadpoles may encounter these same toxins in food material, and differential exposure routes and distribution of toxic chemicals can yield variable downstream effects on animals. To date, most research understanding the interactions between dietary plant toxins and herbivores has been conducted in terrestrial systems. Despite the abundance of plant toxins in food and water sources, the effects of dietary plant toxins on larval amphibians have not been studied, and tannins could negatively affect these species. Here, green frog tadpoles (Lithobates clamitans) were fed diets with or without 2% tannic acid to test how their growth, development, behavior, and gut microbiome respond to dietary tannins. At the end of the trial, we conducted a behavioral assay to measure tadpole activity and boldness and inventoried the gut microbiome using 16S rRNA sequencing. Dietary tannins significantly decreased body mass by 66% and length by 28%, without influencing tadpole developmental stage. We found significant differences in exploratory behavior and boldness during the first minute of our behavioral assay, demonstrating that tannins have the potential to influence behavior during novel or stressful events. Finally, tannins significantly sculpted the gut microbiome, with an increase in the measurement of Shannon entropy. We observed 7 microbial phyla and 153 microbial genera that exhibited significantly differential abundances differences between control and tannic acid-fed tadpoles. Collectively, our results demonstrate that dietary tannins have the potential to alter amphibian growth, behavior, and microbiome.
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Affiliation(s)
- Maya L Maurer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - José F Goyco-Blas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Semertzidou A, Whelan E, Smith A, Ng S, Roberts L, Brosens JJ, Marchesi JR, Bennett PR, MacIntyre DA, Kyrgiou M. Microbial signatures and continuum in endometrial cancer and benign patients. MICROBIOME 2024; 12:118. [PMID: 38951935 PMCID: PMC11218081 DOI: 10.1186/s40168-024-01821-0] [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: 06/20/2023] [Accepted: 04/22/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Endometrial cancer is a multifactorial disease with inflammatory, metabolic and potentially microbial cues involved in disease pathogenesis. The endometrial cancer microbiome has been poorly characterised so far and studies have often overestimated bacterial biomass due to lack of integration of appropriate contamination controls. There is also a scarcity of evidence on the functionality of microbial microenvironments in endometrial cancer. This work addresses that knowledge gap by interrogating the genuine, contamination-free microbial signatures in the female genital tract and rectum of women with endometrial cancer and the mechanistic role of microbiome on carcinogenic processes. RESULTS Here we sampled different regions of the reproductive tract (vagina, cervix, endometrium, fallopian tubes and ovaries) and rectum of 61 patients (37 endometrial cancer; 24 benign controls). We performed 16S rRNA gene sequencing of the V1-V2 hypervariable regions and qPCR of the 16S rRNA gene to qualitatively and quantitatively assess microbial communities and used 3D benign and endometrial cancer organoids to evaluate the effect of microbial products of L. crispatus, which was found depleted in endometrial cancer patients following primary analysis, on endometrial cell proliferation and inflammation. We found that the upper genital tract of a subset of women with and without endometrial cancer harbour microbiota quantitatively and compositionally distinguishable from background contaminants. Endometrial cancer was associated with reduced cervicovaginal and rectal bacterial load together with depletion of Lactobacillus species relative abundance, including L. crispatus, increased bacterial diversity and enrichment of Porphyromonas, Prevotella, Peptoniphilus and Anaerococcus in the lower genital tract and endometrium. Treatment of benign and malignant endometrial organoids with L. crispatus conditioned media exerted an anti-proliferative effect at high concentrations but had minimal impact on cytokine and chemokine profiles. CONCLUSIONS Our findings provide evidence that the upper female reproductive tract of some women contains detectable levels of bacteria, the composition of which is associated with endometrial cancer. Whether this is a cause or consequence of cancer pathophysiology and what is the functional significance of this finding remain to be elucidated to guide future screening tools and microbiome-based therapeutics. Video Abstract.
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Affiliation(s)
- Anita Semertzidou
- Institute of Reproductive and Developmental Biology, Department of Digestion, Metabolism and Reproduction, Department of Surgery and Cancer, Imperial College Faculty of Medicine, Room 3006, 3rd Floor, Du Cane Road, London, W12 0NN, UK
- Department of Obstetrics & Gynaecology, Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Eilbhe Whelan
- Institute of Reproductive and Developmental Biology, Department of Digestion, Metabolism and Reproduction, Department of Surgery and Cancer, Imperial College Faculty of Medicine, Room 3006, 3rd Floor, Du Cane Road, London, W12 0NN, UK
- Department of Obstetrics & Gynaecology, Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Ann Smith
- Faculty of Health and Applied Sciences, University West of England, Glenside Campus, Bristol, BS16 1DD, UK
| | - Sherrianne Ng
- Institute of Reproductive and Developmental Biology, Department of Digestion, Metabolism and Reproduction, Department of Surgery and Cancer, Imperial College Faculty of Medicine, Room 3006, 3rd Floor, Du Cane Road, London, W12 0NN, UK
| | - Lauren Roberts
- Institute of Reproductive and Developmental Biology, Department of Digestion, Metabolism and Reproduction, Department of Surgery and Cancer, Imperial College Faculty of Medicine, Room 3006, 3rd Floor, Du Cane Road, London, W12 0NN, UK
| | - Jan J Brosens
- Division of Reproductive Health, Warwick Medical School, Clinical Sciences Research Laboratories, University Hospital, Coventry, CV2 2DX, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Digestion, Metabolism and Reproduction, Imperial College London, London, W2 1NY, UK
| | - Phillip R Bennett
- Institute of Reproductive and Developmental Biology, Department of Digestion, Metabolism and Reproduction, Department of Surgery and Cancer, Imperial College Faculty of Medicine, Room 3006, 3rd Floor, Du Cane Road, London, W12 0NN, UK
- Department of Obstetrics & Gynaecology, Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - David A MacIntyre
- Institute of Reproductive and Developmental Biology, Department of Digestion, Metabolism and Reproduction, Department of Surgery and Cancer, Imperial College Faculty of Medicine, Room 3006, 3rd Floor, Du Cane Road, London, W12 0NN, UK
| | - Maria Kyrgiou
- Institute of Reproductive and Developmental Biology, Department of Digestion, Metabolism and Reproduction, Department of Surgery and Cancer, Imperial College Faculty of Medicine, Room 3006, 3rd Floor, Du Cane Road, London, W12 0NN, UK.
- Department of Obstetrics & Gynaecology, Imperial College Healthcare NHS Trust, London, W12 0HS, UK.
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Tawfik MM, Lorgen-Ritchie M, Król E, McMillan S, Norambuena F, Bolnick DI, Douglas A, Tocher DR, Betancor MB, Martin SAM. Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages. Anim Microbiome 2024; 6:38. [PMID: 38951941 PMCID: PMC11218362 DOI: 10.1186/s42523-024-00321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/05/2024] [Indexed: 07/03/2024] Open
Abstract
To promote sustainable aquaculture, the formulation of Atlantic salmon (Salmo salar) feeds has changed in recent decades, focusing on replacing standard marine-based ingredients with plant-based alternatives, increasingly demonstrating successful outcomes in terms of fish performance. However, little is known about how these plant-based diets may impact the gut microbiota at first feeding and onwards. Nutritional programming (NP) is one strategy applied for exposing fish to a plant-based (V) diet at an early stage in life to promote full utilisation of plant-based ingredients and prevent potential adverse impacts of exposure to a plant-rich diet later in life. We investigated the impact of NP on gut microbiota by introducing fish to plant ingredients (V fish) during first feeding for a brief period of two weeks (stimulus phase) and compared those to fish fed a marine-based diet (M fish). Results demonstrated that V fish not only maintained growth performance at 16 (intermediate phase) and 22 (challenge phase) weeks post first feeding (wpff) when compared to M fish but also modulated gut microbiota. PERMANOVA general effects revealed gut microbiota dissimilarity by fish group (V vs. M fish) and phases (stimulus vs. intermediate vs. challenge). However, no interaction effect of both groups and phases was demonstrated, suggesting a sustained impact of V diet (nutritional history) on fish across time points/phases. Moreover, the V diet exerted a significant cumulative modulatory effect on the Atlantic salmon gut microbiota at 16 wpff that was not demonstrated at two wpff, although both fish groups were fed the M diet at 16 wpff. The nutritional history/dietary regime is the main NP influencing factor, whereas environmental and host factors significantly impacted microbiota composition in M fish. Microbial metabolic reactions of amino acid metabolism were higher in M fish when compared to V fish at two wpff suggesting microbiota played a role in digesting the essential amino acids of M feed. The excessive mucin O-degradation revealed in V fish at two wpff was mitigated in later life stages after NP, suggesting physiological adaptability and tolerance to V diet. Future studies are required to explore more fully how the microbiota functionally contributes to the NP.
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Affiliation(s)
- Marwa Mamdouh Tawfik
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
- Hydrobiology Department, Veterinary Research Institute, National Research Centre, Giza, 12622, Egypt.
| | - Marlene Lorgen-Ritchie
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Elżbieta Król
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Stuart McMillan
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | | | - Daniel I Bolnick
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Alex Douglas
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Douglas R Tocher
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Mónica B Betancor
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
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46
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Li G, Shen Q, Gao Y, Ma C, Song B, Wang C, Tang D, He X, Cao Y. The microbiota continuum along the upper reproductive tract of male rat and its relation to semen parameters. Heliyon 2024; 10:e32556. [PMID: 39183864 PMCID: PMC11341332 DOI: 10.1016/j.heliyon.2024.e32556] [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: 10/26/2023] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 08/27/2024] Open
Abstract
Given the physiological function and anatomical location of the reproductive tract, studying the upper reproductive tract microbiota may be essential for studying male infertility and other male diseases. This study aimed to characterize the microbiota of the upper reproductive tract male rats and investigate whether specific microbial compositions are associated with sperm parameters. 16S rRNA gene sequencing was used to characterize the microbial composition in the testis, epididymis, seminal vesicles, vas deferens and prostate tissues of the rats. The results showed significant enrichment of Methyloperoxococcus spp. in testicular tissues, Jeotgalicoccus spp. in epididymal tissues. Spearman's correlation analysis revealed that the abundance of several bacterial genera in epididymal, testicular, and seminal vesicle gland tissues correlated with several sperm activity parameters. Our findings provide detailed information on characterizing the upper reproductive tract microbiome in male rats, as well as a potentially crucial link between the reproductive system microbiota and sperm quality.
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Affiliation(s)
- Guanjian Li
- Reproductive Medicine Center, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- National Health Commission Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, Anhui, China
| | - Qunshan Shen
- Reproductive Medicine Center, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Ministry of Education of the People's Republic of China, Hefei, Anhui, China
| | - Yang Gao
- Reproductive Medicine Center, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Ministry of Education of the People's Republic of China, Hefei, Anhui, China
| | - Cong Ma
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, Anhui, China
| | - Bing Song
- Reproductive Medicine Center, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- National Health Commission Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, Anhui, China
| | - Chao Wang
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, Anhui, China
| | - Dongdong Tang
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, Anhui, China
| | - Xiaojin He
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, Anhui, China
- Reproductive Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunxia Cao
- Reproductive Medicine Center, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- National Health Commission Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, Anhui, China
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47
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Li H, Li J, Hu J, Chen J, Zhou W. High-performing cross-dataset machine learning reveals robust microbiota alteration in secondary apical periodontitis. Front Cell Infect Microbiol 2024; 14:1393108. [PMID: 38975327 PMCID: PMC11224960 DOI: 10.3389/fcimb.2024.1393108] [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: 02/28/2024] [Accepted: 05/22/2024] [Indexed: 07/09/2024] Open
Abstract
Multiple research groups have consistently underscored the intricate interplay between the microbiome and apical periodontitis. However, the presence of variability in experimental design and quantitative assessment have added a layer of complexity, making it challenging to comprehensively assess the relationship. Through an unbiased methodological refinement analysis, we re-analyzed 4 microbiota studies including 120 apical samples from infected teeth (with/without root canal treatment), healthy teeth, using meta-analysis and machine learning. With high-performing machine-learning models, we discover disease signatures of related species and enriched metabolic pathways, expanded understanding of apical periodontitis with potential therapeutic implications. Our approach employs uniform computational tools across datasets to leverage statistical power and define a reproducible signal potentially linked to the development of secondary apical periodontitis (SAP).
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Affiliation(s)
- Hao Li
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiehang Li
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiani Hu
- Research and Development Department, Beijing Xunzhu Biotechnology Co. Ltd., Beijing, China
- School of Chemistry Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jionglin Chen
- Research and Development Department, Beijing Xunzhu Biotechnology Co. Ltd., Beijing, China
| | - Wei Zhou
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
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48
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Kourout M, Espich S, Fisher C, Tiper I, Purkayastha A, Smith S, Santana-Quintero L, Duncan R. Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using an expanded high-density resequencing microarray platform. Front Mol Biosci 2024; 11:1419213. [PMID: 38966129 PMCID: PMC11222771 DOI: 10.3389/fmolb.2024.1419213] [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: 04/17/2024] [Accepted: 05/23/2024] [Indexed: 07/06/2024] Open
Abstract
Introduction: Nucleic acid tests for blood donor screening have improved the safety of the blood supply; however, increasing numbers of emerging pathogen tests are burdensome. Multiplex testing platforms are a potential solution. Methods: The Blood Borne Pathogen Resequencing Microarray Expanded (BBP-RMAv.2) can perform multiplex detection and identification of 80 viruses, bacteria and parasites. This study evaluated pathogen detection in human blood or plasma. Samples spiked with selected pathogens, each with one of 6 viruses, 2 bacteria and 5 protozoans were tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of primers, and hybridized to a microarray. The reported sequences were aligned to a database to identify the pathogen. To directly compare the microarray to an emerging molecular approach, the amplified nucleic acids were also submitted to nanopore next generation sequencing (NGS). Results: The BBP-RMAv.2 detected viral pathogens at a concentration as low as 100 copies/ml and a range of concentrations from 1,000 to 100,000 copies/ml for all the spiked pathogens. Coded specimens were identified correctly demonstrating the effectiveness of the platform. The nanopore sequencing correctly identified most samples and the results of the two platforms were compared. Discussion: These results indicated that the BBP-RMAv.2 could be employed for multiplex detection with potential for use in blood safety or disease diagnosis. The NGS was nearly as effective at identifying pathogens in blood and performed better than BBP-RMAv.2 at identifying pathogen-negative samples.
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Affiliation(s)
- Moussa Kourout
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Scott Espich
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Carolyn Fisher
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Irina Tiper
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | | | - Sean Smith
- HIVE Team, Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Luis Santana-Quintero
- HIVE Team, Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Robert Duncan
- Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
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49
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Dean CJ, Deng Y, Wehri TC, Pena-Mosca F, Ray T, Crooker BA, Godden SM, Caixeta LS, Noyes NR. The impact of kit, environment, and sampling contamination on the observed microbiome of bovine milk. mSystems 2024; 9:e0115823. [PMID: 38785438 PMCID: PMC11237780 DOI: 10.1128/msystems.01158-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
In low-microbial biomass samples such as bovine milk, contaminants can outnumber endogenous bacteria. Because of this, milk microbiome research suffers from a critical knowledge gap, namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelia and stripped and cisternal milk and used numerous negative controls, including air and sampling controls and extraction and library preparation blanks, to identify the potential sources of contamination. Two algorithms were used to mathematically remove contaminants and track the potential movement of microbes among samples. Results suggest that the majority (i.e., >75%) of sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. Contaminants in milk samples were primarily sourced from DNA extraction kits and the internal and external skin of the teat, while teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse, and compositionally distinct bacterial profile compared with epithelial samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in milk sample sequences, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during sample collection and processing workflows.IMPORTANCEObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.
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Affiliation(s)
- C. J. Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Y. Deng
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T. C. Wehri
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - F. Pena-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T. Ray
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - B. A. Crooker
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - S. M. Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - L. S. Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - N. R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
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50
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Sequeira SO, Pasnak E, Viegas C, Gomes B, Dias M, Cervantes R, Pena P, Twarużek M, Kosicki R, Viegas S, Caetano LA, Penetra MJ, Silva I, Caldeira AT, Pinheiro C. Microbial Assessment in A Rare Norwegian Book Collection: A One Health Approach to Cultural Heritage. Microorganisms 2024; 12:1215. [PMID: 38930597 PMCID: PMC11206040 DOI: 10.3390/microorganisms12061215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Microbial contamination poses a threat to both the preservation of library and archival collections and the health of staff and users. This study investigated the microbial communities and potential health risks associated with the UNESCO-classified Norwegian Sea Trade Archive (NST Archive) collection exhibiting visible microbial colonization and staff health concerns. Dust samples from book surfaces and the storage environment were analysed using culturing methods, qPCR, Next Generation Sequencing, and mycotoxin, cytotoxicity, and azole resistance assays. Penicillium sp., Aspergillus sp., and Cladosporium sp. were the most common fungi identified, with some potentially toxic species like Stachybotrys sp., Toxicladosporium sp., and Aspergillus section Fumigati. Fungal resistance to azoles was not detected. Only one mycotoxin, sterigmatocystin, was found in a heavily contaminated book. Dust extracts from books exhibited moderate to high cytotoxicity on human lung cells, suggesting a potential respiratory risk. The collection had higher contamination levels compared to the storage environment, likely due to improved storage conditions. Even though overall low contamination levels were obtained, these might be underestimated due to the presence of salt (from cod preservation) that could have interfered with the analyses. This study underlines the importance of monitoring microbial communities and implementing proper storage measures to safeguard cultural heritage and staff well-being.
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Affiliation(s)
- Sílvia O. Sequeira
- LAQV-REQUIMTE, Department of Conservation and Restoration, NOVA School of Sciences and Technology, NOVA University of Lisbon, Campus da Caparica, 2829-516 Caparica, Portugal;
- Laboratório José de Figueiredo, Museus e Monumentos de Portugal, Rua das Janelas Verdes, 1249-018 Lisbon, Portugal;
| | - Ekaterina Pasnak
- LAQV-REQUIMTE, Department of Conservation and Restoration, NOVA School of Sciences and Technology, NOVA University of Lisbon, Campus da Caparica, 2829-516 Caparica, Portugal;
| | - Carla Viegas
- H&TRC—Health & Technology Research Center, ESTeSL—Escola Superior de Tecnologia e Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal; (B.G.); (M.D.); (R.C.); (P.P.); (L.A.C.)
- Public Health Research Centre, Comprehensive Health Research Center, CHRC, REAL, CCAL, NOVA National School of Public Health, NOVA University Lisbon, 1099-085 Lisbon, Portugal;
| | - Bianca Gomes
- H&TRC—Health & Technology Research Center, ESTeSL—Escola Superior de Tecnologia e Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal; (B.G.); (M.D.); (R.C.); (P.P.); (L.A.C.)
- CE3C—Center for Ecology, Evolution and Environmental Change, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Marta Dias
- H&TRC—Health & Technology Research Center, ESTeSL—Escola Superior de Tecnologia e Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal; (B.G.); (M.D.); (R.C.); (P.P.); (L.A.C.)
- Public Health Research Centre, Comprehensive Health Research Center, CHRC, REAL, CCAL, NOVA National School of Public Health, NOVA University Lisbon, 1099-085 Lisbon, Portugal;
| | - Renata Cervantes
- H&TRC—Health & Technology Research Center, ESTeSL—Escola Superior de Tecnologia e Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal; (B.G.); (M.D.); (R.C.); (P.P.); (L.A.C.)
- Public Health Research Centre, Comprehensive Health Research Center, CHRC, REAL, CCAL, NOVA National School of Public Health, NOVA University Lisbon, 1099-085 Lisbon, Portugal;
| | - Pedro Pena
- H&TRC—Health & Technology Research Center, ESTeSL—Escola Superior de Tecnologia e Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal; (B.G.); (M.D.); (R.C.); (P.P.); (L.A.C.)
- Public Health Research Centre, Comprehensive Health Research Center, CHRC, REAL, CCAL, NOVA National School of Public Health, NOVA University Lisbon, 1099-085 Lisbon, Portugal;
| | - Magdalena Twarużek
- Department of Physiology and Toxicology, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (M.T.); (R.K.)
| | - Robert Kosicki
- Department of Physiology and Toxicology, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (M.T.); (R.K.)
| | - Susana Viegas
- Public Health Research Centre, Comprehensive Health Research Center, CHRC, REAL, CCAL, NOVA National School of Public Health, NOVA University Lisbon, 1099-085 Lisbon, Portugal;
| | - Liliana Aranha Caetano
- H&TRC—Health & Technology Research Center, ESTeSL—Escola Superior de Tecnologia e Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal; (B.G.); (M.D.); (R.C.); (P.P.); (L.A.C.)
- Research Institute for Medicines (iMed.uLisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisbon, Portugal
| | - Maria João Penetra
- HERCULES Laboratory, Évora University, Palácio do Vimioso, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; (M.J.P.); (I.S.); (A.T.C.)
| | - Inês Silva
- HERCULES Laboratory, Évora University, Palácio do Vimioso, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; (M.J.P.); (I.S.); (A.T.C.)
- IN2PAST—Associate Laboratory for Research and Innovation in Heritage, Arts, Sustainability and Territory, University of Évora, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal
| | - Ana Teresa Caldeira
- HERCULES Laboratory, Évora University, Palácio do Vimioso, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; (M.J.P.); (I.S.); (A.T.C.)
- IN2PAST—Associate Laboratory for Research and Innovation in Heritage, Arts, Sustainability and Territory, University of Évora, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal
| | - Catarina Pinheiro
- Laboratório José de Figueiredo, Museus e Monumentos de Portugal, Rua das Janelas Verdes, 1249-018 Lisbon, Portugal;
- HERCULES Laboratory, Évora University, Palácio do Vimioso, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; (M.J.P.); (I.S.); (A.T.C.)
- IN2PAST—Associate Laboratory for Research and Innovation in Heritage, Arts, Sustainability and Territory, University of Évora, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal
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