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Dou S, Ma G, Liang Y, Fu G, Shen J, Fu L, Wang Q, Li T, Cong B, Li S. Preliminary exploratory research on the application value of oral and intestinal meta-genomics in predicting subjects' occupations-A case study of the distinction between students and migrant workers. Front Microbiol 2024; 14:1330603. [PMID: 38390220 PMCID: PMC10883652 DOI: 10.3389/fmicb.2023.1330603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/26/2023] [Indexed: 02/24/2024] Open
Abstract
Background In the field of forensic science, accurately determining occupation of an individual can greatly assist in resolving cases such as criminal investigations or disaster victim identifications. However, estimating occupation can be challenging due to the intricate relationship between occupation and various factors, including gender, age, living environment, health status, medication use, and lifestyle habits such as alcohol consumption and smoking. All of these factors can impact the composition of oral or gut microbial community of an individual. Methods and results In this study, we collected saliva and feces samples from individuals representing different occupational sectors, specifically students and manual laborers. We then performed metagenomic sequencing on the DNA extracted from these samples to obtain data that could be analyzed for taxonomic and functional annotations in five different databases. The correlation between occupation with microbial information was assisted from the perspective of α and β diversity, showing that individuals belonging to the two occupations hold significantly different oral and gut microbial communities, and that this correlation is basically not affected by gender, drinking, and smoking in our datasets. Finally, random forest (RF) models were built with recursive feature elimination (RFE) processes. Models with 100% accuracy in both training and testing sets were constructed based on three species in saliva samples or on a single pathway annotated by the KEGG database in fecal samples, namely, "ko04145" or Phagosome. Conclusion Although this study may have limited representativeness due to its small sample size, it provides preliminary evidence of the potential of using microbiome information for occupational inference.
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Affiliation(s)
- Shujie Dou
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, China
| | - Guanju Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, China
| | - Yu Liang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, China
| | - Guangping Fu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, China
| | - Jie Shen
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, China
| | - Lihong Fu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, China
| | - Qian Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, China
| | - Tao Li
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, China
- Hainan Tropical Forensic Medicine Academician Workstation, Haikou, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, China
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Chen D, Cheng K, Wan L, Cui C, Li G, Zhao D, Yu Y, Liao X, Liu Y, D'Souza AW, Lian X, Sun J. Daily occupational exposure in swine farm alters human skin microbiota and antibiotic resistome. IMETA 2024; 3:e158. [PMID: 38868515 PMCID: PMC10989081 DOI: 10.1002/imt2.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 06/14/2024]
Abstract
Antimicrobial resistance (AMR) is a major threat to global public health, and antibiotic resistance genes (ARGs) are widely distributed across humans, animals, and environment. Farming environments are emerging as a key research area for ARGs and antibiotic resistant bacteria (ARB). While the skin is an important reservoir of ARGs and ARB, transmission mechanisms between farming environments and human skin remain unclear. Previous studies confirmed that swine farm environmental exposures alter skin microbiome, but the timeline of these changes is ill defined. To improve understanding of these changes and to determine the specific time, we designed a cohort study of swine farm workers and students through collected skin and environmental samples to explore the impact of daily occupational exposure in swine farm on human skin microbiome. Results indicated that exposure to livestock-associated environments where microorganisms are richer than school environment can reshape the human skin microbiome and antibiotic resistome. Exposure of 5 h was sufficient to modify the microbiome and ARG structure in workers' skin by enriching microorganisms and ARGs. These changes were preserved once formed. Further analysis indicated that ARGs carried by host microorganisms may transfer between the environment with workers' skin and have the potential to expand to the general population using farm workers as an ARG vector. These results raised concerns about potential transmission of ARGs to the broader community. Therefore, it is necessary to take corresponding intervention measures in the production process to reduce the possibility of ARGs and ARB transmission.
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Affiliation(s)
- Dong‐Rui Chen
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
- Veterinary CenterGuangxi State Farms Yongxin Animal Husbandry Group Co., Ltd.NanningChina
| | - Ke Cheng
- Veterinary CenterGuangxi State Farms Yongxin Animal Husbandry Group Co., Ltd.NanningChina
| | - Lei Wan
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Chao‐Yue Cui
- Laboratory Animal CentreWenzhou Medical UniversityWenzhouChina
| | - Gong Li
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Dong‐Hao Zhao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Yang Yu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Xiao‐Ping Liao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Ya‐Hong Liu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Alaric W. D'Souza
- Department of PediatricsBoston Children's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Xin‐Lei Lian
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
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Gul F, Herrema H, Davids M, Keating C, Nasir A, Ijaz UZ, Javed S. Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathog 2024; 16:5. [PMID: 38254227 PMCID: PMC10801943 DOI: 10.1186/s13099-024-00596-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC). METHODS 16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through [Formula: see text] test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment. RESULTS A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history. CONCLUSIONS This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings.
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Affiliation(s)
- Farzana Gul
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Mark Davids
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Ciara Keating
- School of Biodiversity, One Health & Veterinary Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Arshan Nasir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
- Moderna, Inc., Cambridge, MA, USA
| | - Umer Zeeshan Ijaz
- Water & Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, G11 6EW, UK.
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, L69 7BE, UK.
- National University of Ireland, Galway, University Road, Galway, H91 TK33, Ireland.
| | - Sundus Javed
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan.
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4
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Zeng X, Jin H, Wang C, Li M, Wang R, Li W, Lin F, Chen Y, Chen W, Huang X, Liu J, Zheng M, Jiang X, Chen Q. Establishment of a Standard Tongue Coating Collection Method for Microbiome Studies. Biopreserv Biobank 2023; 21:599-609. [PMID: 36730760 DOI: 10.1089/bio.2022.0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Objective: Recently, researchers have been focusing on characterizing the tongue coating microbiome from patients with digestive tract disease. However, to the best of our knowledge, the tongue coating collection methods have not been standardized until now. This article focuses on bridging this gap by exploring and validating the conditions suitable for the collection of tongue coating samples. Methods: One hundred forty-one healthy subjects were involved in the standardization of the tongue coating collection method. We conducted our standardization experiment by comparing different sampling tools, different preservation solutions, different scraping times, and different storage days with preservation at room temperature. The tongue coating samples from 59 normal individuals were analyzed using 16S ribosomal RNA (rRNA) gene-sequencing technology. The assessment of the quality of extracted DNA was used to verify our established method. We separated the 59 subjects into two groups (aged and younger), and the sequencing results were used to explore the age-related changes in microbiome. Results: Sterile oral swab B is suitable for the collection of tongue coating samples. To obtain a sufficient amount of DNA from a tongue coating sample, we recommend 30 times of tongue coating scraping. Normal saline, phosphate-buffered saline, and commercial preservation solution are all suitable for short-term sample storage (<1 hour). The commercial long-term preservation solution, which stores samples at room temperature (0 hour to 7 days) and can provide for fast commercial transportation, ensures the integrity of the sample DNA as well as the stability of the DNA quality. By using the established method, extracted DNA from all the 59 normal individuals' tongue coating samples passed an appropriate quality bar for microbiome studies. The average value of OD 260/280 is 1.72 ± 0.10; the average total DNA amount is 334.92 ng (±183.81 ng). The bacterial diversity of the tongue coating is increased and the bacterial community composition changes greatly in the NC group (aged normal subjects). Fusobacteriota is found as the dominant bacteria phyla in aged normal subjects with the 16S rRNA gene-sequencing technology. At the genus level, the relative abundance of Fusobacterium, Haemophilus, and Leptotrichia are significantly higher in aged individuals (all p < 0.05), and Neisseria, Streptococcus, and Porphyromonas are significantly higher in younger individuals (all p < 0.05). Conclusion: A participant-friendly tongue coating collection method for microbiome analyses can be established with good reliability and reproducibility. By taking advantage of our established method and 16S rRNA gene sequencing, significant differences were found in diversity and composition of tongue coating microbiota between aged and younger individuals, which contributes to a better understanding of the age-related composition of tongue coating microbiota.
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Affiliation(s)
- Xuan Zeng
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huihui Jin
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chuyang Wang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Man Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruohan Wang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wanhua Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fengye Lin
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weicheng Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoting Huang
- Medical Research Center, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Jun Liu
- Scientific Research Department, The First Affiliated Hospital of Shaoyang University, Shaoyang, China
| | - Mingzhu Zheng
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, China
| | - Xuanting Jiang
- Department of Scientific Research, Kangmeihuada GeneTech Co., Ltd., (KMHD), Shenzhen, China
| | - Qubo Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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5
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Siddiqui R, Badran Z, Boghossian A, Alharbi AM, Alfahemi H, Khan NA. The increasing importance of the oral microbiome in periodontal health and disease. Future Sci OA 2023; 9:FSO856. [PMID: 37621848 PMCID: PMC10445586 DOI: 10.2144/fsoa-2023-0062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/30/2023] [Indexed: 08/26/2023] Open
Abstract
Herein, the aim is to discuss the current knowledge of microbiome and periodontal diseases. Current treatment strategies include mechanical therapy such as root planing, scaling, deep pocket debridement and antimicrobial chemotherapy as an adjuvant therapy. Among promising therapeutic strategies, dental probiotics and oral microbiome transplantation have gained attention, and may be used to treat bacterial imbalances by competing with pathogenic bacteria for nutrients and adhesion surfaces, as well as probiotics targeting the gut microbiome. Development of strategies to prevent and treat periodontal diseases are warranted as both are highly prevalent and can affect human health. Further studies are necessary to better comprehend the microbiome in order to develop innovative preventative measures as well as efficacious therapies against periodontal diseases.
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Affiliation(s)
- Ruqaiyyah Siddiqui
- College of Arts & Sciences, American University of Sharjah, Sharjah, 26666, United Arab Emirates
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey
| | - Zahi Badran
- Periodontology Unit, Department of Preventive & Restorative Dentistry, College of Dental Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Anania Boghossian
- College of Arts & Sciences, American University of Sharjah, Sharjah, 26666, United Arab Emirates
| | - Ahmad M Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, 21944, Saudi Arabia
| | - Hasan Alfahemi
- Department of Medical Microbiology, Faculty of Medicine, Al-Baha University, Al-Baha, 65799, Saudi Arabia
| | - Naveed Ahmed Khan
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey
- Department of Clinical Sciences, College of Medicine, University of Sharjah, University City, Sharjah, United Arab Emirates
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6
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Yan D, Li M, Si W, Ni S, Liu X, Chang Y, Guo X, Wang J, Bai J, Chen Y, Jia H, Zhang T, Wu M, Song X, Tian Z, Yu L. Haze Exposure Changes the Skin Fungal Community and Promotes the Growth of Talaromyces Strains. Microbiol Spectr 2023; 11:e0118822. [PMID: 36507683 PMCID: PMC10269824 DOI: 10.1128/spectrum.01188-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
Haze pollution has been a public health issue. The skin microbiota, as a component of the first line of defense, is disturbed by environmental pollutants, which may have an impact on human health. A total of 74 skin samples from healthy students were collected during haze and nonhaze days in spring and winter. Significant differences of skin fungal community composition between haze and nonhaze days were observed in female and male samples in spring and male samples in winter based on unweighted UniFrac distance analysis. Phylogenetic diversity whole-tree indices and observed features were significantly increased during haze days in male samples in winter compared to nonhaze days, but no significant difference was observed in other groups. Dothideomycetes, Capnodiales, Mycosphaerellaceae, etc. were significantly enriched during nonhaze days, whereas Trichocomaceae, Talaromyces, and Pezizaceae were significantly enriched during haze days. Thus, five Talaromyces strains were isolated, and an in vitro culture experiment revealed that the growth of representative Talaromyces strains was increased at high concentrations of particulate matter, confirming the sequencing results. Furthermore, during haze days, the fungal community assembly was better fitted to a niche-based assembly model than during nonhaze days. Talaromyces enriched during haze days deviated from the neutral assembly process. Our findings provided a comprehensive characterization of the skin fungal community during haze and nonhaze days and elucidated novel insights into how haze exposure influences the skin fungal community. IMPORTANCE Skin fungi play an important role in human health. Particulate matter (PM), the main haze pollutant, has been a public environmental threat. However, few studies have assessed the effects of air pollutants on skin fungi. Here, haze exposure influenced the diversity and composition of the skin fungal community. In an in vitro experiment, a high concentration of PM promoted the growth of Talaromyces strains. The fungal community assembly is better fitted to a niche-based assembly model during haze days. We anticipate that this study may provide new insights on the role of haze exposure disturbing the skin fungal community. It lays the groundwork for further clarifying the association between the changes of the skin fungal community and adverse health outcomes. Our study is the first to report the changes in the skin fungal community during haze and nonhaze days, which expands the understanding of the relationship between haze and skin fungi.
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Affiliation(s)
- Dong Yan
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Min Li
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Wenhao Si
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
- Department of Dermatology, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Shijun Ni
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xin Liu
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yahan Chang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiaochan Guo
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Jingjing Wang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Jie Bai
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yuanhang Chen
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Haoyue Jia
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Minna Wu
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiangfeng Song
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhongwei Tian
- Department of Dermatology, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Liyan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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7
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The dynamic balance of the skin microbiome across the lifespan. Biochem Soc Trans 2023; 51:71-86. [PMID: 36606709 PMCID: PMC9988004 DOI: 10.1042/bst20220216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
For decades research has centered on identifying the ideal balanced skin microbiome that prevents disease and on developing therapeutics to foster this balance. However, this single idealized balance may not exist. The skin microbiome changes across the lifespan. This is reflected in the dynamic shifts of the skin microbiome's diverse, inter-connected community of microorganisms with age. While there are core skin microbial taxa, the precise community composition for any individual person is determined by local skin physiology, genetics, microbe-host interactions, and microbe-microbe interactions. As a key interface with the environment, the skin surface and its appendages are also constantly exchanging microbes with close personal contacts and the environment. Hormone fluctuations and immune system maturation also drive age-dependent changes in skin physiology that support different microbial community structures over time. Here, we review recent insights into the factors that shape the skin microbiome throughout life. Collectively, the works summarized within this review highlight how, depending on where we are in lifespan, our skin supports robust microbial communities, while still maintaining microbial features unique to us. This review will also highlight how disruptions to this dynamic microbial balance can influence risk for dermatological diseases as well as impact lifelong health.
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8
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Gaike AH, Kalamkar SD, Gajjar V, Divate U, Karandikar-Iyer S, Goel P, Shouche YS, Ghaskadbi SS. Effect of long-term oral glutathione supplementation on gut microbiome of type 2 diabetic individuals. FEMS Microbiol Lett 2023; 370:fnad116. [PMID: 37935462 DOI: 10.1093/femsle/fnad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
The aim of this study was to check the effect of long-term oral glutathione (GSH) supplementation on alteration in gut microbiome of Indian diabetic individuals. Early morning fresh stool sample of diabetic individuals recruited in a randomized clinical trial wherein they were given 500 mg GSH supplementation orally once a day for a period of 6 months was collected and gut microbiome was analysed using high throughput 16S rRNA metagenomic sequencing. Long-term GSH supplementation as reported in our earlier work showed significant increase in body stores of GSH and stabilized decreased glycated haemoglobin (HbA1c). Analysis of gut microbiome revealed that abundance of phylum Proteobacteria significantly decreased (P < 0.05) in individuals with GSH supplementation after 6 months compared to those without it. Beneficial dominant genera such as Megasphaera, Bacteroides, and Megamonas were found to be significantly enriched (P < 0.05), while pathogenic Escherichia/Shigella was found to be depleted (P < 0.05) after supplementation. Data clearly demonstrate that GSH supplementation along with antidiabetic treatment helps restore the gut microbiome by enriching beneficial bacteria of healthy gut and reducing significantly the load of pathogenic bacteria of diabetic gut.
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Affiliation(s)
- Akshay H Gaike
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
- National Centre for Cell Science, Pune 411007, India
| | - Saurabh D Kalamkar
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| | | | | | | | - Pranay Goel
- Biology Division, Indian Institute of Science Education and Research, Pune 411008, India
| | - Yogesh S Shouche
- National Centre for Cell Science, Pune 411007, India
- SKAN Research Trust, Bengaluru 560034, India
| | - Saroj S Ghaskadbi
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
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9
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D'Aloisio LD, Shetty V, Ballal M, Gibson DL. Following the Indian Immigrant: adoption of westernization results in a western gut microbiome and an increased risk of inflammatory bowel diseases. FEMS Microbiol Ecol 2022; 98:6825449. [PMID: 36370451 DOI: 10.1093/femsec/fiac133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/01/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
Abstract
Indians who migrate to westernized countries such as Canada, the USA, and the UK are at an increased risk of developing inflammatory bowel disease (IBD). While the underlying aetiology of IBD remains unclear, a gut microbiome, i.e. no longer symbiotic with its host, is a major player. Increasing IBD incidence in Indian immigrants may be due to the adoption of western practices that result in loss of tolerance of a symbiotic community in the gut and its underlying immune responses. However, little is known about the microbial changes in the Indian gut, including shifts in the microbiome when they migrate to westernized countries. In this Current Opinion, we discuss what is known about the Indian gut microbiome and how living in a westernized environment may be impeding what was once a symbiotic relationship with their gut microbiome and intestinal mucosae, which may be the driving factor in their increased risk of IBD.
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Affiliation(s)
- Leah D D'Aloisio
- Department of Biology, University of British Columbia- Okanagan Campus, V1V 1V7 Kelowna, Canada
| | - Vignesh Shetty
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, 576104 Manipal, India.,Department of Medicine, University of Cambridge, CB2 2QQ Cambridge, United Kingdom
| | - Mamatha Ballal
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, 576104 Manipal, India
| | - Deanna L Gibson
- Department of Biology, University of British Columbia- Okanagan Campus, V1V 1V7 Kelowna, Canada.,Department of Medicine, University of British Columbia- Okanagan Campus, V1V 1V7 Kelowna, Canada
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10
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Poulsen CS, Nygaard N, Constancias F, Stankevic E, Kern T, Witte DR, Vistisen D, Grarup N, Pedersen OB, Belstrøm D, Hansen T. Association of general health and lifestyle factors with the salivary microbiota - Lessons learned from the ADDITION-PRO cohort. Front Cell Infect Microbiol 2022; 12:1055117. [PMID: 36467723 PMCID: PMC9709502 DOI: 10.3389/fcimb.2022.1055117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/24/2022] [Indexed: 07/20/2023] Open
Abstract
INTRODUCTION Previous research indicates that the salivary microbiota may be a biomarker of oral as well as systemic disease. However, clarifying the potential bias from general health status and lifestyle-associated factors is a prerequisite of using the salivary microbiota for screening. MATERIALS & METHODS ADDDITION-PRO is a nationwide Danish cohort, nested within the Danish arm of the Anglo-Danish-Dutch Study of Intensive treatment in People with Screen-Detected Diabetes in Primary Care. Saliva samples from n=746 individuals from the ADDITION-PRO cohort were characterized using 16s rRNA sequencing. Alpha- and beta diversity as well as relative abundance of genera was examined in relation to general health and lifestyle-associated variables. Permutational multivariate analysis of variance (PERMANOVA) was performed on individual variables and all variables together. Classification models were created using sparse partial-least squares discriminant analysis (sPLSDA) for variables that showed statistically significant differences based on PERMANOVA analysis (p < 0.05). RESULTS Glycemic status, hemoglobin-A1c (HbA1c) level, sex, smoking and weekly alcohol intake were found to be significantly associated with salivary microbial composition (individual variables PERMANOVA, p < 0.05). Collectively, these variables were associated with approximately 5.8% of the observed differences in the composition of the salivary microbiota. Smoking status was associated with 3.3% of observed difference, and smoking could be detected with good accuracy based on salivary microbial composition (AUC 0.95, correct classification rate 79.6%). CONCLUSIONS Glycemic status, HbA1c level, sex, smoking and weekly alcohol intake were significantly associated with the composition of the salivary microbiota. Despite smoking only being associated with 3.3% of the difference in overall salivary microbial composition, it was possible to create a model for detection of smoking status with a high correct classification rate. However, the lack of information on the oral health status of participants serves as a limitation in the present study. Further studies in other cohorts are needed to validate the external validity of these findings.
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Affiliation(s)
- Casper Sahl Poulsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Nikoline Nygaard
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
- Institute of Odontology, Section of Oral Microbiology, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Florentin Constancias
- Swiss Federal Institute of Technology in Zürich, Department of Health Sciences and Technology, Zürich, Switzerland
| | - Evelina Stankevic
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Timo Kern
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Daniel R. Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus, Denmark
| | - Dorte Vistisen
- Steno Diabetes Center, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Oluf Borbye Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
- Center for Clinical Metabolic Research, Herlev-Gentofte Hospital, Gentofte, Denmark
| | - Daniel Belstrøm
- Institute of Odontology, Section of Oral Microbiology, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
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11
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Saleem A, Ikram A, Dikareva E, Lahtinen E, Matharu D, Pajari AM, de Vos WM, Hasan F, Salonen A, Jian C. Unique Pakistani gut microbiota highlights population-specific microbiota signatures of type 2 diabetes mellitus. Gut Microbes 2022; 14:2142009. [PMID: 36322821 PMCID: PMC9635555 DOI: 10.1080/19490976.2022.2142009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Biogeographic variations in the gut microbiota are pivotal to understanding the global pattern of host-microbiota interactions in prevalent lifestyle-related diseases. Pakistani adults, having an exceptionally high prevalence of type 2 diabetes mellitus (T2D), are one of the most understudied populations in microbiota research to date. The aim of the present study is to examine the gut microbiota across individuals from Pakistan and other populations of non-industrialized and industrialized lifestyles with a focus on T2D. The fecal samples from 94 urban-dwelling Pakistani adults with and without T2D were profiled by bacterial 16S ribosomal RNA gene and fungal internal transcribed spacer (ITS) region amplicon sequencing and eubacterial qPCR, and plasma samples quantified for circulating levels of lipopolysaccharide-binding protein (LBP) and the activation ability of Toll-like receptor (TLR)-signaling. Publicly available datasets generated with comparable molecular methods were retrieved for comparative analysis of the bacterial microbiota. Overall, urbanized Pakistanis' gut microbiota was similar to that of transitional or non-industrialized populations, depleted in Akkermansiaceae and enriched in Prevotellaceae (dominated by the non-Westernized clades of Prevotella copri). The relatively high proportion of Atopobiaceae appeared to be a unique characteristic of the Pakistani gut microbiota. The Pakistanis with T2D had elevated levels of LBP and TLR-signaling in circulation as well as gut microbial signatures atypical of other populations, e.g., increased relative abundance of Libanicoccus/Parolsenella, limiting the inter-population extrapolation of gut microbiota-based classifiers for T2D. Taken together, our findings call for a more global representation of understudied populations to extend the applicability of microbiota-based diagnostics and therapeutics.
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Affiliation(s)
- Afshan Saleem
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan,Department of Microbiology, Faculty of Basic and Applied Sciences, University of Haripur, Haripur, Pakistan
| | - Aamer Ikram
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Evgenia Dikareva
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Emilia Lahtinen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Dollwin Matharu
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anne-Maria Pajari
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Fariha Hasan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ching Jian
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,CONTACT Ching Jian Haartmaninkatu 3, PO box 21, FI-00014Helsinki, Finland
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12
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Reynoso-García J, Miranda-Santiago AE, Meléndez-Vázquez NM, Acosta-Pagán K, Sánchez-Rosado M, Díaz-Rivera J, Rosado-Quiñones AM, Acevedo-Márquez L, Cruz-Roldán L, Tosado-Rodríguez EL, Figueroa-Gispert MDM, Godoy-Vitorino F. A complete guide to human microbiomes: Body niches, transmission, development, dysbiosis, and restoration. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:951403. [PMID: 38993286 PMCID: PMC11238057 DOI: 10.3389/fsysb.2022.951403] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Humans are supra-organisms co-evolved with microbial communities (Prokaryotic and Eukaryotic), named the microbiome. These microbiomes supply essential ecosystem services that play critical roles in human health. A loss of indigenous microbes through modern lifestyles leads to microbial extinctions, associated with many diseases and epidemics. This narrative review conforms a complete guide to the human holobiont-comprising the host and all its symbiont populations- summarizes the latest and most significant research findings in human microbiome. It pretends to be a comprehensive resource in the field, describing all human body niches and their dominant microbial taxa while discussing common perturbations on microbial homeostasis, impacts of urbanization and restoration and humanitarian efforts to preserve good microbes from extinction.
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Affiliation(s)
| | | | | | - Kimil Acosta-Pagán
- Department of Microbiology and Medical Zoology, UPR School of Medicine, San Juan, PR, United States
| | - Mitchell Sánchez-Rosado
- Department of Microbiology and Medical Zoology, UPR School of Medicine, San Juan, PR, United States
| | - Jennifer Díaz-Rivera
- Department of Microbiology and Medical Zoology, UPR School of Medicine, San Juan, PR, United States
| | - Angélica M. Rosado-Quiñones
- Department of Biology, UPR Rio Piedras Campus, San Juan, PR, United States
- Department of Microbiology and Medical Zoology, UPR School of Medicine, San Juan, PR, United States
| | - Luis Acevedo-Márquez
- Department of Microbiology and Medical Zoology, UPR School of Medicine, San Juan, PR, United States
| | - Lorna Cruz-Roldán
- Department of Microbiology and Medical Zoology, UPR School of Medicine, San Juan, PR, United States
| | | | | | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, UPR School of Medicine, San Juan, PR, United States
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13
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Brain Natriuretic Peptide (BNP) Affects Growth and Stress Tolerance of Representatives of the Human Microbiome, Micrococcus luteus C01 and Alcaligenes faecalis DOS7. BIOLOGY 2022; 11:biology11070984. [PMID: 36101364 PMCID: PMC9311935 DOI: 10.3390/biology11070984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary The body of an average person weighing 70 kg contains approximately 39 trillion bacterial cells, which densely inhabit the gastrointestinal tract, skin, mucous membranes, etc. Bacteria respond to the signaling molecules in the human body, regulate the expression of the necessary genes, and thus adapt to the physiology of the host. Signaling molecules include hormones, neurotransmitters, immune system molecules, as well as natriuretic peptides, which are involved in the regulation of the circulatory system, water and electrolyte metabolism, and adipose tissue metabolism. Brain natriuretic peptide (BNP) is secreted by the ventricles during congestion and signals heart failure. This study showed that the presence of BNP in the growth medium of human symbiont bacteria affects their growth characteristics, survival, and stress resistance, including antibiotic resistance. It was concluded that bacterial populations that develop in a healthy person at a BNP level of up to 250 pg/mL will be more stress resistant than in a person suffering from heart failure. Our findings are promising to be used both in clinical medical practice and in the production of bacterial preparations for cosmetology, agriculture, and waste management. Abstract Brain natriuretic peptide (BNP) is secreted by the ventricles of the heart during overload to signal heart failure. Slight bilateral skin itching induced by BNP has been associated with response activity of the skin microbiota. In this work, we studied the effect of 25–250,000 pg BNP/mL on the growth, long-term survival, and stress (H2O2, antibiotics, salinity, heat and pH shock) resistance of human symbiont bacteria: Gram-positive Micrococcus luteus C01 and Gram-negative Alcaligenes faecalis DOS7. The effect of BNP turned out to be dose-dependent. Up to 250 pg BNP/mL made bacteria more stress resistant. At 2500 pg BNP/mL (heart failure) the thermosensitivity of the bacteria increased. Almost all considered BNP concentrations increased the resistance of bacteria to the action of tetracycline and ciprofloxacin. Both bacteria survived 1.3–1.7 times better during long-term (up to 4 months) storage. Our findings are important both for clinical medical practice and for practical application in other areas. For example, BNP can be used to obtain stress-resistant bacteria, which is important in the collection of microorganisms, as well as for the production of bacterial preparations and probiotics for cosmetology, agriculture, and waste management.
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14
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Li Z, Liu Y, Zhang L. Role of the microbiome in oral cancer occurrence, progression and therapy. Microb Pathog 2022; 169:105638. [PMID: 35718272 DOI: 10.1016/j.micpath.2022.105638] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 02/07/2023]
Abstract
The oral cavity, like other digestive or mucosal sites, contains a site-specific microbiome that plays a significant role in maintaining health and homeostasis. Strictly speaking, the gastrointestinal tract starts from the oral cavity, with special attention paid to the specific flora of the oral cavity. In healthy people, the microbiome of the oral microenvironment is governed by beneficial bacteria, that benefit the host by symbiosis. When a microecological imbalance occurs, changes in immune and metabolic signals affect the characteristics of cancer, as well as chronic inflammation, disruption of the epithelial barrier, changes in cell proliferation and cell apoptosis, genomic instability, angiogenesis, and epithelial barrier destruction and metabolic regulation. These pathophysiological changes could result in oral cancer. Rising evidence suggests that oral dysbacteriosis and particular microbes may play a positive role in the evolution, development, progression, and metastasis of oral cancer, for instance, oral squamous cell carcinoma (OSCC) through direct or indirect action.
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Affiliation(s)
- Zhengrui Li
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, China.
| | - Yuan Liu
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, China.
| | - Ling Zhang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, China.
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15
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Herremans KM, Riner AN, Cameron ME, McKinley KL, Triplett EW, Hughes SJ, Trevino JG. The oral microbiome, pancreatic cancer and human diversity in the age of precision medicine. MICROBIOME 2022; 10:93. [PMID: 35701831 PMCID: PMC9199224 DOI: 10.1186/s40168-022-01262-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 03/23/2022] [Indexed: 05/09/2023]
Abstract
Pancreatic cancer is a deadly disease with limited diagnostic and treatment options. Not all populations are affected equally, as disparities exist in pancreatic cancer prevalence, treatment and outcomes. Recently, next-generation sequencing has facilitated a more comprehensive analysis of the human oral microbiome creating opportunity for its application in precision medicine. Oral microbial shifts occur in patients with pancreatic cancer, which may be appreciated years prior to their diagnosis. In addition, pathogenic bacteria common in the oral cavity have been found within pancreatic tumors. Despite these findings, much remains unknown about how or why the oral microbiome differs in patients with pancreatic cancer. As individuals develop, their oral microbiome reflects both their genotype and environmental influences. Genetics, race/ethnicity, smoking, socioeconomics and age affect the composition of the oral microbiota, which may ultimately play a role in pancreatic carcinogenesis. Multiple mechanisms have been proposed to explain the oral dysbiosis found in patients with pancreatic cancer though they have yet to be confirmed. With a better understanding of the interplay between the oral microbiome and pancreatic cancer, improved diagnostic and therapeutic approaches may be implemented to reduce healthcare disparities. Video Abstract.
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Affiliation(s)
- Kelly M. Herremans
- Department of Surgery, University of Florida College of Medicine, P.O. Box 100286, Gainesville, FL 32610 USA
| | - Andrea N. Riner
- Department of Surgery, University of Florida College of Medicine, P.O. Box 100286, Gainesville, FL 32610 USA
| | - Miles E. Cameron
- Department of Surgery, University of Florida College of Medicine, P.O. Box 100286, Gainesville, FL 32610 USA
| | - Kelley L. McKinley
- Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, FL 32611-0700 USA
| | - Eric W. Triplett
- Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, FL 32611-0700 USA
| | - Steven J. Hughes
- Department of Surgery, University of Florida College of Medicine, P.O. Box 100286, Gainesville, FL 32610 USA
| | - Jose G. Trevino
- Division of Surgical Oncology, Virginia Commonwealth University, 1200 E Broad St, Richmond, VA 23298-0645 USA
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16
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Zhou R, Qian S, Cho WCS, Zhou J, Jin C, Zhong Y, Wang J, Zhang X, Xu Z, Tian M, Chan LWC, Zhang H. Microbiota-microglia connections in age-related cognition decline. Aging Cell 2022; 21:e13599. [PMID: 35349746 PMCID: PMC9124309 DOI: 10.1111/acel.13599] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/08/2022] [Accepted: 03/13/2022] [Indexed: 12/13/2022] Open
Abstract
Aging is an inevitable process that all individuals experience, of which the extent differs among individuals. It has been recognized as the risk factor of neurodegenerative diseases by affecting gut microbiota compositions, microglia, and cognition abilities. Aging‐induced changes in gut microbiota compositions have a critical role in orchestrating the morphology and functions of microglia through the gut‐brain axis. Gut microbiota communicates with microglia by its secreted metabolites and neurotransmitters. This is highly associated with age‐related cognitive declines. Here, we review the main composition of microbiota in the aged individuals, outline the changes of the brain in age‐related cognitive decline from a neuroinflammation perspective, especially the changes of morphology and functions of microglia, discuss the crosstalk between microbiota and microglia in the aged brain and further highlight the role of microbiota‐microglia connections in neurodegenerative diseases (Alzheimer's disease and Parkinson's disease).
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Affiliation(s)
- Rui Zhou
- Department of Nuclear Medicine and Medical PET Center The Second Affiliated Hospital of Zhejiang University School of Medicine Hangzhou China
- Department of Health Technology and Informatics The Hong Kong Polytechnic University Hong Kong SAR China
| | - Shufang Qian
- Department of Nuclear Medicine and Medical PET Center The Second Affiliated Hospital of Zhejiang University School of Medicine Hangzhou China
| | - William C. S. Cho
- Department of Clinical Oncology Queen Elizabeth Hospital Hong Kong SAR China
| | - Jinyun Zhou
- Department of Nuclear Medicine and Medical PET Center The Second Affiliated Hospital of Zhejiang University School of Medicine Hangzhou China
| | - Chentao Jin
- Department of Nuclear Medicine and Medical PET Center The Second Affiliated Hospital of Zhejiang University School of Medicine Hangzhou China
| | - Yan Zhong
- Department of Nuclear Medicine and Medical PET Center The Second Affiliated Hospital of Zhejiang University School of Medicine Hangzhou China
| | - Jing Wang
- Department of Nuclear Medicine and Medical PET Center The Second Affiliated Hospital of Zhejiang University School of Medicine Hangzhou China
| | - Xiaohui Zhang
- Department of Nuclear Medicine and Medical PET Center The Second Affiliated Hospital of Zhejiang University School of Medicine Hangzhou China
| | - Zhoujiao Xu
- Department of Nuclear Medicine and Medical PET Center The Second Affiliated Hospital of Zhejiang University School of Medicine Hangzhou China
| | - Mei Tian
- Department of Nuclear Medicine and Medical PET Center The Second Affiliated Hospital of Zhejiang University School of Medicine Hangzhou China
| | - Lawrence W. C. Chan
- Department of Health Technology and Informatics The Hong Kong Polytechnic University Hong Kong SAR China
| | - Hong Zhang
- Department of Nuclear Medicine and Medical PET Center The Second Affiliated Hospital of Zhejiang University School of Medicine Hangzhou China
- Key Laboratory for Biomedical Engineering of Ministry of Education Zhejiang University Hangzhou China
- The College of Biomedical Engineering and Instrument Science of Zhejiang University Hangzhou China
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17
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Liu K, Kong XJ. Altered Salivary Microbiota Following Bifidobacterium animalis Subsp. Lactis BL-11 Supplementation Are Associated with Anthropometric Growth and Social Behavior Severity in Individuals with Prader-Willi Syndrome. Probiotics Antimicrob Proteins 2022; 14:699-711. [PMID: 35474569 PMCID: PMC9246814 DOI: 10.1007/s12602-022-09938-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2022] [Indexed: 12/04/2022]
Abstract
To evaluate the influence of oral probiotic Bifidobacterium animalis subsp. lactis (BL-11) supplementation on salivary microbiota composition and the association with growth parameters, and behavioral symptoms in individuals with Prader-Willi syndrome (PWS). In this post hoc analysis, we included a subset of 36 PWS patients with available saliva samples from our original randomized, double-blinded, placebo-controlled trial (Chinese Clinical Trial Registry, ChiCTR1900022646, April 20, 2019). Among the 36 subjects, 17 subjects were allocated to the probiotic group for daily use of the BL-11 probiotic and 19 subjects were allocated to the placebo group. Groupwise and longitudinal differences in salivary microbiota abundances, biodiversity metrics, and height were analyzed. Linear correlations were found between identified differentially abundant salivary microbiota and clinical parameters. Salivary microbiome α-diversity was found to be higher in the probiotic-treated group at week 12 relative to placebo controls (P < 0.05). Leptotrichia, Paracoccus, and Faecalibacterium were found to be more abundant in the probiotic-treated group (P < 0.05). Salivary microbiota abundance and predicted functional profiling abundance correlations were found to be associated with anti-inflammation, anti-obesity, toxin degradation, and anti-oxidative injury effects (Q < 0.1). Several oral taxa also displayed correlations with social behavior severity scores in the probiotic-treated group (Q < 0.1). The findings suggest novel salivary microbiota compositional changes in response to the oral supplementation of BL-11 probiotic in individuals with PWS. The observed differentially abundant taxa between groups post-treatment were highly correlated with interventional effects on growth and social behaviors, although further investigation is warranted. Clinical Trial Registration The original clinical trial was registered under the Chinese Clinical Trial Registry with registration number ChiCTR1900022646 (April 20, 2019).
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Affiliation(s)
- Kevin Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street, Charlestown, Boston, MA, 02129, USA
| | - Xue-Jun Kong
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street, Charlestown, Boston, MA, 02129, USA. .,Department of Medicine and Psychiatry, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
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18
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Potbhare R, RaviKumar A, Munukka E, Lahti L, Ashma R. Skin microbiota diversity among genetically unrelated individuals of Indian origin. PeerJ 2022; 10:e13075. [PMID: 35313523 PMCID: PMC8934042 DOI: 10.7717/peerj.13075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
Background Human skin harbors complex transient and resident microbial communities that show intra- & inter-individual variation due to various environmental and host-associated factors such as skin site, diet, age, gender, genetics, or the type and use of cosmetics. This variation remains largely uncharacterized in the Indian population; hence, the present study aims to characterize the variation in skin microbiota among individuals of Indian origin and quantify associations with age, diet, and geography. Methods Axillary sweat samples from genetically unrelated individuals (N = 58) residing in the three geographical locations of Maharashtra, India, were collected using a sterile cotton swab. Bacterial DNA was extracted using a standard protocol and checked for quality. Variable regions (V3-V4) of the 16S rRNA gene were sequenced using the Illumina platform. We used standard methods from microbiota bioinformatics, including alpha and beta diversity, community typing, and differential abundance, to quantify the association of skin microbiota with age, diet, and geographical location. Results Our study indicated the prevalence of phyla- Firmicutes, Proteobacteria, and Actinobacteria, consistent with previous reports on skin microbiota composition of the world population level. The alpha diversity (Shannon index) was significantly associated with the age group (Kruskal-Wallis test, p = 0.02), but not with geography (p = 0.62) or diet (p = 0.74). The overall skin microbiota community composition was significantly associated with geographical location based on Community State Types (CST) analysis and PERMANOVA (R2 = 0.07, p = 0.01). Differential abundance analysis at the genus level indicated a distinctively high abundance of Staphylococcus and Corynebacterium among individuals of the Pune district. Pseudomonas and Anaerococcus were abundant in individuals from Ahmednagar whereas, Paenibacillus, Geobacillus, Virgibacillus, Jeotgalicoccus, Pullulanibacillus, Delsulfosporomusa, Citinovibrio, and Calditerricola were abundant in individuals from Nashik district. Conclusion Our work provides one of the first characterizations of skin microbiota variation in different sub-populations in India. The analysis quantifies the level of individuality, as contrasted to the other factors of age, geography, and diet, thus helping to evaluate the applicability of skin microbiota profiles as a potential biomarker to stratify individuals.
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Affiliation(s)
- Renuka Potbhare
- Department of Zoology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ameeta RaviKumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Eveliina Munukka
- Microbiome Biobank, Institute of Biomedicine, University of Turku, Turku, Finland,Biocodex Nordics, Finland
| | - Leo Lahti
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
| | - Richa Ashma
- Department of Zoology, Savitribai Phule Pune University, Pune, Maharashtra, India
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19
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Awad A, Madla CM, McCoubrey LE, Ferraro F, Gavins FK, Buanz A, Gaisford S, Orlu M, Siepmann F, Siepmann J, Basit AW. Clinical translation of advanced colonic drug delivery technologies. Adv Drug Deliv Rev 2022; 181:114076. [PMID: 34890739 DOI: 10.1016/j.addr.2021.114076] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/26/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
Targeted drug delivery to the colon offers a myriad of benefits, including treatment of local diseases, direct access to unique therapeutic targets and the potential for increasing systemic drug bioavailability and efficacy. Although a range of traditional colonic delivery technologies are available, these systems exhibit inconsistent drug release due to physiological variability between and within individuals, which may be further exacerbated by underlying disease states. In recent years, significant translational and commercial advances have been made with the introduction of new technologies that incorporate independent multi-stimuli release mechanisms (pH and/or microbiota-dependent release). Harnessing these advanced technologies offers new possibilities for drug delivery via the colon, including the delivery of biopharmaceuticals, vaccines, nutrients, and microbiome therapeutics for the treatment of both local and systemic diseases. This review details the latest advances in colonic drug delivery, with an emphasis on emerging therapeutic opportunities and clinical technology translation.
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20
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Ahrodia T, Das S, Bakshi S, Das B. Structure, functions, and diversity of the healthy human microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 191:53-82. [DOI: 10.1016/bs.pmbts.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Putative Familial Transmissible Bacteria of Various Body Niches Link with Home Environment and Children's Immune Health. Microbiol Spectr 2021; 9:e0087221. [PMID: 34878304 PMCID: PMC8653841 DOI: 10.1128/spectrum.00872-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Owing to their significant impact on children's long-term health, familial factors in the microbiomes of children have attracted increasing attention. However, the mechanism underlying microbiome transmission across generations remains unclear. A significantly lower alpha diversity was observed in the gut flora of children than in the gut flora of parents and grandparents; the alpha diversity of oral and skin microbiota was relatively higher in children than in their predecessors. Gut, oral, and skin microbiome was more similar between family members than between unrelated individuals. Meanwhile, 55.05%, 61.09%, and 76.73% of amplicon sequence variants (ASVs) in children's gut, oral, and skin microbiomes, respectively, were transmitted from all family members. Among these, the most transmissible ASVs belonged to Methylophilaceae, Solimonadaceae, Neisseriaceae, and Burkholderiaceae, which were defined as "putative familial transmissible bacteria." Furthermore, we found that the time spent with parents/grandparents and children's dietary preferences were important factors that influenced the proportion of the transmissible microbiome. Moreover, the majority of transmissible ASVs (85.06%), especially those of Ruminococcaceae and Lachnospiraceae, were significantly associated with the immune indices, such as CD3+, CD4+, CD8+, IgG, and IgA. IMPORTANCE Our study revealed that the children's microbiota was partially transmitted from their family members and specific putative transmissible ASVs were associated with the immune system of children. These findings suggest that home life plays a key role in the shaping of young children's microbiomes and has long-term health benefits.
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22
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Li Y, Ma H, Xue L, Chen H, Pang R, Shang Y, Luo J, Xie X, Zhang J, Ding Y, Chen M, Wang J, Wu Q. Imbalanced Dermic Microbiome Aggravates Inflammation in Toenail Paronychia. Front Cell Infect Microbiol 2021; 11:781927. [PMID: 34926325 PMCID: PMC8677670 DOI: 10.3389/fcimb.2021.781927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022] Open
Abstract
The commensal microbiome influences skin immunity, but its function in toenail health remains unclear. Paronychia is one of the most common inflammatory toenail diseases, but antibiotic treatment is seldom effective in clinical cases. In this study, we performed 16S rRNA sequencing to investigate the characteristics of microbes associated with paronychia in order to identify the key microorganisms involved in inflammation. Seventy dermic samples were collected from patients with paronychia and the differences in dermic microbiota were analyzed in patients with different inflammation severities. Distinct clustering of dermal microbiota was observed in the dermis with different inflammation severities. A higher relative abundance of anaerobic microorganisms such as Parvimona, Prevotella, and Peptoniphilus was observed in severe paronychia, whereas Lactobacillus disappeared with disease progression. Co-occurring network analysis suggested that the disturbance of the dermic microbiome and attenuation of antagonism by Lactobacillus against anaerobic pathogens may aggravate inflammation in paronychia. Functional analysis showed that dermic microbiome disturbance may worsen microbial metabolism and tissue repair in the skin. In conclusion, we revealed that an increased abundance of anaerobic microorganisms and loss of Lactobacillus in the dermis may promote paronychia progression and microbiological imbalance may aggravate inflammation in patients with paronychia.
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Affiliation(s)
- Ying Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Han Ma
- Department of Dermatology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Huizhen Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yanyan Shang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Juan Luo
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinqiang Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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23
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Lee H, Jeong J, Oh Y, Lee CJ, Mun S, Lee DG, Jo H, Heo YM, Baek C, Heo CY, Kang SM, Han K. Comparative analysis of human facial skin microbiome between topical sites compared to entire face. Genes Genomics 2021; 43:1483-1495. [PMID: 34734352 DOI: 10.1007/s13258-021-01180-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Skin is an essential outer barrier and supports the growth of commensal microorganisms that protects a host from the offense of foreign toxic organisms. With the rapid development of next-generation sequencing (NGS)-based applications, skin microbiome research for facial health care has reached industry growth, such as therapy and cosmetic product development. Despite the acceleration of skin microbiome research, experimental standardization protocol has not yet been established in the facial site and method of sampling. OBJECTIVE Thus, we aimed to investigate the differences in microbial composition at each facial site (cheek, mouth, forehead, and entire face) using comprehensive microbiome analysis. METHODS Twelve specimens from three men (four specimens per one person) were collected. The hypervariable regions (V3-V4) of the bacterial 16S rRNA gene were targeted for 16S amplicon library construction and classification of bacterial taxonomy. Skin microbial composition for all specimens was investigated, and the differences site-by-site in skin microbial composition were analyzed and evaluated by the various statistical tests. RESULTS We were able to validate the independent correlation between the skin microbiome composition and the facial sites. The cheek site showed the highest alpha-diversity in richness and evenness scores compared to the forehead and mouth. The cheek and mouth sites showed a positive correlation (R2 value > 0.93) with the entire face, while the forehead sites were negatively correlated (R2 value < 0.2). Given the relative abundance based on statistical correlation analysis, we estimated that the cheek site could be considered an optimal topical site to replace the entire face. CONCLUSION Our study suggests that skin microbiome profiling of four facial sites confirms that the cheek shows the most similar skin flora with the entire face. This study would be informative for preventing bias caused by sampling methods before researching and understanding skin cosmetics development or skin diseases.
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Affiliation(s)
- Haeun Lee
- Department of Bioconvergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Jinuk Jeong
- Department of Bioconvergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Yunseok Oh
- Department of Bioconvergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Cherl-Jun Lee
- Department of Bioconvergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Dong-Geol Lee
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - HyungWoo Jo
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Young Mok Heo
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Chaeyun Baek
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Chan Yeong Heo
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Bundang-gu, Seongnam, 13620, Republic of Korea.,H&BIO Corporation/R&D CENTER, Bundang-gu, Seongnam, 13605, Republic of Korea
| | - So Min Kang
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Bundang-gu, Seongnam, 13620, Republic of Korea.,H&BIO Corporation/R&D CENTER, Bundang-gu, Seongnam, 13605, Republic of Korea
| | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea. .,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. .,Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
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24
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Jani K, Bandal J, Shouche Y, Shafi S, Azhar EI, Zumla A, Sharma A. Extended Ecological Restoration of Bacterial Communities in the Godavari River During the COVID-19 Lockdown Period: a Spatiotemporal Meta-analysis. MICROBIAL ECOLOGY 2021; 82:365-376. [PMID: 34219185 PMCID: PMC8255117 DOI: 10.1007/s00248-021-01781-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/20/2021] [Indexed: 05/04/2023]
Abstract
The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz. Proteobacteria (70.6%), Bacteroidetes (22.5%), Verrucomicrobia (1.8%), Actinobacteria (1.2%) and Cyanobacteria (1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by - 0.71-fold and - 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.
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Affiliation(s)
- Kunal Jani
- DBT-National Centre for Cell Science, Pune, India
| | | | | | - Shuja Shafi
- Mass Gatherings and Global Health Network, London, UK
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, and Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alimuddin Zumla
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
- NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, UK
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25
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McCoubrey LE, Gaisford S, Orlu M, Basit AW. Predicting drug-microbiome interactions with machine learning. Biotechnol Adv 2021; 54:107797. [PMID: 34260950 DOI: 10.1016/j.biotechadv.2021.107797] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
Pivotal work in recent years has cast light on the importance of the human microbiome in maintenance of health and physiological response to drugs. It is now clear that gastrointestinal microbiota have the metabolic power to promote, inactivate, or even toxify the efficacy of a drug to a level of clinically relevant significance. At the same time, it appears that drug intake has the propensity to alter gut microbiome composition, potentially affecting health and response to other drugs. Since the precise composition of an individual's microbiome is unique, one's drug-microbiome relationship is similarly unique. Thus, in the age of evermore personalised medicine, the ability to predict individuals' drug-microbiome interactions is highly sought. Machine learning (ML) offers a powerful toolkit capable of characterising and predicting drug-microbiota interactions at the individual patient level. ML techniques have the potential to learn the mechanisms operating drug-microbiome activities and measure patients' risk of such occurrences. This review will outline current knowledge at the drug-microbiota interface, and present ML as a technique for examining and forecasting personalised drug-microbiome interactions. When harnessed effectively, ML could alter how the pharmaceutical industry and healthcare professionals consider the drug-microbiome axis in patient care.
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Affiliation(s)
| | | | - Mine Orlu
- University College London, London, United Kingdom
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26
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McCoubrey LE, Elbadawi M, Orlu M, Gaisford S, Basit AW. Machine Learning Uncovers Adverse Drug Effects on Intestinal Bacteria. Pharmaceutics 2021; 13:1026. [PMID: 34371718 PMCID: PMC8308984 DOI: 10.3390/pharmaceutics13071026] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiome, composed of trillions of microorganisms, plays an essential role in human health. Many factors shape gut microbiome composition over the life span, including changes to diet, lifestyle, and medication use. Though not routinely tested during drug development, drugs can exert profound effects on the gut microbiome, potentially altering its functions and promoting disease. This study develops a machine learning (ML) model to predict whether drugs will impair the growth of 40 gut bacterial strains. Trained on over 18,600 drug-bacteria interactions, 13 distinct ML models are built and compared, including tree-based, ensemble, and artificial neural network techniques. Following hyperparameter tuning and multi-metric evaluation, a lead ML model is selected: a tuned extra trees algorithm with performances of AUROC: 0.857 (±0.014), recall: 0.587 (±0.063), precision: 0.800 (±0.053), and f1: 0.666 (±0.042). This model can be used by the pharmaceutical industry during drug development and could even be adapted for use in clinical settings.
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Affiliation(s)
| | | | | | | | - Abdul W. Basit
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; (L.E.M.); (M.E.); (M.O.); (S.G.)
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27
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Nationality and body location alter human skin microbiome. Appl Microbiol Biotechnol 2021; 105:5241-5256. [PMID: 34125277 DOI: 10.1007/s00253-021-11387-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/25/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
Skin microbiomes function directly in human health and are affected by various external and internal factors. However, few studies have showed the variation of human skin microbiota at multiple body sites in individuals of different national origin living in the same environment. Here, using 16S rRNA sequencing, we investigated the diversity and function of skin microbiomes in different body locations of Chinese and Pakistani individuals from a single college in China. Body location and nationality significantly affected community structures, while season and gender only impacted community member. Due to different lifestyles and likely genetic characteristics of the hosts, Proteobacteria was more abundant in Pakistanis than in Chinese individuals. There were significant differences in the Shannon diversity of skin microorganisms among different skin sites of Chinese individuals, but not in Pakistanis. PICRUSt prediction indicated that gene functions involved in carbohydrate metabolism, lipid metabolism, and xenobiotics biodegradation and metabolism were higher in bacteria collected from Pakistanis than those from Chinese individuals, but the amino acid metabolism of skin microorganisms in Chinese people was higher. The relative abundances of potential pathogenic bacteria also differed in different body locations, providing a foundation for studying skin-associated bacterial diseases. Through a meta-analysis of 233 human skin samples from eight elevational sites in western China, we found that skin microbial diversity first decreased and then increased with increasing altitude. Network analysis showed positive correlation between altitude and Lactobacillus, Chryseobacterium, or Acinetobacter. Our results uncover the variation of human skin microbiota allowing future explorations of potential significance for human health. KEY POINTS: • Body location and nationality affect skin microbiota diversity and function. • Proteobacteria was more abundant in Pakistanis than in Chinese. • Skin microbial diversity first decreased and then increased with elevated altitude.
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28
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Exploring the signature gut and oral microbiome in individuals of specific Ayurveda prakriti. J Biosci 2021. [DOI: 10.1007/s12038-021-00182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Dixit K, Davray D, Chaudhari D, Kadam P, Kshirsagar R, Shouche Y, Dhotre D, Saroj SD. Benchmarking of 16S rRNA gene databases using known strain sequences. Bioinformation 2021; 17:377-391. [PMID: 34092959 PMCID: PMC8131573 DOI: 10.6026/97320630017377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/18/2022] Open
Abstract
16S rRNA gene analysis is the most convenient and robust method for microbiome studies. Inaccurate taxonomic assignment of bacterial strains could have deleterious effects as all downstream analyses rely heavily on the accurate assessment of microbial taxonomy. The use of mock communities to check the reliability of the results has been suggested. However, often the mock communities used in most of the studies represent only a small fraction of taxa and are used mostly as validation of sequencing run to estimate sequencing artifacts. Moreover, a large number of databases and tools available for classification and taxonomic assignment of the 16S rRNA gene make it challenging to select the best-suited method for a particular dataset. In the present study, we used authentic and validly published 16S rRNA gene type strain sequences (full length, V3-V4 region) and analyzed them using a widely used QIIME pipeline along with different parameters of OTU clustering and QIIME compatible databases. Data Analysis Measures (DAM) revealed a high discrepancy in ratifying the taxonomy at different taxonomic hierarchies. Beta diversity analysis showed clear segregation of different DAMs. Limited differences were observed in reference data set analysis using partial (V3-V4) and full-length 16S rRNA gene sequences, which signify the reliability of partial 16S rRNA gene sequences in microbiome studies. Our analysis also highlights common discrepancies observed at various taxonomic levels using various methods and databases.
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Affiliation(s)
- Kunal Dixit
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India
| | - Dimple Davray
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India
| | - Diptaraj Chaudhari
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune, India
| | - Pratik Kadam
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune, India
| | - Rudresh Kshirsagar
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune, India
| | - Yogesh Shouche
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune, India
| | - Dhiraj Dhotre
- Reliance Life Sciences Pvt Ltd, Rabale, Mumbai, India
| | - Sunil D Saroj
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India
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30
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Impact of gastrointestinal tract variability on oral drug absorption and pharmacokinetics: An UNGAP review. Eur J Pharm Sci 2021; 162:105812. [PMID: 33753215 DOI: 10.1016/j.ejps.2021.105812] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/19/2021] [Accepted: 03/16/2021] [Indexed: 12/17/2022]
Abstract
The absorption of oral drugs is frequently plagued by significant variability with potentially serious therapeutic consequences. The source of variability can be traced back to interindividual variability in physiology, differences in special populations (age- and disease-dependent), drug and formulation properties, or food-drug interactions. Clinical evidence for the impact of some of these factors on drug pharmacokinetic variability is mounting: e.g. gastric pH and emptying time, small intestinal fluid properties, differences in pediatrics and the elderly, and surgical changes in gastrointestinal anatomy. However, the link of colonic factors variability (transit time, fluid composition, microbiome), sex differences (male vs. female) and gut-related diseases (chronic constipation, anorexia and cachexia) to drug absorption variability has not been firmly established yet. At the same time, a way to decrease oral drug pharmacokinetic variability is provided by the pharmaceutical industry: clinical evidence suggests that formulation approaches employed during drug development can decrease the variability in oral exposure. This review outlines the main drivers of oral drug exposure variability and potential approaches to overcome them, while highlighting existing knowledge gaps and guiding future studies in this area.
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31
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Chumponsuk T, Gruneck L, Gentekaki E, Jitprasertwong P, Kullawong N, Nakayama J, Popluechai S. The salivary microbiota of Thai adults with metabolic disorders and association with diet. Arch Oral Biol 2021; 122:105036. [PMID: 33421657 DOI: 10.1016/j.archoralbio.2020.105036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/24/2020] [Accepted: 12/26/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVE This study aimed to investigate abundance of specific bacterial taxa in the saliva of 105 Thai adults with different BMI (lean, overweight, and obese) and T2DM subjects using qPCR targeting the 16S rRNA gene of various bacteria taxa. DESIGN We employed qPCR targeting 16S rRNA genes to explore the bacterial profiles and abundances in the saliva of Thai adult subjects with different BMI and T2DM. Multivariate statistical analyses (multiple factor analysis (MFA) and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) were performed to assess the associations of salivary bacteria with diet, blood profile, gender, age, and use of antibiotics. RESULTS We found that abundance profiles of the examined salivary bacteria were similar across the four groups. When diet, blood profile, and gender, age, and use of antibiotics were considered, significant differences were noted between subgroups. A positive correlation was also found between consumption of carbonate soft drinks and Bacteroidetes, Gamma-proteobacteria, Veillonella, Fusobacterium and Fusobacterium nucleatum. CONCLUSIONS This is the first study demonstrating the relative abundance of salivary bacteria in adult Thai subjects with different levels of BMI and T2DM. Regardless of the similar pattern of bacterial profiles across groups, sPLS-DA analysis highlighted the influence of host variables (gender, age, and use of antibiotics) on the abundance of salivary microbiota. Our findings pave the way for further hypothesis testing to gain insight into the association between host factors and salivary microbiome.
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Affiliation(s)
| | - Lucsame Gruneck
- Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai, Thailand
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Muang, Chiang Rai, Thailand; Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai, Thailand
| | - Paiboon Jitprasertwong
- School of Geriatric Oral Health, Institute of Dentistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Niwed Kullawong
- School of Health Science, Mae Fah Luang University, Muang, Chiang Rai, Thailand
| | - Jiro Nakayama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Siam Popluechai
- School of Science, Mae Fah Luang University, Muang, Chiang Rai, Thailand; Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai, Thailand.
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32
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McCoubrey LE, Elbadawi M, Orlu M, Gaisford S, Basit AW. Harnessing machine learning for development of microbiome therapeutics. Gut Microbes 2021; 13:1-20. [PMID: 33522391 PMCID: PMC7872042 DOI: 10.1080/19490976.2021.1872323] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023] Open
Abstract
The last twenty years of seminal microbiome research has uncovered microbiota's intrinsic relationship with human health. Studies elucidating the relationship between an unbalanced microbiome and disease are currently published daily. As such, microbiome big data have become a reality that provide a mine of information for the development of new therapeutics. Machine learning (ML), a branch of artificial intelligence, offers powerful techniques for big data analysis and prediction-making, that are out of reach of human intellect alone. This review will explore how ML can be applied for the development of microbiome-targeted therapeutics. A background on ML will be given, followed by a guide on where to find reliable microbiome big data. Existing applications and opportunities will be discussed, including the use of ML to discover, design, and characterize microbiome therapeutics. The use of ML to optimize advanced processes, such as 3D printing and in silico prediction of drug-microbiome interactions, will also be highlighted. Finally, barriers to adoption of ML in academic and industrial settings will be examined, concluded by a future outlook for the field.
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Affiliation(s)
| | - Moe Elbadawi
- UCL School of Pharmacy, University College London, London, UK
| | - Mine Orlu
- UCL School of Pharmacy, University College London, London, UK
| | - Simon Gaisford
- UCL School of Pharmacy, University College London, London, UK
- FabRx Ltd., Ashford, Kent, UK
| | - Abdul W. Basit
- UCL School of Pharmacy, University College London, London, UK
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Zubeldia-Varela E, Barber D, Barbas C, Perez-Gordo M, Rojo D. Sample pre-treatment procedures for the omics analysis of human gut microbiota: Turning points, tips and tricks for gene sequencing and metabolomics. J Pharm Biomed Anal 2020; 191:113592. [PMID: 32947167 DOI: 10.1016/j.jpba.2020.113592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/29/2020] [Accepted: 08/23/2020] [Indexed: 02/06/2023]
Abstract
The connection between gut microbiota and human health is becoming increasingly relevant and the number of groups working in this field is constantly growing. In this context, from high-throughput gene sequencing to metabolomics analysis, the omics technologies have contributed enormously to unveil the secret crosstalk between us and our microbes. All the omics technologies produce a great amount of information, and processing this information is time-consuming and expensive. For this reason, a correct experimental design and a careful pre-analytical planning are crucial. To study the human gut microbiota, faeces are the sample of choice. Faecal material is complex, and procedures for collecting and preserving faeces are not well-established. Furthermore, increasing evidence suggests that multiple confounding factors, such as antibiotics consumption, mode of delivery, diet, aging and several diseases and disorders can alter the composition and functionality of the microbiota. This review is focused on the discussion of critical general issues during the pre-analytical planning, from patient handling to faeces sampling, including collection procedures, transport, storage conditions and possible pre-treatments, which are critical for a successful research in omics with a special attention to metabolomics and gene sequencing. We also point out that the adoption of standard operating procedures in the field is needed to guarantee accuracy and reproducibility of results.
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Affiliation(s)
- Elisa Zubeldia-Varela
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Domingo Barber
- Institute of Applied and Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Marina Perez-Gordo
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Institute of Applied and Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - David Rojo
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain.
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Bhattacharya S, Bhadra R, Schols AMWJ, Sambashivaiah S. Gut microbial dysbiosis as a limiting factor in the management of primary and secondary sarcopenia: an Asian Indian perspective. Curr Opin Clin Nutr Metab Care 2020; 23:404-410. [PMID: 32868683 DOI: 10.1097/mco.0000000000000688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW The article summarizes recent research advances on the role of gut microbiome in primary and secondary sarcopenia. This article also explores the potential contribution of gut dysbiosis to suboptimal sarcopenia management with special focus on factors contributing to gut dysbiosis among Asian Indians. RECENT FINDINGS Aging and chronic diseases contribute to gut dysbiosis and intestinal barrier dysfunction allowing enhanced microbial translocation that may negatively affect muscle strength, physical function, and frailty. Gut microbiome of Asian Indians has shown a unique composition that is affected by multiple factors, such as socioeconomic status, poor hygiene, high rate of infection and infestations, antibiotic overuse and transition towards a westernized eating pattern. Current management approach for sarcopenia (exercise and/or protein supplementation) fails to address gut dysbiosis and intestinal barrier dysfunction. Incorporating a prebiotic or probiotic element to the intervention strategy may improve gut dysbiosis, inflammation and muscle function. SUMMARY Gut dysbiosis and intestinal barrier dysfunction appear to be a significant limitation in sarcopenia management, thus gut centric intervention may be perceived as a (co)intervention strategy to be tested in appropriate clinical trials.
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Affiliation(s)
| | - Rohini Bhadra
- St John's Research Institute, St John's Medical College, Bengaluru, India
| | - Annemie M W J Schols
- NUTRIM School of Nutrition and Translational Research in Metabolism, Department of Respiratory Medicine, Maastricht University, The Netherlands
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Verma D, Srivastava A, Garg PK, Akhter Y, Dubey AK, Mishra S, Deo SVS. Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population. Arch Microbiol 2020; 203:927-939. [PMID: 33084948 DOI: 10.1007/s00203-020-02084-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/26/2020] [Accepted: 10/06/2020] [Indexed: 01/21/2023]
Abstract
Poor oral health has broad consequences that can be seen at personal as well as societal levels, especially in developing countries like India. We have limited information on the healthy oral cavity's inhabitant microorganisms that play a crucial role in overall oral health. In a comprehensive culture-independent approach, the bacterial composition of healthy human oral cavities was determined from a sub-population of northern India. During this study, 20 mouthwash-derived metagenomes were explored for identifying bacterial diversity using the 16S rRNA hypervariable V3 region with the MiSeq Illumina platform. On the taxonomy assignment of operational taxonomic units (OTUs), 20 assigned phyla and 162 genera were recovered among the participants. The mean relative abundance revealed that Streptococcus was the dominant genera among the participants. However, at inter-individual analysis, Neisseria and Haemophilus exhibited first-order dominance among five and three healthy individuals, respectively. Correlation studies indicate that Streptococcus shares a strong relationship with Rothia, Corynebacterium, Prevotella, and Veillonella, whereas it was negatively correlated with Neisseria, Aggregatibacter, Porphyromonas, and Fusobacteria like Gram-negative bacteria. Bacterial diversity showed insignificant differences at the level of age and gender within and between the participants. The results support several of the major findings of previous reports on the healthy oral microbiome of the Indian population, however, the present investigation further illustrates that demographic region leaves an impact on overall bacterial composition. The study will assist in a better understanding of the oral microbiome from region-specific Indian population that was otherwise highly under-represented.
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Affiliation(s)
- Digvijay Verma
- Department of Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India.
| | - Ankita Srivastava
- Department of Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Pankaj Kumar Garg
- Department of Surgical Oncology, All India Institute of Medical Sciences, Rishikesh, Uttrakhand, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Ashok Kumar Dubey
- Division of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
| | - SukhDev Mishra
- Department of Bio-Statistics and Data Management, ICMR-National Institute of Occupational Health, Ahmedabad, India
| | - S V S Deo
- Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, India
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Jnana A, Murali TS, Guruprasad KP, Satyamoorthy K. Prakriti phenotypes as a stratifier of gut microbiome: A new frontier in personalized medicine? J Ayurveda Integr Med 2020; 11:360-365. [PMID: 32718805 PMCID: PMC7527847 DOI: 10.1016/j.jaim.2020.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022] Open
Abstract
Ayurveda has a rich history and its significance woven deeply in the Indian culture. The concept of prakriti (a person’s “nature” or constitutional type determined by the proportion of three doshas, namely - vata, pitta and kapha) in Ayurveda is deeply rooted in personalized health management. While the attributes of prakriti has been established to have a genomic basis, there is dearth of elaborate evidences linking prakriti with manifestation of diseases. Next generation sequencing studies have provided a causal link between variation in the gut microbiome and its effect on an individual’s fitness. Separately, reports have identified gut microbial patterns associated with several host variables such as geography, age, diet and extreme prakriti phenotypes. Recently, few reports have identified a “core gut microbiome” consisting of Bacteroides, Faecalibacterium, Prevotella and Ruminococcus prevalent across the Indian population; however, a few bacterial genera were specifically enriched in certain prakritis. Hence, in this review we aim to analyse the role of prakriti variations on dysbiosis of the gut microbiome and concomitantly its effect on human health. We suggest that prakriti phenotyping can function as a potential stratifier of the gut microbiome in a given population and may provide evidence for the conceptual framework of personalized medicine in Ayurvedic system of medicine.
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Affiliation(s)
- Apoorva Jnana
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Thokur Sreepathy Murali
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Kanive Parashiva Guruprasad
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India; Centre for Ayurvedic Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India; Centre for Ayurvedic Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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