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Cheng G, Westerholm M, Schnürer A. Complete genome sequence of Citroniella saccharovorans DSM 29873, isolated from human fecal sample. Microbiol Resour Announc 2024; 13:e0001524. [PMID: 38466102 PMCID: PMC11008133 DOI: 10.1128/mra.00015-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
A complete genome was recovered from Citroniella saccharovorans, strain DSM 29873, using Oxford Nanopore Technologies. The genome assembly contains 1,413,868 bp with 30.23% G+C content. The species belongs to the family Peptoniphilaceae and, as of yet, is the only cultivated representative of the genus Citroniella.
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Affiliation(s)
- George Cheng
- Department of Molecular Sciences, Biocenter Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Westerholm
- Department of Molecular Sciences, Biocenter Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, Biocenter Swedish University of Agricultural Sciences, Uppsala, Sweden
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Filardo S, Di Pietro M, Sessa R. Current progresses and challenges for microbiome research in human health: a perspective. Front Cell Infect Microbiol 2024; 14:1377012. [PMID: 38638832 PMCID: PMC11024239 DOI: 10.3389/fcimb.2024.1377012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
It is becoming increasingly clear that the human microbiota, also known as "the hidden organ", possesses a pivotal role in numerous processes involved in maintaining the physiological functions of the host, such as nutrient extraction, biosynthesis of bioactive molecules, interplay with the immune, endocrine, and nervous systems, as well as resistance to the colonization of potential invading pathogens. In the last decade, the development of metagenomic approaches based on the sequencing of the bacterial 16s rRNA gene via Next Generation Sequencing, followed by whole genome sequencing via third generation sequencing technologies, has been one of the great advances in molecular biology, allowing a better profiling of the human microbiota composition and, hence, a deeper understanding of the importance of microbiota in the etiopathogenesis of different pathologies. In this scenario, it is of the utmost importance to comprehensively characterize the human microbiota in relation to disease pathogenesis, in order to develop novel potential treatment or preventive strategies by manipulating the microbiota. Therefore, this perspective will focus on the progress, challenges, and promises of the current and future technological approaches for microbiome profiling and analysis.
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Affiliation(s)
| | | | - Rosa Sessa
- Department of Public Health and Infectious Diseases, Section of Microbiology, University of Rome “Sapienza”, Rome, Italy
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3
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Ling J, Hryckowian AJ. Re-framing the importance of Group B Streptococcus as a gut-resident pathobiont. Infect Immun 2024:e0047823. [PMID: 38436256 DOI: 10.1128/iai.00478-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024] Open
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) is a Gram-positive bacterial species that causes disease in humans across the lifespan. While antibiotics are used to mitigate GBS infections, it is evident that antibiotics disrupt human microbiomes (which can predispose people to other diseases later in life), and antibiotic resistance in GBS is on the rise. Taken together, these unintended negative impacts of antibiotics highlight the need for precision approaches for minimizing GBS disease. One possible approach involves selectively depleting GBS in its commensal niches before it can cause disease at other body sites or be transmitted to at-risk individuals. One understudied commensal niche of GBS is the adult gastrointestinal (GI) tract, which may predispose colonization at other body sites in individuals at risk for GBS disease. However, a better understanding of the host-, microbiome-, and GBS-determined variables that dictate GBS GI carriage is needed before precise GI decolonization approaches can be developed. In this review, we synthesize current knowledge of the diverse body sites occupied by GBS as a pathogen and as a commensal. We summarize key molecular factors GBS utilizes to colonize different host-associated niches to inform future efforts to study GBS in the GI tract. We also discuss other GI commensals that are pathogenic in other body sites to emphasize the broader utility of precise de-colonization approaches for mitigating infections by GBS and other bacterial pathogens. Finally, we highlight how GBS treatments could be improved with a more holistic understanding of GBS enabled by continued GI-focused study.
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Affiliation(s)
- Joie Ling
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Healthon, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrew J Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Healthon, Madison, Wisconsin, USA
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4
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Hong BY, Driscoll M, Gratalo D, Jarvie T, Weinstock GM. Improved DNA Extraction and Amplification Strategy for 16S rRNA Gene Amplicon-Based Microbiome Studies. Int J Mol Sci 2024; 25:2966. [PMID: 38474213 DOI: 10.3390/ijms25052966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 02/25/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Next-generation sequencing technology has driven the rapid advancement of human microbiome studies by enabling community-level sequence profiling of microbiomes. Although all microbiome sequencing methods depend on recovering the DNA from a sample as a first critical step, lysis methods can be a major determinant of microbiome profile bias. Gentle enzyme-based DNA preparation methods preserve DNA quality but can bias the results by failing to open difficult-to-lyse bacteria. Mechanical methods like bead beating can also bias DNA recovery because the mechanical energy required to break tougher cell walls may shear the DNA of the more easily lysed microbes, and shearing can vary depending on the time and intensity of beating, influencing reproducibility. We introduce a non-mechanical, non-enzymatic, novel rapid microbial DNA extraction procedure suitable for 16S rRNA gene-based microbiome profiling applications that eliminates bead beating. The simultaneous application of alkaline, heat, and detergent ('Rapid' protocol) to milligram quantity samples provided consistent representation across the population of difficult and easily lysed bacteria equal to or better than existing protocols, producing sufficient high-quality DNA for full-length 16S rRNA gene PCR. The novel 'Rapid' method was evaluated using mock bacterial communities containing both difficult and easily lysed bacteria. Human fecal sample testing compared the novel Rapid method with a standard Human Microbiome Project (HMP) protocol for samples from lung cancer patients and controls. DNA recovered from both methods was analyzed using 16S rRNA gene sequencing of the V1V3 and V4 regions on the Illumina platform and the V1V9 region on the PacBio platform. Our findings indicate that the 'Rapid' protocol consistently yielded higher levels of Firmicutes species, which reflected the profile of the bacterial community structure more accurately, which was confirmed by mock community evaluation. The novel 'Rapid' DNA lysis protocol reduces population bias common to bead beating and enzymatic lysis methods, presenting opportunities for improved microbial community profiling, combined with the reduction in sample input to 10 milligrams or less, and it enables rapid transfer and simultaneous lysis of 96 samples in a standard plate format. This results in a 20-fold reduction in sample handling time and an overall 2-fold time advantage when compared to widely used commercial methods. We conclude that the novel 'Rapid' DNA extraction protocol offers a reliable alternative for preparing fecal specimens for 16S rRNA gene amplicon sequencing.
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Affiliation(s)
- Bo-Young Hong
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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Kamel M, Aleya S, Alsubih M, Aleya L. Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases. J Pers Med 2024; 14:217. [PMID: 38392650 PMCID: PMC10890469 DOI: 10.3390/jpm14020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.
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Affiliation(s)
- Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 11221, Egypt
| | - Sami Aleya
- Faculty of Medecine, Université de Bourgogne Franche-Comté, Hauts-du-Chazal, 25030 Besançon, France
| | - Majed Alsubih
- Department of Civil Engineering, King Khalid University, Guraiger, Abha 62529, Saudi Arabia
| | - Lotfi Aleya
- Laboratoire de Chrono-Environnement, Université de Bourgogne Franche-Comté, UMR CNRS 6249, La Bouloie, 25030 Besançon, France
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Jennings SAV, Clavel T. Synthetic Communities of Gut Microbes for Basic Research and Translational Approaches in Animal Health and Nutrition. Annu Rev Anim Biosci 2024; 12:283-300. [PMID: 37963399 DOI: 10.1146/annurev-animal-021022-025552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Microbes and animals have a symbiotic relationship that greatly influences nutrient uptake and animal health. This relationship can be studied using selections of microbes termed synthetic communities, or SynComs. SynComs are used in many different animal hosts, including agricultural animals, to investigate microbial interactions with nutrients and how these affect animal health. The most common host focuses for SynComs are currently mouse and human, from basic mechanistic research through to translational disease models and live biotherapeutic products (LBPs) as treatments. We discuss SynComs used in basic research models and findings that relate to human and animal health and nutrition. Translational use cases of SynComs are discussed, followed by LBPs, especially within the context of agriculture. SynComs still face challenges, such as standardization for reproducibility and contamination risks. However, the future of SynComs is hopeful, especially in the areas of genome-guided SynCom design and custom SynCom-based treatments.
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Affiliation(s)
- Susan A V Jennings
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany;
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany;
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Mortazavi SMJ, Said-Salman I, Mortazavi AR, El Khatib S, Sihver L. How the adaptation of the human microbiome to harsh space environment can determine the chances of success for a space mission to Mars and beyond. Front Microbiol 2024; 14:1237564. [PMID: 38390219 PMCID: PMC10881706 DOI: 10.3389/fmicb.2023.1237564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/05/2023] [Indexed: 02/24/2024] Open
Abstract
The ability of human cells to adapt to space radiation is essential for the well-being of astronauts during long-distance space expeditions, such as voyages to Mars or other deep space destinations. However, the adaptation of the microbiomes should not be overlooked. Microorganisms inside an astronaut's body, or inside the space station or other spacecraft, will also be exposed to radiation, which may induce resistance to antibiotics, UV, heat, desiccation, and other life-threatening factors. Therefore, it is essential to consider the potential effects of radiation not only on humans but also on their microbiomes to develop effective risk reduction strategies for space missions. Studying the human microbiome in space missions can have several potential benefits, including but not limited to a better understanding of the major effects space travel has on human health, developing new technologies for monitoring health and developing new radiation therapies and treatments. While radioadaptive response in astronauts' cells can lead to resistance against high levels of space radiation, radioadaptive response in their microbiome can lead to resistance against UV, heat, desiccation, antibiotics, and radiation. As astronauts and their microbiomes compete to adapt to the space environment. The microorganisms may emerge as the winners, leading to life-threatening situations due to lethal infections. Therefore, understanding the magnitude of the adaptation of microorganisms before launching a space mission is crucial to be able to develop effective strategies to mitigate the risks associated with radiation exposure. Ensuring the safety and well-being of astronauts during long-duration space missions and minimizing the risks linked with radiation exposure can be achieved by adopting this approach.
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Affiliation(s)
- Seyed Mohammad Javad Mortazavi
- Ionizing and non-ionizing radiation protection research center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ilham Said-Salman
- Department of Biological and Chemical Sciences, School of Arts & Sciences, Lebanese International University, Saida, Lebanon
- Department of Biological and Chemical Sciences, International University of Beirut, Beirut, Lebanon
| | | | - Sami El Khatib
- Department of Biomedical Sciences, School of Arts and Sciences, Lebanese International University, Beirut, Lebanon
- Center for Applied Mathematics and Bioinformatics (CAMB) at Gulf University for Science and Technology, Kuwait City, Kuwait
| | - Lembit Sihver
- Department of Radiation Dosimetry, Nuclear Physics Institute (NPI) of the Czech Academy of Sciences (CAS), Prague, Czechia
- Department of Radiation Physics, Technische Universität Wien Atominstitut, Vienna, Austria
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Tutelyan VA, Nikityuk DB. [Key challenges in the dietary intake structure and cutting edge technologies for optimizing nutrition to protect the health of the Russian рopulation]. Vopr Pitan 2024; 93:6-21. [PMID: 38555606 DOI: 10.33029/0042-8833-2024-93-1-6-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/05/2024] [Indexed: 04/02/2024]
Abstract
This article presents an analysis of some of the results of the work of the Federal Research Center for Nutrition and Biotechnology (Center) in recent years, highlighting the most important, promising areas of Nutrition Science and Food Hygiene that need further development. The priority area of Center functioning is scientific support for the implementation of the Doctrine of Food Security of the Russian Federation (Decree of the President of the Russian Federation dated January 21, 2020 No. 20), Decree of the President of the Russian Federation dated July 21, 2020 No. 474 «On the national development goals of the Russian Federation for the period until 2030 «in terms of ensuring an increase in life expectancy and improving the life quality of the population, the Strategy for Improving the Quality of Food Products in the Russian Federation until 2030 (Order of the Government of the Russian Federation dated June 29, 2016 No. 1364-r). The Center coordinates all research on medical nutrition problems in the Russian Federation within the framework of the work of the Problem Commission on Nutrition Hygiene of the Scientific Council of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare, the Scientific Council of the Russian Academy of Sciences on Medical Nutrition Problems, the Scientific and Technical Committee of the Comprehensive Scientific Program «Priority Research in the Field of Nutrition of the Population», Profile Commission on Dietetics of the Expert Council in the Field of Health of the Ministry of Healthcare of Russian Federation, ensuring the implementation of their results with the participation of members of the Consortium "Healthcare, Nutrition, Demography". The most important area of the Center's work is scientific and expert support in the field of international and national technical regulation of the production and turnover of foods and raw materials, in particular, the work of the Russian national contact point of the Codex Alimentarius Commission (established by FAO and WHO), as well as the work of the Russian side in the Eurasian Economic Commission regarding the preparation of proposals for technical regulations of the Customs Union in the field of food safety, evaluation of draft technical regulations and amendments and additions to them.
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Affiliation(s)
- V A Tutelyan
- Federal Research Center for Nutrition, Biotechnology and Food Safety, 109240, Moscow, Russian Federation
| | - D B Nikityuk
- Federal Research Center for Nutrition, Biotechnology and Food Safety, 109240, Moscow, Russian Federation
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Park H, Joachimiak MP, Jungbluth SP, Yang Z, Riehl WJ, Canon RS, Arkin AP, Dehal PS. A bacterial sensor taxonomy across earth ecosystems for machine learning applications. mSystems 2024; 9:e0002623. [PMID: 38078749 PMCID: PMC10804942 DOI: 10.1128/msystems.00026-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 10/23/2023] [Indexed: 01/24/2024] Open
Abstract
Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes. We hypothesized that an ecosystem's unique stimuli leave a sensor "fingerprint," able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from Host-associated, Environmental, and Engineered ecosystems across the globe. We extracted and clustered the collection's nearly 18M unique sensory domains into 113,712 similar groupings with MMseqs2. We built gradient-boosted decision tree machine learning models and found we could classify the ecosystem type (accuracy: 87%) and predict the levels of different physical parameters (R2 score: 83%) using the sensor cluster abundance as features. Feature importance enables identification of the most predictive sensors to differentiate between ecosystems which can lead to mechanistic interpretations if the sensor domains are well annotated. To demonstrate this, a machine learning model was trained to predict patient's disease state and used to identify domains related to oxygen sensing present in a healthy gut but missing in patients with abnormal conditions. Moreover, since 98.7% of identified sensor domains are uncharacterized, importance ranking can be used to prioritize sensors to determine what ecosystem function they may be sensing. Furthermore, these new predictive sensors can function as targets for novel sensor engineering with applications in biotechnology, ecosystem maintenance, and medicine.IMPORTANCEMicrobes infect, colonize, and proliferate due to their ability to sense and respond quickly to their surroundings. In this research, we extract the sensory proteins from a diverse range of environmental, engineered, and host-associated metagenomes. We trained machine learning classifiers using sensors as features such that it is possible to predict the ecosystem for a metagenome from its sensor profile. We use the optimized model's feature importance to identify the most impactful and predictive sensors in different environments. We next use the sensor profile from human gut metagenomes to classify their disease states and explore which sensors can explain differences between diseases. The sensors most predictive of environmental labels here, most of which correspond to uncharacterized proteins, are a useful starting point for the discovery of important environment signals and the development of possible diagnostic interventions.
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Affiliation(s)
- Helen Park
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- EPSRC/BBSRC Future Biomanufacturing Research Hub, EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcin P. Joachimiak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sean P. Jungbluth
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ziming Yang
- Computational Science Initiative, Brookhaven National Laboratory, Upton, New York, USA
| | - William J. Riehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - R. Shane Canon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Paramvir S. Dehal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Yadav M, Chauhan NS. Role of gut-microbiota in disease severity and clinical outcomes. Brief Funct Genomics 2024; 23:24-37. [PMID: 36281758 DOI: 10.1093/bfgp/elac037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/05/2022] [Accepted: 09/28/2022] [Indexed: 01/21/2024] Open
Abstract
A delicate balance of nutrients, antigens, metabolites and xenobiotics in body fluids, primarily managed by diet and host metabolism, governs human health. Human gut microbiota is a gatekeeper to nutrient bioavailability, pathogens exposure and xenobiotic metabolism. Human gut microbiota starts establishing during birth and evolves into a resilient structure by adolescence. It supplements the host's metabolic machinery and assists in many physiological processes to ensure health. Biotic and abiotic stressors could induce dysbiosis in gut microbiota composition leading to disease manifestations. Despite tremendous scientific advancements, a clear understanding of the involvement of gut microbiota dysbiosis during disease onset and clinical outcomes is still awaited. This would be important for developing an effective and sustainable therapeutic intervention. This review synthesizes the present scientific knowledge to present a comprehensive picture of the role of gut microbiota in the onset and severity of a disease.
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Affiliation(s)
- Monika Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
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Souza CE, Jacobson NE, An MA, Droit L, Vega AA, Rosales M, Mihindukulasuriya KA, Pastrana K, Handley SA, Parkes M, Rimmer J, Wang D, Dinsdale EA, A. Edwards R, Segall AM. Draft genomes of 12 Bifidobacterium isolates from human IBD fecal samples. Microbiol Resour Announc 2024; 13:e0013023. [PMID: 38099679 PMCID: PMC10793331 DOI: 10.1128/mra.00130-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/19/2023] [Indexed: 01/18/2024] Open
Abstract
Twelve Bifidobacterium strains were isolated from fecal samples of inflammatory bowel disease patients and matched "household control" individuals. These include the species Bifidobacterium adolescentis, Bifidobacterium animalis, Bifidobacterium breve, Bifidobacterium catenulatum, Bifidobacterium longum, and Bifidobacterium pseudocatenulatum.
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Affiliation(s)
- Cole E. Souza
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Nicole E. Jacobson
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Michelle A. An
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Lindsay Droit
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Alejandro A. Vega
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Mariel Rosales
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Kathie A. Mihindukulasuriya
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Karina Pastrana
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Scott A. Handley
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Miles Parkes
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, Division of Gastroenterology, Addenbrooke's NHS Trust Hospital, Cambridge, United Kingdom
| | - Joanna Rimmer
- Department of Medicine, Division of Gastroenterology, Addenbrooke's NHS Trust Hospital, Cambridge, United Kingdom
- Academic Department of Military Medicine, Royal Centre for Defence Medicine, Birmingham, United Kingdom
| | - David Wang
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration (FAME), College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration (FAME), College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Anca M. Segall
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, California, USA
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Nguyen VH, Sharon BM, Shipman BM, Zimmern PE, De Nisco NJ. Complete genomes of Limosilactobacillus portuensis and Limosilactobacillus vaginalis isolated from the urine of postmenopausal women. Microbiol Resour Announc 2024; 13:e0088323. [PMID: 38018964 PMCID: PMC10793329 DOI: 10.1128/mra.00883-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/22/2023] [Indexed: 11/30/2023] Open
Abstract
There is frequent evidence that Limosilactobacillus vaginalis colonizes female genitourinary tracts but few reports of Limosilactobacillus portuensis. Their role in urinary tract infection (UTI) is unclear. We present the first complete genome of L. portuensis and a complete genome of L. vaginalis isolated from postmenopausal women with varying UTI histories.
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Affiliation(s)
- Vivian H. Nguyen
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Belle M. Sharon
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Braden M. Shipman
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Philippe E. Zimmern
- Department of Urology, The University of Texas at Southwestern Medical Center, Dallas, Texas, USA
| | - Nicole J. De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
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Blake KS, Schwartz DJ, Paruthiyil S, Wang B, Ning J, Isidean SD, Burns DS, Whiteson H, Lalani T, Fraser JA, Connor P, Troth T, Porter CK, Tribble DR, Riddle MS, Gutiérrez RL, Simons MP, Dantas G. Gut microbiome and antibiotic resistance effects during travelers' diarrhea treatment and prevention. mBio 2024; 15:e0279023. [PMID: 38085102 PMCID: PMC10790752 DOI: 10.1128/mbio.02790-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 10/30/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE The travelers' gut microbiome is potentially assaulted by acute and chronic perturbations (e.g., diarrhea, antibiotic use, and different environments). Prior studies of the impact of travel and travelers' diarrhea (TD) on the microbiome have not directly compared antibiotic regimens, and studies of different antibiotic regimens have not considered travelers' microbiomes. This gap is important to be addressed as the use of antibiotics to treat or prevent TD-even in moderate to severe cases or in regions with high infectious disease burden-is controversial based on the concerns for unintended consequences to the gut microbiome and antimicrobial resistance (AMR) emergence. Our study addresses this by evaluating the impact of defined antibiotic regimens (single-dose treatment or daily prophylaxis) on the gut microbiome and resistomes of deployed servicemembers, using samples collected during clinical trials. Our findings indicate that the antibiotic treatment regimens that were studied generally do not lead to adverse effects on the gut microbiome and resistome and identify the relative risks associated with prophylaxis. These results can be used to inform therapeutic guidelines for the prevention and treatment of TD and make progress toward using microbiome information in personalized medical care.
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Affiliation(s)
- Kevin S. Blake
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Drew J. Schwartz
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Women’s Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Srinand Paruthiyil
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jie Ning
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sandra D. Isidean
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
- Naval Medical Research Command, Silver Spring, Maryland, USA
| | - Daniel S. Burns
- Academic Department of Military Medicine, UK Defence Medical Directorate, Birmingham, United Kingdom
| | - Harris Whiteson
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tahaniyat Lalani
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Jamie A. Fraser
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Patrick Connor
- Academic Department of Military Medicine, UK Defence Medical Directorate, Birmingham, United Kingdom
| | - Tom Troth
- Academic Department of Military Medicine, UK Defence Medical Directorate, Birmingham, United Kingdom
| | - Chad K. Porter
- Naval Medical Research Command, Silver Spring, Maryland, USA
| | - David R. Tribble
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Mark S. Riddle
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | | | - Mark P. Simons
- Naval Medical Research Command, Silver Spring, Maryland, USA
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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14
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Aguirre-García MM, Amedei A, Hernández-Ruiz P, Gómez-García AP, Niccolai E, Moreno-Rodríguez AM, Pinto-Cardoso S, Alviter-Plata A, Escalona-Montaño AR, Ordaz-Robles ER, González-Salazar MDC, Springall Del Villar R, Berrios-Bárcenas EA, Ávila-Vanzzini N. Cytokine and microbiota profiles in obesity-related hypertension patients. Front Cell Infect Microbiol 2024; 13:1325261. [PMID: 38292856 PMCID: PMC10824975 DOI: 10.3389/fcimb.2023.1325261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/30/2023] [Indexed: 02/01/2024] Open
Abstract
Background Systemic arterial hypertension is linked to a heightened risk of cardiovascular diseases on a global scale. In Mexico, nearly half of adults in vulnerable conditions experience hypertension. Imbalance in the oral and intestinal microbiota composition has been observed in patients with hypertension, documented by a decrease of bacteria producing short-chain fatty acids, which play a critical role in blood pressure regulation. Aim To examine the cytokines' profile and assess the characteristics of oral and gut microbiota in obesity-related hypertension in Mexican patients. Methods A cross-sectional, observational, and analytical study was carried out. Twenty-two patients were categorized by their body mass index (BMI) as overweight and obese, and the diagnosis of primary hypertension. DNA from supragingival dental plaque and feces samples was used to carry out 16S rRNA sequencing. Additionally, 13 cytokines were quantified. Results In the oral microbiota, Kluyvera was found to be significantly enriched in obese compared to overweight patients. Instead, the gut microbiota was dominated by Firmicutes. However, the correlation between certain genera and proinflammatory cytokines was noted. Conclusion This exploratory study provides insights into the complex relationship between the oral and gut microbiota and their association with systemic inflammation in obesity-related hypertension.
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Affiliation(s)
- María Magdalena Aguirre-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Interdisciplinary Internal Medicine Unit, Careggi University Hospital, Florence, Italy
| | - Paulina Hernández-Ruiz
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Ana Pamela Gómez-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Aura M. Moreno-Rodríguez
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Sandra Pinto-Cardoso
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Ciudad de México, Mexico
| | - Adriana Alviter-Plata
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Alma R. Escalona-Montaño
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - Erick R. Ordaz-Robles
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
| | - María del C. González-Salazar
- Outpatient Clinic, Cardiovascular Risk Factors Clinic, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, Mexico
| | | | - Enrique A. Berrios-Bárcenas
- Outpatient Clinic, Cardiovascular Risk Factors Clinic, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, Mexico
| | - Nydia Ávila-Vanzzini
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Instituto Nacional de Cardiología "Ignacio Chávez, Ciudad de México, Mexico
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15
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Song L, Rauf F, Hou CW, Qiu J, Murugan V, Chung Y, Lai H, Adam D, Magee DM, Trivino Soto G, Peterson M, Anderson KS, Rice SG, Readhead B, Park JG, LaBaer J. Quantitative assessment of multiple pathogen exposure and immune dynamics at scale. Microbiol Spectr 2024; 12:e0239923. [PMID: 38063388 PMCID: PMC10783028 DOI: 10.1128/spectrum.02399-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/13/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Serology reveals exposure to pathogens, as well as the state of autoimmune and other clinical conditions. It is used to evaluate individuals and their histories and as a public health tool to track epidemics. Employing a variety of formats, studies nearly always perform serology by testing response to only one or a few antigens. However, clinical outcomes of new infections also depend on which previous infections may have occurred. We developed a high-throughput serology method that evaluates responses to hundreds of antigens simultaneously. It can be used to evaluate thousands of samples at a time and provide a quantitative readout. This tool will enable doctors to monitor which pathogens an individual has been exposed to and how that changes in the future. Moreover, public health officials could track populations and look for infectious trends among large populations. Testing many potential antigens at a time may also aid in vaccine development.
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Affiliation(s)
- Lusheng Song
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Femina Rauf
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ching-Wen Hou
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Vel Murugan
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Yunro Chung
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - Huafang Lai
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Deborah Adam
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - D. Mitchell Magee
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Guillermo Trivino Soto
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Milene Peterson
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Karen S. Anderson
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Stephen G. Rice
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Benjamin Readhead
- Arizona State University-Banner Neurodegenerative Disease Research Center, Tempe, Arizona, USA
| | - Jin G. Park
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
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16
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Kim J, Jang H, Koh H. MiMultiCat: A Unified Cloud Platform for the Analysis of Microbiome Data with Multi-Categorical Responses. Bioengineering (Basel) 2024; 11:60. [PMID: 38247937 PMCID: PMC10813402 DOI: 10.3390/bioengineering11010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 12/21/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
The field of the human microbiome is rapidly growing due to the recent advances in high-throughput sequencing technologies. Meanwhile, there have also been many new analytic pipelines, methods and/or tools developed for microbiome data preprocessing and analytics. They are usually focused on microbiome data with continuous (e.g., body mass index) or binary responses (e.g., diseased vs. healthy), yet multi-categorical responses that have more than two categories are also common in reality. In this paper, we introduce a new unified cloud platform, named MiMultiCat, for the analysis of microbiome data with multi-categorical responses. The two main distinguishing features of MiMultiCat are as follows: First, MiMultiCat streamlines a long sequence of microbiome data preprocessing and analytic procedures on user-friendly web interfaces; as such, it is easy to use for many people in various disciplines (e.g., biology, medicine, public health). Second, MiMultiCat performs both association testing and prediction modeling extensively. For association testing, MiMultiCat handles both ecological (e.g., alpha and beta diversity) and taxonomical (e.g., phylum, class, order, family, genus, species) contexts through covariate-adjusted or unadjusted analysis. For prediction modeling, MiMultiCat employs the random forest and gradient boosting algorithms that are well suited to microbiome data while providing nice visual interpretations. We demonstrate its use through the reanalysis of gut microbiome data on obesity with body mass index categories. MiMultiCat is freely available on our web server.
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Affiliation(s)
| | | | - Hyunwook Koh
- Department of Applied Mathematics and Statistics, The State University of New York (SUNY), Incheon 21985, Republic of Korea
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17
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Inglis LK, Roach MJ, Edwards RA. Prophages: an integral but understudied component of the human microbiome. Microb Genom 2024; 10:001166. [PMID: 38264887 PMCID: PMC10868603 DOI: 10.1099/mgen.0.001166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 12/07/2023] [Indexed: 01/25/2024] Open
Abstract
Phages integrated into a bacterial genome - called prophages - continuously monitor the vigour of the host bacteria to determine when to escape the genome and to protect their host from other phage infections, and they may provide genes that promote bacterial growth. Prophages are essential to almost all microbiomes, including the human microbiome. However, most human microbiome studies have focused on bacteria, ignoring free and integrated phages, so we know little about how these prophages affect the human microbiome. To address this gap in our knowledge, we compared the prophages identified in 14 987 bacterial genomes isolated from human body sites to characterize prophage DNA in the human microbiome. Here, we show that prophage DNA is ubiquitous, comprising on average 1-5 % of each bacterial genome. The prophage content per genome varies with the isolation site on the human body, the health of the human and whether the disease was symptomatic. The presence of prophages promotes bacterial growth and sculpts the microbiome. However, the disparities caused by prophages vary throughout the body.
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Affiliation(s)
- Laura K. Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
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18
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Kandalai S, Li H, Zhang N, Peng H, Zheng Q. The human microbiome and cancer: a diagnostic and therapeutic perspective. Cancer Biol Ther 2023; 24:2240084. [PMID: 37498047 PMCID: PMC10376920 DOI: 10.1080/15384047.2023.2240084] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/09/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Recent evidence has shown that the human microbiome is associated with various diseases, including cancer. The salivary microbiome, fecal microbiome, and circulating microbial DNA in blood plasma have all been used experimentally as diagnostic biomarkers for many types of cancer. The microbiomes present within local tissue, other regions, and tumors themselves have been shown to promote and restrict the development and progression of cancer, most often by affecting cancer cells or the host immune system. These microbes have also been shown to impact the efficacy of various cancer therapies, including radiation, chemotherapy, and immunotherapy. Here, we review the research advances focused on how microbes impact these different facets and why they are important to the clinical care of cancer. It is only by better understanding the roles these microbes play in the diagnosis, development, progression, and treatment of cancer, that we will be able to catch and treat cancer early.
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Affiliation(s)
- Shruthi Kandalai
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Huapeng Li
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Nan Zhang
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Haidong Peng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA
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19
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Vänni P, Tejesvi MV, Paalanne N, Aagaard K, Ackermann G, Camargo CA, Eggesbø M, Hasegawa K, Hoen AG, Karagas MR, Kolho KL, Laursen MF, Ludvigsson J, Madan J, Ownby D, Stanton C, Stokholm J, Tapiainen T. Machine-learning analysis of cross-study samples according to the gut microbiome in 12 infant cohorts. mSystems 2023; 8:e0036423. [PMID: 37874156 PMCID: PMC10734493 DOI: 10.1128/msystems.00364-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/13/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE There are challenges in merging microbiome data from diverse research groups due to the intricate and multifaceted nature of such data. To address this, we utilized a combination of machine-learning (ML) models to analyze 16S sequencing data from a substantial set of gut microbiome samples, sourced from 12 distinct infant cohorts that were gathered prospectively. Our initial focus was on the mode of delivery due to its prior association with changes in infant gut microbiomes. Through ML analysis, we demonstrated the effective merging and comparison of various gut microbiome data sets, facilitating the identification of robust microbiome biomarkers applicable across varied study populations.
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Affiliation(s)
- Petri Vänni
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Mysore V. Tejesvi
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
| | - Niko Paalanne
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Kjersti Aagaard
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Merete Eggesbø
- Department of Climate and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Kaija-Leena Kolho
- Children’s Hospital, University of Helsinki and HUS, Helsinki, Finland
| | - Martin F. Laursen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Johnny Ludvigsson
- Crown Princess Victoria Children’s Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Juliette Madan
- Department of Psychiatry, Dartmouth Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
- Department of Pediatrics, Dartmouth Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Dennis Ownby
- Medical College of Georgia, Augusta, Georgia, USA
| | - Catherine Stanton
- Teagasc Food Research Centre & APC Microbiome Ireland, Moorepark, Fermoy, Co. Cork, Ireland
| | - Jakob Stokholm
- Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Terhi Tapiainen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, USA
- Biocenter Oulu, University of Oulu, Oulu, Finland
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20
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Bhattacharjee P, Karim KA, Khan Z. Harnessing the Microbiome: A Comprehensive Review on Advancing Therapeutic Strategies for Rheumatic Diseases. Cureus 2023; 15:e50964. [PMID: 38249228 PMCID: PMC10800157 DOI: 10.7759/cureus.50964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Rheumatic diseases are a group of disorders that affect the joints, muscles, and bones. These diseases, such as rheumatoid arthritis, lupus, and psoriatic arthritis, can cause pain, stiffness, and swelling, leading to reduced mobility and disability. Recent studies have identified the microbiome, the diverse community of microorganisms that live in and on the human body, as a potential factor in the development and progression of rheumatic diseases. Harnessing the microbiome offers a promising new avenue for developing therapeutic strategies for these debilitating conditions. There is growing interest in the role of oral and gut microbiomes in the management of rheumatoid arthritis and other autoimmune disease. Microbial metabolites have immunomodulatory properties that could be exploited for rheumatic disorders. A wide range of microorganisms are present in the oral cavity and are found to be vulnerable to the effects of the environment. The physiology and ecology of the microbiota become intimately connected with those of the host, and they critically influence the promotion of health or progression toward disease. This article aims to provide a comprehensive overview of the current state of knowledge on oral and gut microbiome and its potential future role in the management of rheumatic diseases. This article will also discuss newer treatment strategies such as bioinformatic analyses and fecal transplantation.
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Affiliation(s)
- Priyadarshini Bhattacharjee
- Acute Medicine, Cambridge University Hospital NHS Foundation Trust, Cambridge, GBR
- School of Clinical Medicine, University of Cambridge, Cambridge, GBR
| | - Karim Arif Karim
- Medicine and Surgery, Kamuzu University of Health Sciences, Blantyre, MWI
| | - Zahid Khan
- Acute Medicine, Mid and South Essex NHS Foundation Trust, Southend-on-Sea, GBR
- Cardiology, Bart's Heart Centre, London, GBR
- Cardiology and General Medicine, Barking, Havering and Redbridge University Hospitals NHS Trust, London, GBR
- Cardiology, Royal Free Hospital, London, GBR
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21
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Torres AR, Morris S, Benson M, Wilkinson C, Lyon R. Stimulation of Pro-inflammatory Cytokines in Mixed Cultures of Peripheral Blood Mononuclear Cells and Anaerobic Bacteria. Cureus 2023; 15:e50586. [PMID: 38222203 PMCID: PMC10788116 DOI: 10.7759/cureus.50586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2023] [Indexed: 01/16/2024] Open
Abstract
In the last couple of decades, much progress has been made in studying bacteria living in humans. However, there is much more to learn about bacteria immune cell interactions. Here, we show that anaerobic bacteria do not grow when cultured overnight with human cells under atmospheric air. Air contains about 18% oxygen, which inhibits the growth of these bacteria while supporting the cultivation of human cells. The bacteria cultured with human peripheral blood mononuclear cells (PBMCs) inflamed with phytohemagglutinin (PHA) greatly increased the production of proinflammatory cytokines like tumor necrosis factor-alpha (TNFα) while inhibiting the production of monocyte chemoattractant protein-1 (MCP-1), an important chemokine.
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22
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Kim J, Koh H. MiTree: A Unified Web Cloud Analytic Platform for User-Friendly and Interpretable Microbiome Data Mining Using Tree-Based Methods. Microorganisms 2023; 11:2816. [PMID: 38004827 PMCID: PMC10672986 DOI: 10.3390/microorganisms11112816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/05/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
The advent of next-generation sequencing has greatly accelerated the field of human microbiome studies. Currently, investigators are seeking, struggling and competing to find new ways to diagnose, treat and prevent human diseases through the human microbiome. Machine learning is a promising approach to help such an effort, especially due to the high complexity of microbiome data. However, many of the current machine learning algorithms are in a "black box", i.e., they are difficult to understand and interpret. In addition, clinicians, public health practitioners and biologists are not usually skilled at computer programming, and they do not always have high-end computing devices. Thus, in this study, we introduce a unified web cloud analytic platform, named MiTree, for user-friendly and interpretable microbiome data mining. MiTree employs tree-based learning methods, including decision tree, random forest and gradient boosting, that are well understood and suited to human microbiome studies. We also stress that MiTree can address both classification and regression problems through covariate-adjusted or unadjusted analysis. MiTree should serve as an easy-to-use and interpretable data mining tool for microbiome-based disease prediction modeling, and should provide new insights into microbiome-based diagnostics, treatment and prevention. MiTree is an open-source software that is available on our web server.
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Hisatomi A, Tourlousse DM, Hamajima M, Ohkuma M, Sekiguchi Y, Sakamoto M. Complete genome sequences of Ruminococcus torques strains JCM 36208 and JCM 36209, isolated from the feces of a healthy Japanese male. Microbiol Resour Announc 2023; 12:e0063223. [PMID: 37800929 PMCID: PMC10652952 DOI: 10.1128/mra.00632-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/25/2023] [Indexed: 10/07/2023] Open
Abstract
Here, we report the complete genome sequences of two Ruminococcus torques strains (JCM 36208 and JCM 36209) that were newly isolated from the feces of a healthy Japanese male. Both genomes consist of a single circular chromosome with a length of ~2.8 Mbp and a G+C content of 41.8%.
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Affiliation(s)
- Atsushi Hisatomi
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Dieter M. Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Mayu Hamajima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
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Blanco-Míguez A, Gálvez EJC, Pasolli E, De Filippis F, Amend L, Huang KD, Manghi P, Lesker TR, Riedel T, Cova L, Punčochář M, Thomas AM, Valles-Colomer M, Schober I, Hitch TCA, Clavel T, Berry SE, Davies R, Wolf J, Spector TD, Overmann J, Tett A, Ercolini D, Segata N, Strowig T. Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions. Cell Host Microbe 2023; 31:1804-1819.e9. [PMID: 37883976 PMCID: PMC10635906 DOI: 10.1016/j.chom.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
The Segatella copri (formerly Prevotella copri) complex (ScC) comprises taxa that are key members of the human gut microbiome. It was previously described to contain four distinct phylogenetic clades. Combining targeted isolation with large-scale metagenomic analysis, we defined 13 distinct Segatella copri-related species, expanding the ScC complex beyond four clades. Complete genome reconstruction of thirteen strains from seven species unveiled the presence of genetically diverse large circular extrachromosomal elements. These elements are consistently present in most ScC species, contributing to intra- and inter-species diversities. The nine species-level clades present in humans display striking differences in prevalence and intra-species genetic makeup across human populations. Based on a meta-analysis, we found reproducible associations between members of ScC and the male sex and positive correlations with lower visceral fat and favorable markers of cardiometabolic health. Our work uncovers genomic diversity within ScC, facilitating a better characterization of the human microbiome.
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Affiliation(s)
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kun D Huang
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Till-Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Linda Cova
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | | | | | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Technical University of Braunschweig, Braunschweig, Germany
| | - Adrian Tett
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Wien, Austria
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Centre for Individualized Infection Medicine, Hannover, Germany.
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25
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Frey-Furtado L, Magalhães I, Sampaio-Maia B, Azevedo MJ. Oral microbiome characterization in oral mucositis patients-A systematic review. J Oral Pathol Med 2023; 52:911-918. [PMID: 37839408 DOI: 10.1111/jop.13492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND Oral mucositis (OM) is a severe and common adverse effect of cancer treatment. The oral microbiome appears to play a role on the onset and severity of OM. Therefore, this systematic review aims to characterize the oral dysbiosis associated with OM. METHODS The PRISMA checklist was followed and PubMed, Web of Science, and Scopus were screened for clinical studies characterizing the oral microbiome alterations in patients with OM. RESULTS From a total of 2500 articles retrieved, we included nine articles in this systematic review. Certain types of bacteria, as Fusobacterium, were recognized as predictors of the onset of OM. In addition, it was reported that patients with severe OM presented a reduction in alpha-diversity, an increase in beta-diversity. The abundance of some taxa significantly changed with OM severity, with Bacillota phylum and genera Leptotrichia, Actinomyces, and Prevotella decreasing and Treponema increasing with disease progression. Additionally, during cancer treatment, changes in the oral microbiome have been observed in OM patients, with an increase in Candida and nosocomial pathogens, including Staphylococcus species. CONCLUSION Our review indicates that cancer treatment can significantly alter the oral microbiome, with more pronounced changes observed in patients with severe OM in all relevant oral phyla, but more pronounced in Bacillota phylum.
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Affiliation(s)
- Leonor Frey-Furtado
- Faculdade de Medicina Dentária, Universidade do Porto, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Inês Magalhães
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- Escola Superior de Biotecnologia - Universidade Católica Portuguesa, Porto, Portugal
| | - Benedita Sampaio-Maia
- Faculdade de Medicina Dentária, Universidade do Porto, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Maria João Azevedo
- Faculdade de Medicina Dentária, Universidade do Porto, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- Academic Center for Dentistry Amsterdam, Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
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Cauwenberghs E, Oerlemans E, Wittouck S, Allonsius CN, Gehrmann T, Ahannach S, De Boeck I, Spacova I, Bron PA, Donders G, Verhoeven V, Lebeer S. Salivary microbiome of healthy women of reproductive age. mBio 2023; 14:e0030023. [PMID: 37655878 PMCID: PMC10653790 DOI: 10.1128/mbio.00300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/10/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE The salivary microbiome has been proven to play a crucial role in local and systemic diseases. Moreover, the effects of biological and lifestyle factors such as oral hygiene and smoking on this microbial community have already been explored. However, what was not yet well understood was the natural variation of the saliva microbiome in healthy women and how this is associated with specific use of hormonal contraception and with the number of different sexual partners with whom microbiome exchange is expected regularly. In this paper, we characterized the salivary microbiome of 255 healthy women of reproductive age using an in-depth questionnaire and self-sampling kits. Using the large metadata set, we were able to investigate the associations of several host-related and lifestyle variables with the salivary microbiome profiles. Our study shows a high preservation between individuals.
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Affiliation(s)
- Eline Cauwenberghs
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Eline Oerlemans
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Stijn Wittouck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Camille Nina Allonsius
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Thies Gehrmann
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Sarah Ahannach
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Ilke De Boeck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Peter A. Bron
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Gilbert Donders
- Department of Obstetrics and Gynaecology, University Hospital Antwerp, Edegem, Belgium
- Regional Hospital Heilig Hart, Tienen, Belgium
- Femicare, Clinical Research for Women, Tienen, Belgium
| | - Veronique Verhoeven
- Department of Family medicine and population health (FAMPOP), University of Antwerp, Antwerp, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
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27
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Blaustein RA, Shen Z, Kashaf SS, Lee-Lin S, Conlan S, Bosticardo M, Delmonte OM, Holmes CJ, Taylor ME, Banania G, Nagao K, Dimitrova D, Kanakry JA, Su H, Holland SM, Bergerson JRE, Freeman AF, Notarangelo LD, Kong HH, Segre JA. Expanded microbiome niches of RAG-deficient patients. Cell Rep Med 2023; 4:101205. [PMID: 37757827 PMCID: PMC10591041 DOI: 10.1016/j.xcrm.2023.101205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize skin, nares, and gut microbiota of patients with recombination-activating gene (RAG) deficiency-a rare genetically defined inborn error of immunity (IEI) that results in a broad spectrum of clinical phenotypes. Integrating de novo assembly of metagenomes from RAG-deficient patients with reference genome catalogs provides an expansive multi-kingdom view of microbial diversity. RAG-deficient patient microbiomes exhibit inter-individual variation, including expansion of opportunistic pathogens (e.g., Corynebacterium bovis, Haemophilus influenzae), and a relative loss of body site specificity. We identify 35 and 27 bacterial species derived from skin/nares and gut microbiomes, respectively, which are distinct to RAG-deficient patients compared to healthy individuals. Underscoring IEI patients as potential reservoirs for viral persistence and evolution, we further characterize the colonization of eukaryotic RNA viruses (e.g., Coronavirus 229E, Norovirus GII) in this patient population.
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Affiliation(s)
- Ryan A Blaustein
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Zeyang Shen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - ShihQueen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Cassandra J Holmes
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Monica E Taylor
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Glenna Banania
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Keisuke Nagao
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Dimana Dimitrova
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jennifer A Kanakry
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Helen Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
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Ibrahimi E, Lopes MB, Dhamo X, Simeon A, Shigdel R, Hron K, Stres B, D’Elia D, Berland M, Marcos-Zambrano LJ. Overview of data preprocessing for machine learning applications in human microbiome research. Front Microbiol 2023; 14:1250909. [PMID: 37869650 PMCID: PMC10588656 DOI: 10.3389/fmicb.2023.1250909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023] Open
Abstract
Although metagenomic sequencing is now the preferred technique to study microbiome-host interactions, analyzing and interpreting microbiome sequencing data presents challenges primarily attributed to the statistical specificities of the data (e.g., sparse, over-dispersed, compositional, inter-variable dependency). This mini review explores preprocessing and transformation methods applied in recent human microbiome studies to address microbiome data analysis challenges. Our results indicate a limited adoption of transformation methods targeting the statistical characteristics of microbiome sequencing data. Instead, there is a prevalent usage of relative and normalization-based transformations that do not specifically account for the specific attributes of microbiome data. The information on preprocessing and transformations applied to the data before analysis was incomplete or missing in many publications, leading to reproducibility concerns, comparability issues, and questionable results. We hope this mini review will provide researchers and newcomers to the field of human microbiome research with an up-to-date point of reference for various data transformation tools and assist them in choosing the most suitable transformation method based on their research questions, objectives, and data characteristics.
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Affiliation(s)
- Eliana Ibrahimi
- Department of Biology, Faculty of Natural Sciences, University of Tirana, Tirana, Albania
| | - Marta B. Lopes
- Department of Mathematics, Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
- UNIDEMI, Department of Mechanical and Industrial Engineering, NOVA School of Science and Technology, Caparica, Portugal
| | - Xhilda Dhamo
- Department of Applied Mathematics, Faculty of Natural Sciences, University of Tirana, Tirana, Albania
| | - Andrea Simeon
- BioSense Institute, University of Novi Sad, Novi Sad, Serbia
| | - Rajesh Shigdel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Karel Hron
- Department of Mathematical Analysis and Applications of Mathematics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Blaž Stres
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Ljubljana, Slovenia
- Faculty of Civil and Geodetic Engineering, Institute of Sanitary Engineering, Ljubljana, Slovenia
- Department of Automation, Biocybernetics and Robotics, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Domenica D’Elia
- Department of Biomedical Sciences, National Research Council, Institute for Biomedical Technologies, Bari, Italy
| | - Magali Berland
- INRAE, MetaGenoPolis, Université Paris-Saclay, Jouy-en-Josas, France
| | - Laura Judith Marcos-Zambrano
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, Madrid, Spain
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Jang H, Park S, Koh H. Comprehensive microbiome causal mediation analysis using MiMed on user-friendly web interfaces. Biol Methods Protoc 2023; 8:bpad023. [PMID: 37840574 PMCID: PMC10576642 DOI: 10.1093/biomethods/bpad023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/19/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
It is a central goal of human microbiome studies to see the roles of the microbiome as a mediator that transmits environmental, behavioral, or medical exposures to health or disease outcomes. Yet, mediation analysis is not used as much as it should be. One reason is because of the lack of carefully planned routines, compilers, and automated computing systems for microbiome mediation analysis (MiMed) to perform a series of data processing, diversity calculation, data normalization, downstream data analysis, and visualizations. Many researchers in various disciplines (e.g. clinicians, public health practitioners, and biologists) are not also familiar with related statistical methods and programming languages on command-line interfaces. Thus, in this article, we introduce a web cloud computing platform, named as MiMed, that enables comprehensive MiMed on user-friendly web interfaces. The main features of MiMed are as follows. First, MiMed can survey the microbiome in various spheres (i) as a whole microbial ecosystem using different ecological measures (e.g. alpha- and beta-diversity indices) or (ii) as individual microbial taxa (e.g. phyla, classes, orders, families, genera, and species) using different data normalization methods. Second, MiMed enables covariate-adjusted analysis to control for potential confounding factors (e.g. age and gender), which is essential to enhance the causality of the results, especially for observational studies. Third, MiMed enables a breadth of statistical inferences in both mediation effect estimation and significance testing. Fourth, MiMed provides flexible and easy-to-use data processing and analytic modules and creates nice graphical representations. Finally, MiMed employs ChatGPT to search for what has been known about the microbial taxa that are found significantly as mediators using artificial intelligence technologies. For demonstration purposes, we applied MiMed to the study on the mediating roles of oral microbiome in subgingival niches between e-cigarette smoking and gingival inflammation. MiMed is freely available on our web server (http://mimed.micloud.kr).
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Affiliation(s)
- Hyojung Jang
- Department of Applied Mathematics and Statistics, The State University of New York, Korea, Incheon, South Korea
| | - Solha Park
- Department of Applied Mathematics and Statistics, The State University of New York, Korea, Incheon, South Korea
| | - Hyunwook Koh
- Department of Applied Mathematics and Statistics, The State University of New York, Korea, Incheon, South Korea
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Kaliamoorthy S, Priya Sayeeram S, SundarRaj S, Balakrishnan J, Nagarajan M, Samidorai A. Investigating the Association Between Fusobacterium nucleatum and Oral Squamous Cell Carcinoma: A Pilot Case-Control Study on Tissue Samples. Cureus 2023; 15:e47238. [PMID: 38022043 PMCID: PMC10654264 DOI: 10.7759/cureus.47238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Background Fusobacterium nucleatum (F. nucleatum) has been increasingly linked to oral squamous cell carcinoma (OSCC), prompting this study to explore its presence using polymerase chain reaction (PCR) and evaluate its clinical significance. Methods In this pilot case-control study, 12 OSCC tissue samples and 12 non-cancerous oral mucosal tissue samples were analyzed. Total RNA extraction and complementary DNA (cDNA) synthesis were performed using Trizol-based methods, followed by PCR amplification and gel electrophoresis. The clinical characteristics of participants and PCR results were recorded. Results Among the OSCC tissue samples, three out of 12 tested positive for F. nucleatum, while none of the control samples showed its presence. The detection rate of F. nucleatum in OSCC was 25%. Gel analysis confirmed specific amplicon amplification, and ImageJ software enabled copy number quantification. Discussion Our findings support previous research indicating a potential association between F. nucleatum and OSCC. Understanding the etiological significance of F. nucleatum in OSCC has clinical implications, including early detection, risk stratification, and prognostication. However, the limited sample size and the need for further research to elucidate underlying mechanisms are acknowledged. Conclusion This pilot study provides initial evidence of F. nucleatum's presence in a subset of OSCC samples, supporting its potential association with oral cancer. Detecting F. nucleatum in OSCC tissues holds promise for future research and clinical applications as a diagnostic and prognostic biomarker. Understanding its role in oral carcinogenesis will facilitate the development of targeted therapeutic strategies. Larger studies are warranted to validate these findings and investigate the precise mechanisms involved.
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Affiliation(s)
- Sriram Kaliamoorthy
- Dentistry, Vinayaka Mission's Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Karaikal, IND
| | - Sugantha Priya Sayeeram
- Dental Surgery, Thanjavur Medical College, The Tamilnadu Dr. M.G.R Medical University, Thanjavur, IND
| | - Shanmugapriya SundarRaj
- Dental Surgery, Thanjavur Medical College, The Tamilnadu Dr. M.G.R Medical University, Thanjavur, IND
| | - Jeyakumar Balakrishnan
- Central Research Laboratory, Vinayaka Mission's Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Karaikal, IND
| | - Mahendirakumar Nagarajan
- Prosthodontics and Crown & Bridge, Cuddalore Government Dental College, The Tamilnadu Dr. M.G.R Medical University, Chidambaram, IND
| | - Agila Samidorai
- Periodontics, Chettinad Dental College and Research Institute, The Tamilnadu Dr. M.G.R Medical University, Chennai, IND
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Walker JN, Hanson BM, Hunter T, Simar SR, Duran Ramirez JM, Obernuefemann CLP, Parikh RP, Tenenbaum MM, Margenthaler JA, Hultgren SJ, Myckatyn TM. A prospective randomized clinical trial to assess antibiotic pocket irrigation on tissue expander breast reconstruction. Microbiol Spectr 2023; 11:e0143023. [PMID: 37754546 PMCID: PMC10581127 DOI: 10.1128/spectrum.01430-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/31/2023] [Indexed: 09/28/2023] Open
Abstract
Bacterial infection is the most common complication following staged post-mastectomy breast reconstruction initiated with a tissue expander (TE). To limit bacterial infection, antibiotic irrigation of the surgical site is commonly performed despite little high-quality data to support this practice. We performed a prospective randomized control trial to compare the impact of saline irrigation alone to a triple antibiotic irrigation regimen (1 g cefazolin, 80 mg gentamicin, and 50,000 units of bacitracin in 500 mL of saline) for breast implant surgery. The microbiome in breasts with cancer (n = 16) was compared to those without (n = 16), as all patients (n = 16) had unilateral cancers but bilateral mastectomies (n = 32). Biologic and prosthetic specimens procured both at the time of mastectomy and during TE removal months later were analyzed for longitudinal comparison. Outcomes included clinical infection, bacterial abundance, and relative microbiome composition. No patient in either group suffered a reconstructive failure or developed an infection. Triple antibiotic irrigation administered at the time of immediate TE reconstruction did not reduce bacterial abundance or impact microbial diversity relative to saline irrigation at the time of planned exchange. Implanted prosthetic material adopted the microbial composition of the surrounding host tissue. In cancer-naïve breasts, relative to saline, antibiotic irrigation increased bacterial abundance on periprosthetic capsules (P = 0.03) and acellular dermal matrices (P = 0.04) and altered the microbiota on both. These data show that, relative to saline only, the use of triple antibiotic irrigation in TE breast reconstruction does impact the bacterial abundance and diversity of certain biomaterials from cancer-naïve breasts. IMPORTANCE The lifetime risk of breast cancer is ~13% in women and is treated with a mastectomy in ~50% of cases. The majority are reconstructed, usually starting with a tissue expander to help restore the volume for a subsequent permanent breast implant or the women's own tissues. The biopsychosocial benefits of breast reconstruction, though, can be tempered by a high complication rate of at least 7% but over 30% in some women. Bacterial infection is the most common complication, and can lead to treatment delays, patient physical and emotional distress and escalating health care cost. To limit this risk, plastic surgeons have tried a variety of strategies to limit bacterial infection including irrigating the pocket created after removing the breast implant with antibiotic solutions, but good-quality data are scarce. Herein, we study the value of antibiotics in pocket irrigation using a robust randomized clinical trial design and molecular microbiology approaches.
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Affiliation(s)
- Jennifer N. Walker
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Sciences Center, Houston, Texas, USA
- Department of Epidemiology, Human Genetics & Environmental Sciences, Center for Infectious Diseases, School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA
| | - Blake M. Hanson
- Department of Epidemiology, Human Genetics & Environmental Sciences, Center for Infectious Diseases, School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA
- Division of Infectious Disease, Department of Pediatrics, McGovern Medical School, University of Texas Health Sciences Center, Houston, Texas, USA
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Sciences Center, Houston, Texas, USA
| | - Tayler Hunter
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Sciences Center, Houston, Texas, USA
| | - Shelby R. Simar
- Department of Epidemiology, Human Genetics & Environmental Sciences, Center for Infectious Diseases, School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA
- Division of Infectious Disease, Department of Pediatrics, McGovern Medical School, University of Texas Health Sciences Center, Houston, Texas, USA
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Sciences Center, Houston, Texas, USA
| | - Jesus M. Duran Ramirez
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Sciences Center, Houston, Texas, USA
| | - Chloe L. P. Obernuefemann
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Rajiv P. Parikh
- Division of Plastic and Reconstructive Surgery, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Marissa M. Tenenbaum
- Division of Plastic and Reconstructive Surgery, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Julie A. Margenthaler
- Division of Surgical Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Scott J. Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Terence M. Myckatyn
- Division of Plastic and Reconstructive Surgery, Washington University School of Medicine, Saint Louis, Missouri, USA
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Singh A, Amod A, Mulpuru V, Mishra N, Sahoo AK, Samanta SK. Finding Novel AMPs Secreted from the Human Microbiome as Potent Antibacterial and Antibiofilm Agents and Studying Their Synergistic Activity with Ag NCs. ACS Appl Bio Mater 2023; 6:3674-3682. [PMID: 37603700 DOI: 10.1021/acsabm.3c00302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Due to the enhanced resistance of bacteria to antibiotics, researchers always try to find effective alternatives to treat drug-resistant bacterial infections. In this context, we have explored antimicrobial peptides (AMPs), which are a broad class of small peptide molecules, and investigated their efficacy as potent antibacterial and antibiofilm agents. AMPs can cause cell death either through disruption of the cell membrane or by inhibiting vital intracellular functions, by binding to RNA, DNA, or intracellular components upon transversion through the cell membrane. We attempted to find potent intracellular cationic AMPs that can demonstrate antibacterial activity through interaction with DNA. As a source of AMPs, we have utilized those that are secreted from the human microbiome with the anticipation that these will be non-toxic in nature. Out of the total 1087 AMPs, 27 were screened on the basis of amino acid length and efficacy to cross the cell membrane barrier. From the list of 27 peptides, 4 candidates were selected through the docking score of these peptides with the DNA binding domain of H2A proteins. Further, the molecular dynamics simulation analysis demonstrated that 2 AMPs, i.e., peptides 7 and 25, are having considerable membrane permeation and DNA binding ability. Further, the in vitro analysis indicated that both peptides 7 and 25 could exhibit potent antibacterial and antibiofilm activities. In order to further enhance the antibiofilm potency, the above AMPs were used as supplements to silver nanoclusters (Ag NCs) to get synergistic activity. The synergistic activity of Ag NCs was found to be significantly increased with both the above AMPs.
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Affiliation(s)
- Anirudh Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211012, Uttar Pradesh, India
| | - Ayush Amod
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211012, Uttar Pradesh, India
| | - Viswajit Mulpuru
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211012, Uttar Pradesh, India
| | - Nidhi Mishra
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211012, Uttar Pradesh, India
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211012, Uttar Pradesh, India
| | - Sintu Kumar Samanta
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211012, Uttar Pradesh, India
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Sampaio S, Araujo R, Merino-Riba A, Lelouvier B, Servant F, Quelhas-Santos J, Pestana M, Sampaio-Maia B. Blood, Gut, and Oral Microbiome in Kidney Transplant Recipients. Indian J Nephrol 2023; 33:366-370. [PMID: 37881747 PMCID: PMC10593307 DOI: 10.4103/ijn.ijn_168_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/31/2023] [Indexed: 10/27/2023] Open
Abstract
Background and Objective Recent reports describe the existence of a blood microbiome profile not associated with an infection state. Given the high impact that the dysbiotic human microbiome appears to have in chronic kidney disease and, in particular, in the outcome of kidney transplant recipients (KTRs), we aimed to explore the variations and correlations of the gut, oral, and blood microbiome of recipients, 3 months after kidney transplantation. Materials and Methods We conducted a cross-sectional study where the microbiome of stool, saliva, and blood collected from recipients 3 months after kidney transplantation (N = 6) was analyzed by polymerase chain reaction (PCR) amplification and sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene using MiSeq Illumina® technology. Results Blood of KTRs harbors a distinct low-abundance microbiome dominated by Proteobacteria and Firmicutes. Gut and oral microbiome of KTRs also present distinct profiles. The existence of a proportion of shared operational taxonomic units among the different body sites is reported, mainly classified as Proteobacteria and Firmicutes. Conclusions This study provides evidence of existence a blood microbiome in KTRs, different from the gut and the oral microbiome profiles, with a small number of operational taxonomic units representing a shared microbiome. The clinical relevance of this observation should be further explored in these patients.
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Affiliation(s)
- Susana Sampaio
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
- Faculty of Medicine, University of Porto, EPE, Portugal
- Department of Nephrology, São João Hospital Center, EPE, Portugal
| | - Ricardo Araujo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
| | - Ana Merino-Riba
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Nephrology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | | | | | - Janete Quelhas-Santos
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
- Faculty of Medicine, University of Porto, EPE, Portugal
| | - Manuel Pestana
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
- Faculty of Medicine, University of Porto, EPE, Portugal
- Department of Nephrology, São João Hospital Center, EPE, Portugal
| | - Benedita Sampaio-Maia
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
- Faculty of Dental Medicine, University of Porto, Porto, Portugal
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Hurst JH, Kelly MS. Leveraging the human microbiota to target bacterial respiratory pathogens: new paths toward an expanded antimicrobial armamentarium. mBio 2023; 14:e0085423. [PMID: 37338299 PMCID: PMC10470731 DOI: 10.1128/mbio.00854-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Acute respiratory infections are the most frequent infections across the lifespan and are the leading infectious cause of death among children globally. Bacterial respiratory infections are routinely treated with antibiotics, nearly all of which are derived from microbial natural products. Unfortunately, antibiotic-resistant bacteria are an increasingly frequent cause of respiratory infections, and there are few new antibiotics in development that target these pathogens. In the article by Stubbendieck et al., the authors identified Rothia species that demonstrate in vitro and ex vivo growth inhibition of the respiratory pathobiont Moraxella catarrhalis. The authors present experiments suggesting that this activity is mediated at least in part through the secretion of a novel peptidoglycan endopeptidase that targets the M. catarrhalis cell wall. In this commentary, we discuss these findings in the context of the urgent threat of antimicrobial resistance and highlight the promise of the human respiratory microbiota as a source of novel biotherapeutics.
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Affiliation(s)
- Jillian H. Hurst
- Department of Pediatrics, Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Matthew S. Kelly
- Department of Pediatrics, Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
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Montelongo Hernandez C, Putonti C, Wolfe AJ. Urinary Plasmids Reduce Permissivity to Coliphage Infection. Microbiol Spectr 2023; 11:e0130923. [PMID: 37409956 PMCID: PMC10433841 DOI: 10.1128/spectrum.01309-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
The microbial community of the urinary tract (urinary microbiota or urobiota) has been associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. While urinary Escherichia coli strains associated with urinary tract infection (UTI) and their phages have been catalogued for the urobiome, bacterium-plasmid-phage interactions have yet to be explored. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Putative F plasmids were predicted in 47 of 67 urinary E. coli isolates, and most of these plasmids carried genes that encode toxin-antitoxin (TA) modules, antibiotic resistance, and/or virulence. Urinary E. coli plasmids, from urinary microbiota strains UMB0928 and UMB1284, were conjugated into E. coli K-12 strains. These transconjugants included genes for antibiotic resistance and virulence, and they decreased permissivity to coliphage infection by the laboratory phage P1vir and the urinary phages Greed and Lust. Plasmids in one transconjugant were maintained in E. coli K-12 for up to 10 days in the absence of antibiotic resistance selection; this included the maintenance of the antibiotic resistance phenotype and decreased permissivity to phage. Finally, we discuss how F plasmids present in urinary E. coli strains could play a role in coliphage dynamics and the maintenance of antibiotic resistance in urinary E. coli. IMPORTANCE The urinary tract contains a resident microbial community called the urinary microbiota or urobiota. Evidence exists that it is associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. Bacterium-plasmid-phage interactions have been studied primarily in laboratory settings and are yet to be thoroughly tested in complex communities. This is especially true of the urinary tract, where the bacterial genetic determinants of phage infection are not well understood. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Urinary E. coli plasmids, encoding antibiotic resistance and transferred by conjugation into naive laboratory E. coli K-12 strains, decreased permissivity to coliphage infection. We propose a model by which urinary plasmids present in urinary E. coli strains could help to decrease phage infection susceptibility and maintain the antibiotic resistance of urinary E. coli. This has consequences for phage therapy, which could inadvertently select for plasmids that encode antibiotic resistance.
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Affiliation(s)
- Cesar Montelongo Hernandez
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
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Miya TV, Marima R, Damane BP, Ledet EM, Dlamini Z. Dissecting Microbiome-Derived SCFAs in Prostate Cancer: Analyzing Gut Microbiota, Racial Disparities, and Epigenetic Mechanisms. Cancers (Basel) 2023; 15:4086. [PMID: 37627114 PMCID: PMC10452611 DOI: 10.3390/cancers15164086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Prostate cancer (PCa) continues to be the most diagnosed cancer and the second primary cause of fatalities in men globally. There is an abundance of scientific evidence suggesting that the human microbiome, together with its metabolites, plays a crucial role in carcinogenesis and has a significant impact on the efficacy of anticancer interventions in solid and hematological cancers. These anticancer interventions include chemotherapy, immune checkpoint inhibitors, and targeted therapies. Furthermore, the microbiome can influence systemic and local immune responses using numerous metabolites such as short-chain fatty acids (SCFAs). Despite the lack of scientific data in terms of the role of SCFAs in PCa pathogenesis, recent studies show that SCFAs have a profound impact on PCa progression. Several studies have reported racial/ethnic disparities in terms of bacterial content in the gut microbiome and SCFA composition. These studies explored microbiome and SCFA racial/ethnic disparities in cancers such as colorectal, colon, cervical, breast, and endometrial cancer. Notably, there are currently no published studies exploring microbiome/SCFA composition racial disparities and their role in PCa carcinogenesis. This review discusses the potential role of the microbiome in PCa development and progression. The involvement of microbiome-derived SCFAs in facilitating PCa carcinogenesis and their effect on PCa therapeutic response, particularly immunotherapy, are discussed. Racial/ethnic differences in microbiome composition and SCFA content in various cancers are also discussed. Lastly, the effects of SCFAs on PCa progression via epigenetic modifications is also discussed.
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Affiliation(s)
- Thabiso Victor Miya
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa
| | - Rahaba Marima
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa
| | - Botle Precious Damane
- Department of Surgery, Level 7, Bridge E, Steve Biko Academic Hospital, Faculty of Health Sciences, University of Pretoria, Pretoria 0007, South Africa
| | - Elisa Marie Ledet
- Tulane Cancer Center, Tulane Medical School, New Orleans, LA 70112, USA
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria 0028, South Africa
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Hsu TY, Nzabarushimana E, Wong D, Luo C, Beiko RG, Langille M, Huttenhower C, Nguyen LH, Franzosa EA. Profiling novel lateral gene transfer events in the human microbiome. bioRxiv 2023:2023.08.08.552500. [PMID: 37609252 PMCID: PMC10441418 DOI: 10.1101/2023.08.08.552500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope and dynamics of novel LGT events arising in personal microbiomes are not well understood, as there are no widely adopted computational methods to detect, quantify, and characterize LGT from complex microbial communities. We addressed this by developing, benchmarking, and experimentally validating a computational method (WAAFLE) to profile novel LGT events from assembled metagenomes. Applying WAAFLE to >2K human metagenomes from diverse body sites, we identified >100K putative high-confidence but previously uncharacterized LGT events (~2 per assembled microbial genome-equivalent). These events were enriched for mobile elements (as expected), as well as restriction-modification and transport functions typically associated with the destruction of foreign DNA. LGT frequency was quantifiably influenced by biogeography, the phylogenetic similarity of the involved taxa, and the ecological abundance of the donor taxon. These forces manifest as LGT networks in which hub species abundant in a community type donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT may be a more ubiquitous process in the human microbiome than previously described. The open-source WAAFLE implementation, documentation, and data from this work are available at http://huttenhower.sph.harvard.edu/waafle.
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Affiliation(s)
- Tiffany Y Hsu
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Etienne Nzabarushimana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dennis Wong
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Chengwei Luo
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan Langille
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Suryavanshi M, Agudelo J, Miller A. Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease. Front Mol Biosci 2023; 10:1210225. [PMID: 37602324 PMCID: PMC10436313 DOI: 10.3389/fmolb.2023.1210225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction: In complex microbial communities, the importance of microbial species at very low abundance levels and their prevalence for overall community structure and function is increasingly being recognized. Clinical microbiome studies on urinary stone disease (USD) have indicated that both the gut and urinary tract microbiota are associated with the onset of the disease and that kidney stones them-selves harbor a complex, yet consistent and viable, microbiome. However, how rare phylotypes contribute to this association remains unclear. Delineating the contribution of rare and common phylotypes to urinary stone disease is important for the development of bacteriotherapies to promote urologic health. Methods: The objectives of the current report were to conduct a metaanalysis of 16S rRNA datasets derived from the kidney stone, stool, and urine samples of participants with or without urinary stone disease. To delineate the impact of rare and common phylotypes, metaanalyses were conducted by first separating rare and common taxa determined by both the frequency and abundance of amplicon sequence variants. Results: Consistent with previous analyses, we found that gut, upper urinary, and lower urinary tract microbiomes were all unique. Rare phylotypes comprised the majority of species observed in all sample types, with kidney stones exhibiting the greatest bias toward rarity, followed by urine and stool. Both rare and common fractions contributed significantly to the differences observed between sample types and health disparity. Furthermore, the rare and common fractions were taxonomically unique across all sample types. A total of 222 and 320 unique rare phylotypes from urine and stool samples were found to be significantly associated with USD. A co-occurrence correlation analysis revealed that rare phylotypes are most important for microbiome structure in stones, followed by urine and stool. Discussion: Collectively, the results indicate that rare phylotypes may be important for the pathophysiology of USD, particularly in the kidney stone matrix, which is inherently a very low microbial biomass niche that can have implications for the diagnosis and treatment of kidney stones. Further studies are needed to investigate the functional significance of rare phylotypes in kidney stone pathogenesis.
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Affiliation(s)
- Mangesh Suryavanshi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, United States
| | - Jose Agudelo
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, United States
| | - Aaron Miller
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, United States
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, United States
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Reuben RC, Beugnon R, Jurburg SD. COVID-19 alters human microbiomes: a meta-analysis. Front Cell Infect Microbiol 2023; 13:1211348. [PMID: 37600938 PMCID: PMC10433767 DOI: 10.3389/fcimb.2023.1211348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/23/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected a substantial portion of the world's population, and novel consequences of COVID-19 on the human body are continuously being uncovered. The human microbiome plays an essential role in host health and well-being, and multiple studies targeting specific populations have reported altered microbiomes in patients infected with SARS-CoV-2. Given the global scale and massive incidence of COVID on the global population, determining whether the effects of COVID-19 on the human microbiome are consistent and generalizable across populations is essential. Methods We performed a synthesis of human microbiome responses to COVID-19. We collected 16S rRNA gene amplicon sequence data from 11 studies sampling the oral and nasopharyngeal or gut microbiome of COVID-19-infected and uninfected subjects. Our synthesis included 1,159 respiratory (oral and nasopharyngeal) microbiome samples and 267 gut microbiome samples from patients in 11 cities across four countries. Results Our reanalyses revealed communitywide alterations in the respiratory and gut microbiomes across human populations. We found significant overall reductions in the gut microbial diversity of COVID-19-infected patients, but not in the respiratory microbiome. Furthermore, we found more consistent community shifts in the gut microbiomes of infected patients than in the respiratory microbiomes, although the microbiomes in both sites exhibited higher host-to-host variation in infected patients. In respiratory microbiomes, COVID-19 infection resulted in an increase in the relative abundance of potentially pathogenic bacteria, including Mycoplasma. Discussion Our findings shed light on the impact of COVID-19 on the human-associated microbiome across populations, and highlight the need for further research into the relationship between long-term effects of COVID-19 and altered microbiota.
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Affiliation(s)
- Rine Christopher Reuben
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Rémy Beugnon
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leipzig Institute for Meteorology, Universität Leipzig, Leipzig, Germany
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Stephanie D. Jurburg
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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Naud S, Valles C, Abdillah A, Abou Chacra L, Mekhalif FZ, Ibrahim A, Caputo A, Baudoin JP, Gouriet F, Bittar F, Lagier JC, Ranque S, Fenollar F, Tidjani Alou M, Raoult D. Preliminary landscape of Candidatus Saccharibacteria in the human microbiome. Front Cell Infect Microbiol 2023; 13:1195679. [PMID: 37577371 PMCID: PMC10414567 DOI: 10.3389/fcimb.2023.1195679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date. Methods In this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics. Results Using Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples. Conclusion This study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.
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Affiliation(s)
- Sabrina Naud
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Camille Valles
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Abdourahim Abdillah
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Linda Abou Chacra
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Fatima Zouina Mekhalif
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Ahmad Ibrahim
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Aurelia Caputo
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Pierre Baudoin
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Frédérique Gouriet
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Fadi Bittar
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Stéphane Ranque
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Florence Fenollar
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Maryam Tidjani Alou
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
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Mendes I, Vale N. How Can the Microbiome Induce Carcinogenesis and Modulate Drug Resistance in Cancer Therapy? Int J Mol Sci 2023; 24:11855. [PMID: 37511612 PMCID: PMC10380870 DOI: 10.3390/ijms241411855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Over the years, cancer has been affecting the lives of many people globally and it has become one of the most studied diseases. Despite the efforts to understand the cell mechanisms behind this complex disease, not every patient seems to respond to targeted therapies or immunotherapies. Drug resistance in cancer is one of the limiting factors contributing to unsuccessful therapies; therefore, understanding how cancer cells acquire this resistance is essential to help cure individuals affected by cancer. Recently, the altered microbiome was observed to be an important hallmark of cancer and therefore it represents a promising topic of cancer research. Our review aims to provide a global perspective of some cancer hallmarks, for instance how genetic and epigenetic modifications may be caused by an altered human microbiome. We also provide information on how an altered human microbiome can lead to cancer development as well as how the microbiome can influence drug resistance and ultimately targeted therapies. This may be useful to develop alternatives for cancer treatment, i.e., future personalized medicine that can help in cases where traditional cancer treatment is unsuccessful.
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Affiliation(s)
- Inês Mendes
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- School of Life and Environmental Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Edifício de Geociências, 5000-801 Vila Real, Portugal
| | - Nuno Vale
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal
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Neidhöfer C, Bagniceva M, Wetzig N, Sieber MA, Thiele R, Parčina M. Pragmatic Considerations When Extracting DNA for Metagenomics Analyses of Clinical Samples. Int J Mol Sci 2023; 24:11262. [PMID: 37511022 PMCID: PMC10379426 DOI: 10.3390/ijms241411262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Microbiome analyses are essential for understanding microorganism composition and diversity, but interpretation is often challenging due to biological and technical variables. DNA extraction is a critical step that can significantly bias results, particularly in samples containing a high abundance of challenging-to-lyse microorganisms. Taking into consideration the distinctive microenvironments observed in different bodily locations, our study sought to assess the extent of bias introduced by suboptimal bead-beating during DNA extraction across diverse clinical sample types. The question was whether complex targeted extraction methods are always necessary for reliable taxonomic abundance estimation through amplicon sequencing or if simpler alternatives are effective for some sample types. Hence, for four different clinical sample types (stool, cervical swab, skin swab, and hospital surface swab samples), we compared the results achieved from extracting targeted manual protocols routinely used in our research lab for each sample type with automated protocols specifically not designed for that purpose. Unsurprisingly, we found that for the stool samples, manual extraction protocols with vigorous bead-beating were necessary in order to avoid erroneous taxa proportions on all investigated taxonomic levels and, in particular, false under- or overrepresentation of important genera such as Blautia, Faecalibacterium, and Parabacteroides. However, interestingly, we found that the skin and cervical swab samples had similar results with all tested protocols. Our results suggest that the level of practical automation largely depends on the expected microenvironment, with skin and cervical swabs being much easier to process than stool samples. Prudent consideration is necessary when extending the conclusions of this study to applications beyond rough estimations of taxonomic abundance.
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Affiliation(s)
- Claudio Neidhöfer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - Maria Bagniceva
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - Nina Wetzig
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Martin A Sieber
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Ralf Thiele
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Marijo Parčina
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany
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Eggers S, Midya V, Bixby M, Gennings C, Torres-Olascoaga LA, Walker RW, Wright RO, Arora M, Téllez-Rojo MM. Prenatal lead exposure is negatively associated with the gut microbiome in childhood. Front Microbiol 2023; 14:1193919. [PMID: 37426026 PMCID: PMC10325945 DOI: 10.3389/fmicb.2023.1193919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/23/2023] [Indexed: 07/11/2023] Open
Abstract
Background Metal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role of the GM in association with many adverse health outcomes, understanding the relationship between prenatal metal exposures and the GM is critically important. However, there is sparse knowledge of the association between prenatal metal exposure and GM later in childhood. Objectives This analysis aims to identify associations between prenatal lead (Pb) exposure and GM composition and function in children 9-11 years old. Methods Data come from the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) cohort based in Mexico City, Mexico. Prenatal metal concentrations were measured in maternal whole blood drawn during the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the GM. This analysis uses multiple statistical modeling approaches, including linear regression, permutational analysis of variance, weighted quantile sum regression (WQS), and individual taxa regressions, to estimate the association between maternal blood Pb during pregnancy and multiple aspects of the child GM at 9-11 years old, adjusting for relevant confounders. Results Of the 123 child participants in this pilot data analysis, 74 were male and 49 were female. Mean prenatal maternal blood Pb was 33.6 (SE = 2.1) ug/L and 34.9 (SE = 2.1) ug/L at second and third trimesters, respectively. Analysis suggests a consistent negative relationship between prenatal maternal blood Pb and the GM at age 9-11, including measures of alpha and beta diversity, microbiome mixture analysis, and individual taxa. The WQS analysis showed a negative association between prenatal Pb exposure and the gut microbiome, for both second and third trimester exposures (2Tβ = -0.17, 95%CI = [-0.46,0.11]; 3Tβ = -0.17, 95%CI = [-0.44,0.10]). Ruminococcus gnavus, Bifidobacterium longum, Alistipes indistinctus, Bacteroides caccae, and Bifidobacterium bifidum all had weights above the importance threshold from 80% or more of the WQS repeated holdouts in association with both second and third trimester Pb exposure. Discussion Pilot data analysis suggests a negative association between prenatal Pb exposure and the gut microbiome later in childhood; however, additional investigation is needed.
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Affiliation(s)
- Shoshannah Eggers
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Epidemiology, University of Iowa College of Public Health, Iowa City, IA, United States
| | - Vishal Midya
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Moira Bixby
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Chris Gennings
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Libni A. Torres-Olascoaga
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca, Mexico
| | - Ryan W. Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Robert O. Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Martha María Téllez-Rojo
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca, Mexico
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Nowicki C, Ray L, Engen P, Madrigrano A, Witt T, Lad T, Cobleigh M, Mutlu EA. Comparison of gut microbiome composition in colonic biopsies, endoscopically-collected and at-home-collected stool samples. Front Microbiol 2023; 14:1148097. [PMID: 37323911 PMCID: PMC10264612 DOI: 10.3389/fmicb.2023.1148097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Aim The goal of this study is to compare microbiome composition in three different sample types in women, namely stool brought from home vs. solid stool samples obtained at the time of an unprepped sigmoidoscopy vs. biopsies of the colonic mucosa at the time of an unprepped sigmoidoscopy, using alpha- and beta-diversity metrics following bacterial 16S rRNA sequencing. The findings may have relevance to health and disease states in which bacterial metabolism has a significant impact on molecules/metabolites that are recirculated between the gut lumen and mucosa and systemic circulation, such as estrogens (as in breast cancer) or bile acids. Methods Concomitant at-home-collected stool, endoscopically-collected stool, and colonic biopsy samples were collected from 48 subjects (24 breast cancer, 24 control.) After 16S rRNA sequencing, an amplicon sequence variant (ASV) based approach was used to analyze the data. Alpha diversity metrics (Chao1, Pielou's Evenness, Faith PD, Shannon, and Simpson) and beta diversity metrics (Bray-Curtis, Weighted and Unweighted Unifrac) were calculated. LEfSe was used to analyze differences in the abundance of various taxa between sample types. Results Alpha and beta diversity metrics were significantly different between the three sample types. Biopsy samples were different than stool samples in all metrics. The highest variation in microbiome diversity was noted in the colonic biopsy samples. At-home and endoscopically-collected stool showed more similarities in count-based and weighted beta diversity metrics. There were significant differences in rare taxa and phylogenetically-diverse taxa between the two types of stool samples. Generally, there were higher levels of Proteobacteria in biopsy samples, with significantly more Actinobacteria and Firmicutes in stool (all p < 0.001, q-value < 0.05). Overall, there was a significantly higher relative abundance of Lachnospiraceae and Ruminococcaceae in stool samples (at-home collected and endoscopically-collected) and higher abundances of Tisserellaceae in biopsy samples (all p < 0.001, q-value < 0.05). Conclusion Our data shows that different sampling methods can impact results when looking at the composition of the gut microbiome using ASV-based approaches.
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Affiliation(s)
- Christina Nowicki
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Lucille Ray
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Philip Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Andrea Madrigrano
- Department of Surgery, Rush Medical College, Rush University Medical Center, Chicago, IL, United States
| | - Thomas Witt
- Department of Surgery, Rush Medical College, Rush University Medical Center, Chicago, IL, United States
| | - Thomas Lad
- Department of Oncology, Cook County Health and Hospital Systems, Chicago, IL, United States
| | - Melody Cobleigh
- Department of Internal Medicine, Division of Hematology, Oncology, and Cell Therapy, Rush University Medical Center, Chicago, IL, United States
| | - Ece A. Mutlu
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
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Abstract
INTRODUCTION Investigating the taxonomic and functional composition of human microbiomes can aid in the understanding of disease etiologies, diagnosis, and therapy monitoring for several diseases, including inflammatory bowel disease or obesity. One method for microbiome monitoring is metaproteomics, which assesses human and microbial proteins and thus enables the study of host-microbiome interactions. This advantage led to increased interest in metaproteome analyses and significant developments to introduce this method into a clinical context. AREAS COVERED This review summarizes the recent progress from a technical side and an application-related point of view. EXPERT OPINION Numerous publications imply the massive potential of metaproteomics to impact human health care. However, the key challenges of standardization and validation of experimental and bioinformatic workflows and accurate quantification methods must be overcome.
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Affiliation(s)
- Maximilian Wolf
- Multidimensional omics analysis group, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Kay Schallert
- Multidimensional omics analysis group, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, Germany
| | - Luca Knipper
- Multidimensional omics analysis group, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Albert Sickmann
- Department of Bioanalytics, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, Germany
- Medizinisches Proteom-Center (MPC), Ruhr University, Bochum, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, UK
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- Computational Metagenomics, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Dirk Benndorf
- Applied Biosciences and Process Engineering, Anhalt University of Applied Science, Köthen, Germany
| | - Robert Heyer
- Multidimensional omics analysis group, Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Multidimensional omics analysis group, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, Germany
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Zhang Y, Chen T, Hao X, Hu Y, Chen M, Zhang D, Cai H, Luo J, Kong L, Huang S, Huang Y, Yang N, Liu R, Li Q, Yuan C, Wang C, Zhou H, Huang W, Zhang W. Mapping the regulatory effects of herbal organic compounds on gut bacteria. Pharmacol Res 2023; 193:106804. [PMID: 37244386 DOI: 10.1016/j.phrs.2023.106804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Affiliation(s)
- Yulong Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Ting Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Xiaoqing Hao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, P. R. China; The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, P. R. China
| | - Yuanjia Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, P. R. China; DPM, Faculty of Health Sciences, University of Macau, Macao SAR 999078, P. R. China
| | - Manyun Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Daiyan Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, P. R. China
| | - Hong Cai
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, P. R. China
| | - Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Sutianzi Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, P. R. China
| | - Yuanfei Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, P. R. China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, P. R. China
| | - Nian Yang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, P. R. China
| | - Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, P. R. China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, P. R. China
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, P. R. China; The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, P. R. China
| | - Chunsu Yuan
- Tang Center of Herbal Medicine Research and Department of Anesthesia & Critical Care, University of Chicago, Chicago, IL 60637, USA
| | - Chongzhi Wang
- Tang Center of Herbal Medicine Research and Department of Anesthesia & Critical Care, University of Chicago, Chicago, IL 60637, USA
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, P. R. China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, P. R. China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China; Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, P. R. China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, P. R. China.
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, P. R. China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, P. R. China; The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, P. R. China; Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha 410006, P. R. China.
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Koizumi Y, Maruyama F. Editorial: Ecology, environment, and human microbiome interaction with infection. Front Public Health 2023; 11:1217927. [PMID: 37287813 PMCID: PMC10242724 DOI: 10.3389/fpubh.2023.1217927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 05/12/2023] [Indexed: 06/09/2023] Open
Affiliation(s)
- Yukiko Koizumi
- Applied Research, American Dental Association Science and Research Institute, Chicago, IL, United States
| | - Fumito Maruyama
- Microbial Genomics and Ecology, Center for the Planetary Health and Innovation Science, The IDEC Institute, Hiroshima University, Higashihiroshima, Japan
- Project Research Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashihiroshima, Japan
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Stevens E, Marco M. Bacterial extracellular electron transfer in plant and animal ecosystems. FEMS Microbiol Rev 2023:7163210. [PMID: 37188642 DOI: 10.1093/femsre/fuad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Extracellular electron transfer (EET) is a bioelectrochemical process performed by electrochemically active bacteria (EAB) found in host-associated environments, including plant and animal ecosystems and fermenting plant- and animal-derived foods. Through direct or mediated electron transfer pathways, certain bacteria use EET to enhance ecological fitness with host-impacting effects. In the plant rhizosphere, electron acceptors support the growth of EAB such as members of the Geobacter, cable bacteria, and some clostridia with the capacity to influence iron and heavy metal uptake by plants. In animal microbiomes, EET is associated with diet-derived iron in the intestines of soil-dwelling termites, earthworms, and beetle larvae. EET is also associated with the colonization and metabolism of some bacteria in human and animal microbiomes, such as Streptococcus mutans in the mouth, Enterococcus faecalis and Listeria monocytogenes in the intestine, and Pseudomonas aeruginosa in the lungs. During the fermentation of plant tissues and bovine milk, lactic acid bacteria like Lactiplantibacillus plantarum and Lactococcus lactis may use EET to increase their growth and food acidification, as well as decrease environmental oxidation-reduction potential. EET is thus likely an important metabolic pathway for host-associated bacteria and has implications for ecosystem function, health and disease, and biotechnological applications.
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Affiliation(s)
- Eric Stevens
- Department of Food Science & Technology, University of California, Davis, CA, USA
| | - Maria Marco
- Department of Food Science & Technology, University of California, Davis, CA, USA
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Eggers S, Midya V, Bixby M, Gennings C, Torres-Olascoaga LA, Walker RW, Wright RO, Arora M, Téllez-Rojo MM. Prenatal Lead Exposure is Negatively Associated with the Gut Microbiome in Childhood. medRxiv 2023:2023.05.10.23289802. [PMID: 37214901 PMCID: PMC10197792 DOI: 10.1101/2023.05.10.23289802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Metal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role of the GM in association with many adverse health outcomes, understanding the relationship between prenatal metal exposures and the GM is critically important. However, there is sparse knowledge of the association between prenatal metal exposure and GM later in childhood. Objectives This analysis aims to identify associations between prenatal lead (Pb) exposure and GM composition and function in children 9-11 years old. Methods Data come from the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) cohort based in Mexico City, Mexico. Prenatal metal concentrations were measured in maternal whole blood drawn during the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the GM. This analysis uses multiple statistical modeling approaches, including linear regression, permutational analysis of variance, weighted quantile sum regression (WQS), and individual taxa regressions, to estimate the association between maternal blood Pb during pregnancy and multiple aspects of the child GM at 9-11 years old, adjusting for relevant confounders. Results Of the 123 child participants in this pilot data analysis, 74 were male and 49 were female. Mean prenatal maternal blood Pb was 33.6(SE=2.1) ug/L and 34.9(SE=2.1) ug/L at second and third trimesters, respectively. Analysis suggests a consistent negative relationship between prenatal maternal blood Pb and the GM at age 9-11, including measures of alpha and beta diversity, microbiome mixture analysis, and individual taxa. The WQS analysis showed a negative association between prenatal Pb exposure and the gut microbiome, for both second and third trimester exposures (2Tβ=-0.17,95%CI=[-0.46,0.11]; 3Tβ=-0.17,95%CI=[-0.44,0.10]). Ruminococcus gnavus, Bifidobacterium longum, Alistipes indistinctus, Bacteroides caccae, and Bifidobacterium bifidum all had weights above the importance threshold from 80% or more of the WQS repeated holdouts in association with both second and third trimester Pb exposure. Discussion Pilot data analysis suggests a negative association between prenatal Pb exposure and the gut microbiome later in childhood; however, additional investigation is needed.
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Affiliation(s)
- Shoshannah Eggers
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Epidemiology, University of Iowa College of Public Health, Iowa City, Iowa, USA
| | - Vishal Midya
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Moira Bixby
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chris Gennings
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Libni A Torres-Olascoaga
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca, Mexico
| | - Ryan W. Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert O. Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Martha María Téllez-Rojo
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca, Mexico
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Inglis LK, Roach MJ, Edwards RA. Prophage rates in the human microbiome vary by body site and host health. bioRxiv 2023:2023.05.04.539508. [PMID: 37205434 PMCID: PMC10187302 DOI: 10.1101/2023.05.04.539508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Phages integrated into a bacterial genome-called prophages-continuously monitor the health of the host bacteria to determine when to escape the genome, protect their host from other phage infections, and may provide genes that promote bacterial growth. Prophages are essential to almost all microbiomes, including the human microbiome. However, most human microbiome studies focus on bacteria, ignoring free and integrated phages, so we know little about how these prophages affect the human microbiome. We compared the prophages identified in 11,513 bacterial genomes isolated from human body sites to characterise prophage DNA in the human microbiome. Here, we show that prophage DNA comprised an average of 1-5% of each bacterial genome. The prophage content per genome varies with the isolation site on the human body, the health of the human, and whether the disease was symptomatic. The presence of prophages promotes bacterial growth and sculpts the microbiome. However, the disparities caused by prophages vary throughout the body.
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Affiliation(s)
- Laura K. Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
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