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Cena JAD, Belmok A, Kyaw CM, Dame-Teixeira N. The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry. Arch Oral Biol 2024; 161:105936. [PMID: 38422909 DOI: 10.1016/j.archoralbio.2024.105936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases. DESIGN This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites. RESULTS Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla. CONCLUSIONS Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.
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Affiliation(s)
| | - Aline Belmok
- Institute of Biology, University of Brasilia, Brazil
| | | | - Naile Dame-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brazil; Division of Oral Biology, School of Dentistry, University of Leeds, UK.
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Kuehnast T, Kumpitsch C, Mohammadzadeh R, Weichhart T, Moissl-Eichinger C, Heine H. Exploring the human archaeome: its relevance for health and disease, and its complex interplay with the human immune system. FEBS J 2024. [PMID: 38555566 DOI: 10.1111/febs.17123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
This Review aims to coalesce existing knowledge on the human archaeome, a less-studied yet critical non-bacterial component of the human microbiome, with a focus on its interaction with the immune system. Despite a largely bacteria-centric focus in microbiome research, archaea present unique challenges and opportunities for understanding human health. We examine the archaeal distribution across different human body sites, such as the lower gastrointestinal tract (LGT), upper aerodigestive tract (UAT), urogenital tract (UGT), and skin. Variability in archaeal composition exists between sites; methanogens dominate the LGT, while Nitrososphaeria are prevalent on the skin and UAT. Archaea have yet to be classified as pathogens but show associations with conditions such as refractory sinusitis and vaginosis. In the LGT, methanogenic archaea play critical metabolic roles by converting bacterial end-products into methane, correlating with various health conditions, including obesity and certain cancers. Finally, this work looks at the complex interactions between archaea and the human immune system at the molecular level. Recent research has illuminated the roles of specific archaeal molecules, such as RNA and glycerolipids, in stimulating immune responses via innate immune receptors like Toll-like receptor 8 (TLR8) and 'C-type lectin domain family 4 member E' (CLEC4E; also known as MINCLE). Additionally, metabolic by-products of archaea, specifically methane, have demonstrated immunomodulatory effects through anti-inflammatory and anti-oxidative pathways. Despite these advancements, the mechanistic underpinnings of how archaea influence immune activity remain a fertile area for further investigation.
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Affiliation(s)
- Torben Kuehnast
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Christina Kumpitsch
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Rokhsareh Mohammadzadeh
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Thomas Weichhart
- Institute of Medical Genetics, Medical University of Vienna, Austria
| | - Christine Moissl-Eichinger
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
- BioTechMed Graz, Austria
| | - Holger Heine
- Research Center Borstel - Leibniz Lung Center, Division of Innate Immunity, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
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Gani M, Mohd-Ridwan AR, Sitam FT, Kamarudin Z, Selamat SS, Awang NMZ, Karuppannan KV, Md-Zain BM. Habitat shapes the gut microbiome diversity of Malayan tigers (Panthera tigris jacksoni) as revealed through metabarcoding 16S rRNA profiling. World J Microbiol Biotechnol 2024; 40:111. [PMID: 38416247 DOI: 10.1007/s11274-023-03868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 02/29/2024]
Abstract
The gut microbiome refers to the microorganism community living within the digestive tract. The environment plays a crucial role in shaping the gut microbiome composition of animals. The gut microbiome influences the health and behavior of animals, including the critically endangered Malayan tiger (Panthera tigris jacksoni). However, the gut microbiome composition of Malayan tigers, especially those living in their natural habitats, remains poorly understood. To address this knowledge gap, we used next-generation sequencing DNA metabarcoding techniques to analyze the gut microbiome of wild Malayan tigers using fecal samples collected from their natural habitats and in captivity. Our aim was to determine the gut microbiota composition of the Malayan tiger, considering the different types of habitat environments. The results revealed a diverse microbial community within the gut microbiome of Malayan tigers. The prominent phyla that were observed included Firmicutes, Proteobacteria, Actinobacteriota, Fusobacteriota and Bacteroidota. Beta diversity analysis revealed significant differences in gut microbiome composition of Malayan tigers that inhabited oil palm plantations, in villages and protected areas. Diversity analysis also revealed significant difference in the gut microbiome between wild and captive Malayan tigers. However, the distinctions of gut microbiome between wild and captive alpha diversity did not yield significant differences. The differences in microbiome diversity resulted from the interplay of dietary intake and environmental factors. This information will facilitate the establishment of focused conservation approaches and enhance our understanding of the effect of microbiome composition on Malayan tiger health.
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Affiliation(s)
- Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Zubaidah Kamarudin
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Siti Suzana Selamat
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Nik Mohd Zamani Awang
- National Wildlife Rescue Centre (NWRC), Department of Wildlife and National Parks (PERHILITAN), 35600, Sungkai, Perak, Malaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100, Kuala Lumpur, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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4
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Pagan L, Huisman BW, van der Wurff M, Naafs RGC, Schuren FHJ, Sanders IMJG, Smits WK, Zwittink RD, Burggraaf J, Rissmann R, Piek JMJ, Henderickx JGE, van Poelgeest MIE. The vulvar microbiome in lichen sclerosus and high-grade intraepithelial lesions. Front Microbiol 2023; 14:1264768. [PMID: 38094635 PMCID: PMC10716477 DOI: 10.3389/fmicb.2023.1264768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/01/2023] [Indexed: 01/25/2024] Open
Abstract
Background The role of the vulvar microbiome in the development of (pre)malignant vulvar disease is scarcely investigated. The aim of this exploratory study was to analyze vulvar microbiome composition in lichen sclerosus (LS) and vulvar high-grade squamous intraepithelial lesions (HSIL) compared to healthy controls. Methods Women with vulvar lichen sclerosus (n = 10), HSIL (n = 5) and healthy controls (n = 10) were included. Swabs were collected from the vulva, vagina and anal region for microbiome characterization by metagenomic shotgun sequencing. Both lesional and non-lesional sites were examined. Biophysical assessments included trans-epidermal water loss for evaluation of the vulvar skin barrier function and vulvar and vaginal pH measurements. Results Healthy vulvar skin resembled vaginal, anal and skin-like microbiome composition, including the genera Prevotella, Lactobacillus, Gardnerella, Staphylococcus, Cutibacterium, and Corynebacterium. Significant differences were observed in diversity between vulvar skin of healthy controls and LS patients. Compared to the healthy vulvar skin, vulvar microbiome composition of both LS and vulvar HSIL patients was characterized by significantly higher proportions of, respectively, Papillomaviridae (p = 0.045) and Alphapapillomavirus (p = 0.002). In contrast, the Prevotella genus (p = 0.031) and Bacteroidales orders (p = 0.038) were significantly less abundant in LS, as was the Actinobacteria class (p = 0.040) in vulvar HSIL. While bacteria and viruses were most abundant, fungal and archaeal taxa were scarcely observed. Trans-epidermal water loss was higher in vulvar HSIL compared to healthy vulvar skin (p = 0.043). Conclusion This study is the first to examine the vulvar microbiome through metagenomic shotgun sequencing in LS and HSIL patients. Diseased vulvar skin presents a distinct signature compared to healthy vulvar skin with respect to bacterial and viral fractions of the microbiome. Key findings include the presence of papillomaviruses in LS as well as in vulvar HSIL, although LS is generally considered an HPV-independent risk factor for vulvar dysplasia. This exploratory study provides clues to the etiology of vulvar premalignancies and may act as a steppingstone for expanding the knowledge on potential drivers of disease progression.
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Affiliation(s)
- Lisa Pagan
- Centre for Human Drug Research, Leiden, Netherlands
- Department of Gynaecology and Obstetrics, Leiden University Medical Center, Leiden, Netherlands
| | - Bertine W. Huisman
- Centre for Human Drug Research, Leiden, Netherlands
- Department of Gynaecology and Obstetrics, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Frank H. J. Schuren
- Netherlands Organisation for Applied Scientific Research (TNO), Zeist, Netherlands
| | - Ingrid M. J. G. Sanders
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
- Department of Medical Microbiology, Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
| | - Romy D. Zwittink
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
- Department of Medical Microbiology, Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
| | - Jacobus Burggraaf
- Centre for Human Drug Research, Leiden, Netherlands
- Leiden Amsterdam Center for Drug Research, Leiden University, Leiden, Netherlands
| | - Robert Rissmann
- Centre for Human Drug Research, Leiden, Netherlands
- Leiden Amsterdam Center for Drug Research, Leiden University, Leiden, Netherlands
- Department of Dermatology, Leiden University Medical Center, Leiden, Netherlands
| | - Jurgen M. J. Piek
- Department of Obstetrics and Gynaecology, Catharina Cancer Institute, Eindhoven, Netherlands
| | - Jannie G. E. Henderickx
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
- Department of Medical Microbiology, Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
| | - Mariëtte I. E. van Poelgeest
- Centre for Human Drug Research, Leiden, Netherlands
- Department of Gynaecology and Obstetrics, Leiden University Medical Center, Leiden, Netherlands
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Saha S, Boesch C, Maycock J, Wood S, Do T. Sweet Orange Juice Processing By-Product Extracts: A Caries Management Alternative to Chlorhexidine. Biomolecules 2023; 13:1607. [PMID: 38002290 PMCID: PMC10669069 DOI: 10.3390/biom13111607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Dental caries is one of the most prevalent chronic diseases globally in both children and adults. This study investigated the potential of industrial sweet orange waste extracts (ISOWE) as a substitute for chlorhexidine (CHX) in managing dental caries. First, the cytotoxicity of ISOWE (40, 80, 120 mg/mL) and CHX (0.1 and 0.2%) on buccal epithelial cells was determined. ISOWE exhibited no overall toxicity, whereas CHX strongly affected cell viability. The combination of ISOWE and CHX significantly enhanced cell proliferation compared to CHX alone. Next, the antimicrobial efficacy of ISOWE, CHX, and their combination was assessed against a 7-day complex biofilm model inoculated with oral samples from human volunteers. CHX exhibited indiscriminate antimicrobial action, affecting both pathogenic and health-associated oral microorganisms. ISOWE demonstrated lower antimicrobial efficacy than CHX but showed enhanced efficacy against pathogenic species while preserving the oral microbiome's balance. When applied to a cariogenic biofilm, the combined treatment of ISOWE with 0.1% CHX showed similar efficacy to 0.2% CHX treatment alone. Overall, the findings suggest that ISOWE is a promising natural anti-cariogenic agent with lower toxicity and enhanced selectivity for pathogenic species compared to CHX.
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Affiliation(s)
- Suvro Saha
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds LS2 9JT, UK; (S.S.)
- School of Dentistry, Division of Oral Biology, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Christine Boesch
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds LS2 9JT, UK; (S.S.)
| | - Joanne Maycock
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds LS2 9JT, UK; (S.S.)
| | - Simon Wood
- School of Dentistry, Division of Oral Biology, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Thuy Do
- School of Dentistry, Division of Oral Biology, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
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Garcia-Bonete MJ, Rajan A, Suriano F, Layunta E. The Underrated Gut Microbiota Helminths, Bacteriophages, Fungi, and Archaea. Life (Basel) 2023; 13:1765. [PMID: 37629622 PMCID: PMC10455619 DOI: 10.3390/life13081765] [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: 06/30/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
The microbiota inhabits the gastrointestinal tract, providing essential capacities to the host. The microbiota is a crucial factor in intestinal health and regulates intestinal physiology. However, microbiota disturbances, named dysbiosis, can disrupt intestinal homeostasis, leading to the development of diseases. Classically, the microbiota has been referred to as bacteria, though other organisms form this complex group, including viruses, archaea, and eukaryotes such as fungi and protozoa. This review aims to clarify the role of helminths, bacteriophages, fungi, and archaea in intestinal homeostasis and diseases, their interaction with bacteria, and their use as therapeutic targets in intestinal maladies.
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Affiliation(s)
- Maria Jose Garcia-Bonete
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Anandi Rajan
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Francesco Suriano
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Elena Layunta
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Instituto de Investigación Sanitaria de Aragón (IIS Aragón), 50009 Zaragoza, Spain
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Kerem G, Yu X, Ismayi A, Teng B, Udduttula A, Liu C, Yu Z, Tohty D, Zhang JV, Ren PG. Small intestinal microbiota composition altered in obesity-T2DM mice with high salt fed. Sci Rep 2023; 13:8256. [PMID: 37217529 DOI: 10.1038/s41598-023-33909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Obesity has become a global concern because of increasing the risk of many diseases. Alterations in human gut microbiota have been proven to be associated with obesity, yet the mechanism of how the microbiota are altered by high salt diet (HSD) remains obscure. In this study, the changes of Small Intestinal Microbiota (SIM) in obesity-T2DM mice were investigated. High-throughput sequencing was applied for the jejunum microbiota analysis. Results revealed that high salt intake (HS) could suppress the body weight (B.W.) in some extent. In addition, significant T2DM pathological features were revealed in high salt-high food diet (HS-HFD) group, despite of relatively lower food intake. High-throughput sequencing analysis indicated that the F/B ratio in HS intake groups increased significantly (P < 0.001), whereas beneficial bacteria, such as lactic acid or short chain fatty acid producing bacteria, were significantly decreased in HS-HFD group (P < 0.01 or P < 0.05). Furthermore, Halorubrum luteum were observed in small intestine for the first time. Above results preliminary suggested that in obesity-T2DM mice, high dietary salt could aggravate the imbalance of composition of SIM to unhealthy direction.
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Affiliation(s)
- Goher Kerem
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiangfang Yu
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, China
| | - Aynur Ismayi
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bin Teng
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Anjaneyulu Udduttula
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chang Liu
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, China
| | - Zhongjia Yu
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, China
| | - Dilbar Tohty
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Jian V Zhang
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Guangdong Key Laboratory of Nanomedicine, Shenzhen, China
| | - Pei-Gen Ren
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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Li T, Feng Y, Wang C, Shi T, Abudurexiti A, Zhang M, Gao F. Assessment of causal associations among gut microbiota, metabolites, and celiac disease: a bidirectional Mendelian randomization study. Front Microbiol 2023; 14:1087622. [PMID: 37250054 PMCID: PMC10213403 DOI: 10.3389/fmicb.2023.1087622] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Background A growing number of studies have implicated that gut microbial abundance and metabolite concentration alterations are associated with celiac disease (CD). However, the causal relationship underlying these associations is unclear. Here, we used Mendelian randomization (MR) to reveal the causal effect of gut microbiota and metabolites on CD. Methods Genome-wide association study (GWAS) summary-level data for gut microbiota, metabolites, and CD were extracted from published GWASs. Causal bacterial taxa and metabolites for CD were determined by two-sample MR analyses. The robustness of the results was assessed with sensitivity analyses. Finally, reverse causality was investigated with a reverse MR analysis. Results Genetically, increased genus Bifidobacterium was potentially associated with higher CD risk (odds ratio [OR] = 1.447, 95% confidence interval [CI]: 1.054-1.988, p = 0.022) while phylum Lentisphaerae (OR = 0.798, 95% CI: 0.648-0.983, p = 0.034) and genus Coprobacter (OR = 0.683, 95% CI: 0.531-0.880, p = 0.003) were related to lower CD risk. Moreover, there were suggestive associations between CD and the following seven metabolites: 1-oleoylglycerophosphoethanolamine, 1-palmitoylglycerophosphoethanolamine, 1,6-anhydroglucose, phenylacetylglutamine, tryptophan betaine, 10-undecenoate, and tyrosine. Sensitivity analyses deemed the results reliable without pleiotropy. Conclusion We investigated the causal relationships between gut microbiota, metabolites, and CD with two-sample MR. Our findings suggest several novel potential therapeutic targets for CD treatment. Further understanding of the underlying mechanism may provide insights into CD pathogenesis.
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Affiliation(s)
- Ting Li
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Yan Feng
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Chun Wang
- Department of Pathology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Tian Shi
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Adilai Abudurexiti
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Mengxia Zhang
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Feng Gao
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, Xinjiang, China
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Bartlett A, Padfield D, Lear L, Bendall R, Vos M. A comprehensive list of bacterial pathogens infecting humans. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748702 DOI: 10.1099/mic.0.001269] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There exists an enormous diversity of bacteria capable of human infection, but no up-to-date, publicly accessible list is available. Combining a pragmatic definition of pathogenicity with an extensive search strategy, we report 1513 bacterial pathogens known to infect humans described pre-2021. Of these, 73 % were regarded as established (have infected at least three persons in three or more references) and 27 % as putative (fewer than three known cases). Pathogen species belong to 10 phyla and 24 classes scattered throughout the bacterial phylogeny. We show that new human pathogens are discovered at a rapid rate. Finally, we discuss how our results could be expanded to a database, which could provide a useful resource for microbiologists. Our list is freely available and archived on GitHub and Zenodo and we have provided walkthroughs to facilitate access and use.
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Affiliation(s)
- Abigail Bartlett
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, UK
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, UK
| | - Luke Lear
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, UK
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Krawczyk KT, Locht C, Kowalewicz-Kulbat M. Halophilic Archaea Halorhabdus Rudnickae and Natrinema Salaciae Activate Human Dendritic Cells and Orient T Helper Cell Responses. Front Immunol 2022; 13:833635. [PMID: 35720372 PMCID: PMC9204267 DOI: 10.3389/fimmu.2022.833635] [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: 12/11/2021] [Accepted: 04/28/2022] [Indexed: 12/03/2022] Open
Abstract
Halophilic archaea are procaryotic organisms distinct from bacteria, known to thrive in hypersaline environments, including salt lakes, salterns, brines and salty food. They have also been identified in the human microbiome. The biological significance of halophiles for human health has rarely been examined. The interactions between halophilic archaea and human dendritic cells (DCs) and T cells have not been identified so far. Here, we show for the first time that the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae activate human monocyte-derived DCs, induce DC maturation, cytokine production and autologous T cell activation. In vitro both strains induced DC up-regulation of the cell-surface receptors CD86, CD80 and CD83, and cytokine production, including IL-12p40, IL-10 and TNF-α, but not IL-23 and IL-12p70. Furthermore, autologous CD4+ T cells produced significantly higher amounts of IFN-γ and IL-13, but not IL-17A when co-cultured with halophile-stimulated DCs in comparison to T cells co-cultured with unstimulated DCs. IFN-γ was almost exclusively produced by naïve T cells, while IL-13 was produced by both naïve and memory CD4+ T cells. Our findings thus show that halophilic archaea are recognized by human DCs and are able to induce a balanced cytokine response. The immunomodulatory functions of halophilic archaea and their potential ability to re-establish the immune balance may perhaps participate in the beneficial effects of halotherapies.
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Affiliation(s)
- Krzysztof T Krawczyk
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Camille Locht
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Magdalena Kowalewicz-Kulbat
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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11
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Azli B, Razak MN, Omar AR, Mohd Zain NA, Abdul Razak F, Nurulfiza I. Metagenomics Insights Into the Microbial Diversity and Microbiome Network Analysis on the Heterogeneity of Influent to Effluent Water. Front Microbiol 2022; 13:779196. [PMID: 35495647 PMCID: PMC9048743 DOI: 10.3389/fmicb.2022.779196] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Sanitizing the water sources of local communities is important to control the spread of microbial resistance genes, especially those for water-borne illnesses. The activities of antibiotic resistance gene (ARG)-host pathogens pose a threat to public health, and it has been estimated that the infection will lead up to 10 million deaths globally by the year 2050. Hence, in this study, we aim to analyze the efficiency of our municipal wastewater treatment plant (WWTP) process in producing pathogen-free water by investigating the microbial composition between influent and effluent water sites. Shotgun metagenomics sequencing using the Illumina platform was performed on the influent and effluent samples of six different WWTP sites located in Johore, Malaysia. After raw data pre-processing, the non-redundant contigs library was then aligned against BLASTP for taxonomy profiling and the Comprehensive Antibiotic Resistance Database for ARG annotation. Interestingly, the alpha-diversity result reported that effluent site samples showed higher abundance and diverse heterogeneity compared to the influent site. The principal component analysis (PCA) and non-metric multidimensional scaling (NMDS) plots also suggested that effluent sites showed high variation in the genetic material due to loosely clustered sample plots, as compared to the tightly clustered influent samples. This study has successfully identified the top three abundant phyla in influent-Proteobacteria, Firmicutes, and Bacteroidetes-and effluent-Proteobacteria, Actinobacteria, and Bacteroidetes-water. Despite the overlap within the top three abundant phyla in influent and effluent sites (Proteobacteria and Bacteroidetes), the ARG composition heat map and drug class phenotype plot bar exhibits a general trend of a downward shift, showing the efficiency of WWTP in reducing opportunistic pathogens. Overall, it was demonstrated that our municipal WWTP efficiently eliminated pathogenic microbes from the influent water before its total discharge to the environment, though not with the total elimination of microorganisms. This metagenomics study allowed for an examination of our water source and showed the potential interaction of species and ARGs residing in the influent and effluent environment. Both microbial profile structure and co-occurrence network analysis provide integrated understanding regarding the diversity of microorganisms and interactions for future advanced water sanitation treatments.
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Affiliation(s)
- Bahiyah Azli
- Laboratory of Vaccines and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Seri Kembangan, Malaysia
| | - Mohd Nasharudin Razak
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Seri Kembangan, Malaysia
| | - Abdul Rahman Omar
- Laboratory of Vaccines and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Seri Kembangan, Malaysia.,Faculty of Veterinary Medicine, Universiti Putra Malaysia, Seri Kembangan, Malaysia
| | - Nor Azimah Mohd Zain
- Department of Biosciences, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Malaysia.,Research Institute for Sustainable Environment, Universiti Teknologi Malaysia, Skudai, Malaysia
| | - Fatimah Abdul Razak
- Department of Mathematical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - I Nurulfiza
- Laboratory of Vaccines and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Seri Kembangan, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Seri Kembangan, Malaysia
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12
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Cai M, Kandalai S, Tang X, Zheng Q. Contributions of Human-Associated Archaeal Metabolites to Tumor Microenvironment and Carcinogenesis. Microbiol Spectr 2022; 10:e0236721. [PMID: 35225671 PMCID: PMC9045267 DOI: 10.1128/spectrum.02367-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
There is increasing awareness that archaea are interrelated with human diseases (including cancer). Archaea utilize unique metabolic pathways to produce a variety of metabolites that serve as a direct link to host-microbe interactions. However, knowledge on the diversity of human-associated archaea is still extremely limited, and less is known about the pathological effects of their metabolites to the tumor microenvironment and carcinogenesis. In the present study, we performed a large-scale analysis of archaea and their cancer-related metabolites across different body sites using >44,000 contigs with length >1,000 bp. Taxonomy annotation revealed that the occurrence and diversity of archaea are higher in two body sites, the gut and the oral cavity. Unlike other human-associated microbes, the nonmetric multidimensional scaling (NMDS) and permutational multivariate analysis of variance (PERMANOVA) analyses have shown no difference of archaeal compositions between Easterners and Westerners. Likewise, protein annotation suggests that genes encoding cancer-related metabolites (e.g., short-chain fatty acids and polyamines) are more prevalent and diverse in gut and oral samples. Archaea carrying these metabolites are restricted to Euryarchaeota and the TACK superphylum (Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota), especially methanogenic archaea, such as Methanobacteria. IMPORTANCE More evidence suggests that archaea are associated with human disease, including cancer. Here, we present the first framework of the diversity and distribution of human-associated archaea across human body sites, such as gut and oral cavity, using long contigs. Furthermore, we unveiled the potential archaeal metabolites linking to different lineages that might influence the tumor microenvironment and carcinogenesis. These results could open a new door to the guidance of diagnosing cancer and developing new treatment strategies.
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Affiliation(s)
- Mingwei Cai
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Shruthi Kandalai
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
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13
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Meta-analyses on the Periodontal Archaeome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1373:69-93. [DOI: 10.1007/978-3-030-96881-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Maruyama H, Nambu T, Mashimo C, Okinaga T, Takeyasu K. Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life. Int J Mol Sci 2021; 22:13432. [PMID: 34948225 PMCID: PMC8707338 DOI: 10.3390/ijms222413432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/21/2022] Open
Abstract
Comparative structural/molecular biology by single-molecule analyses combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution have been powerful tools for elucidating the mechanisms underlying genome DNA folding. All genomes in the three domains of life undergo stepwise folding from DNA to 30-40 nm fibers. Major protein players are histone (Eukarya and Archaea), Alba (Archaea), and HU (Bacteria) for fundamental structural units of the genome. In Euryarchaeota, a major archaeal phylum, either histone or HTa (the bacterial HU homolog) were found to wrap DNA. This finding divides archaea into two groups: those that use DNA-wrapping as the fundamental step in genome folding and those that do not. Archaeal transcription factor-like protein TrmBL2 has been suggested to be involved in genome folding and repression of horizontally acquired genes, similar to bacterial H-NS protein. Evolutionarily divergent SMC proteins contribute to the establishment of higher-order structures. Recent results are presented, including the use of Hi-C technology to reveal that archaeal SMC proteins are involved in higher-order genome folding, and the use of single-molecule tracking to reveal the detailed functions of bacterial and eukaryotic SMC proteins. Here, we highlight the similarities and differences in the DNA-folding mechanisms in the three domains of life.
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Affiliation(s)
- Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Takayuki Nambu
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Chiho Mashimo
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Toshinori Okinaga
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Kunio Takeyasu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan;
- Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan
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15
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Herrera G, Vega L, Patarroyo MA, Ramírez JD, Muñoz M. Gut microbiota composition in health-care facility-and community-onset diarrheic patients with Clostridioides difficile infection. Sci Rep 2021; 11:10849. [PMID: 34035404 PMCID: PMC8149855 DOI: 10.1038/s41598-021-90380-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/04/2021] [Indexed: 02/04/2023] Open
Abstract
The role of gut microbiota in the establishment and development of Clostridioides difficile infection (CDI) has been widely discussed. Studies showed the impact of CDI on bacterial communities and the importance of some genera and species in recovering from and preventing infection. However, most studies have overlooked important components of the intestinal ecosystem, such as eukaryotes and archaea. We investigated the bacterial, archaea, and eukaryotic intestinal microbiota of patients with health-care-facility- or community-onset (HCFO and CO, respectively) diarrhea who were positive or negative for CDI. The CDI-positive groups (CO/+, HCFO/+) showed an increase in microorganisms belonging to Bacteroidetes, Firmicutes, Proteobacteria, Ascomycota, and Opalinata compared with the CDI-negative groups (CO/-, HCFO/-). Patients with intrahospital-acquired diarrhea (HCFO/+, HCFO/-) showed a marked decrease in bacteria beneficial to the intestine, and there was evidence of increased Archaea and Candida and Malassezia species compared with the CO groups (CO/+, CO/-). Characteristic microbiota biomarkers were established for each group. Finally, correlations between bacteria and eukaryotes indicated interactions among the different kingdoms making up the intestinal ecosystem. We showed the impact of CDI on microbiota and how it varies with where the infection is acquired, being intrahospital-acquired diarrhea one of the most influential factors in the modulation of bacterial, archaea, and eukaryotic populations. We also highlight interactions between the different kingdoms of the intestinal ecosystem, which need to be evaluated to improve our understanding of CDI pathophysiology.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Laura Vega
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, 111321, Bogotá D.C., Colombia
- Health Sciences Division, Main Campus, Universidad Santo Tomás, 110231, Bogotá D.C., Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
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16
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Abstract
Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host-archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease.
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17
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Lathe R, St Clair D. From conifers to cognition: Microbes, brain and behavior. GENES BRAIN AND BEHAVIOR 2020; 19:e12680. [PMID: 32515128 DOI: 10.1111/gbb.12680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/12/2020] [Accepted: 05/29/2020] [Indexed: 12/25/2022]
Abstract
A diversity of bacteria, protozoans and viruses ("endozoites") were recently uncovered within healthy tissues including the human brain. By contrast, it was already recognized a century ago that healthy plants tissues contain abundant endogenous microbes ("endophytes"). Taking endophytes as an informative precedent, we overview the nature, prevalence, and role of endozoites in mammalian tissues, centrally focusing on the brain, concluding that endozoites are ubiquitous in diverse tissues. These passengers often remain subclinical, but they are not silent. We address their routes of entry, mechanisms of persistence, tissue specificity, and potential to cause long-term behavioral changes and/or immunosuppression in mammals, where rabies virus is the exemplar. We extend the discussion to Herpesviridae, Coronaviridae, and Toxoplasma, as well as to diverse bacteria and yeasts, and debate the advantages and disadvantages that endozoite infection might afford to the host and to the ecosystem. We provide a clinical perspective in which endozoites are implicated in neurodegenerative disease, anxiety/depression, and schizophrenia. We conclude that endozoites are instrumental in the delicate balance between health and disease, including age-related brain disease, and that endozoites have played an important role in the evolution of brain function and human behavior.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, University of Edinburgh Medical School, Edinburgh, UK
| | - David St Clair
- Institute of Medical Sciences, School of Medicine, University of Aberdeen, Aberdeen, UK
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18
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Quereda JJ, Barba M, Mocé ML, Gomis J, Jiménez-Trigos E, García-Muñoz Á, Gómez-Martín Á, González-Torres P, Carbonetto B, García-Roselló E. Vaginal Microbiota Changes During Estrous Cycle in Dairy Heifers. Front Vet Sci 2020; 7:371. [PMID: 32719814 PMCID: PMC7350931 DOI: 10.3389/fvets.2020.00371] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/28/2020] [Indexed: 01/04/2023] Open
Abstract
The vaginal microbiota plays an important role in the health of dairy cattle, and it could be manipulated for the prevention and treatment of reproduction-related infections. The present study profiles and compares the vaginal microbiota of healthy dairy heifers during the estrous cycle focusing the results in follicular (estrus) and luteal (diestrus) phases using 16S rRNA sequencing of the V3-V4 hypervariable region. Twenty 13-16-months-old virgin dairy heifers from a single farm were included in this study. Vaginal swabs and blood samples were obtained during estrus (6-8 h before artificial insemination) and diestrus (14 days after insemination). Estrus was evaluated by an activity monitoring system and confirmed with plasma progesterone immunoassay. Results showed that the taxonomic composition of the vaginal microbiota was different during the follicular and luteal phases. At the phylum level, the most abundant bacterial phyla were Tenericutes, Firmicutes, and Bacteroidetes which comprised more than 75% of the vaginal microbiota composition. The next more abundant phyla, in order of decreasing abundance, were Proteobacteria, Actinobacteria, Fusobacteria, Epsilonbacteraeota, and Patescibacteria. Together with Tenericutes, Firmicutes, and Bacteroidetes represented more than 96% of the bacterial composition. Ureaplasma, Histophilus, f_Corynebacteriaceae, Porphyromonas, Mycoplasma, Ruminococcaceae UCG-005, were the most abundant genera or families. The results also showed that the vaginal microbiota of dairy heifers was non-lactobacillus dominant. The genus Lactobacillus was always found at a low relative abundance during the estrous cycle being more abundant in the follicular than in the luteal phase. Despite more research is needed to explore the potential use of native vaginal microbiota members as probiotics in dairy heifers, this study represents an important step forward. Understanding how the microbiota behaves in healthy heifers will help to identify vaginal dysbiosis related to disease.
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Affiliation(s)
- Juan J. Quereda
- Microbiological Agents Associated With Animal Reproduction (ProVaginBio), Faculty of Veterinary Sciences, University Cardenal Herrera CEU, CEU Universities, Valencia, Spain
| | - Marta Barba
- Microbiological Agents Associated With Animal Reproduction (ProVaginBio), Faculty of Veterinary Sciences, University Cardenal Herrera CEU, CEU Universities, Valencia, Spain
| | - María Lorena Mocé
- Microbiological Agents Associated With Animal Reproduction (ProVaginBio), Faculty of Veterinary Sciences, University Cardenal Herrera CEU, CEU Universities, Valencia, Spain
| | - Jesús Gomis
- Microbiological Agents Associated With Animal Reproduction (ProVaginBio), Faculty of Veterinary Sciences, University Cardenal Herrera CEU, CEU Universities, Valencia, Spain
| | - Estrella Jiménez-Trigos
- Microbiological Agents Associated With Animal Reproduction (ProVaginBio), Faculty of Veterinary Sciences, University Cardenal Herrera CEU, CEU Universities, Valencia, Spain
| | - Ángel García-Muñoz
- Microbiological Agents Associated With Animal Reproduction (ProVaginBio), Faculty of Veterinary Sciences, University Cardenal Herrera CEU, CEU Universities, Valencia, Spain
| | - Ángel Gómez-Martín
- Microbiological Agents Associated With Animal Reproduction (ProVaginBio), Faculty of Veterinary Sciences, University Cardenal Herrera CEU, CEU Universities, Valencia, Spain
| | | | | | - Empar García-Roselló
- Microbiological Agents Associated With Animal Reproduction (ProVaginBio), Faculty of Veterinary Sciences, University Cardenal Herrera CEU, CEU Universities, Valencia, Spain
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19
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Ramezani A, Nolin TD, Barrows IR, Serrano MG, Buck GA, Regunathan-Shenk R, West RE, Latham PS, Amdur R, Raj DS. Gut Colonization with Methanogenic Archaea Lowers Plasma Trimethylamine N-oxide Concentrations in Apolipoprotein e-/- Mice. Sci Rep 2018; 8:14752. [PMID: 30283097 PMCID: PMC6170401 DOI: 10.1038/s41598-018-33018-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/20/2018] [Indexed: 01/19/2023] Open
Abstract
A mechanistic link between trimethylamine N-oxide (TMAO) and atherogenesis has been reported. TMAO is generated enzymatically in the liver by the oxidation of trimethylamine (TMA), which is produced from dietary choline, carnitine and betaine by gut bacteria. It is known that certain members of methanogenic archaea (MA) could use methylated amines such as trimethylamine as growth substrates in culture. Therefore, we investigated the efficacy of gut colonization with MA on lowering plasma TMAO concentrations. Initially, we screened for the colonization potential and TMAO lowering efficacy of five MA species in C57BL/6 mice fed with high choline/TMA supplemented diet, and found out that all five species could colonize and lover plasma TMAO levels, although with different efficacies. The top performing MA, Methanobrevibacter smithii, Methanosarcina mazei, and Methanomicrococcus blatticola, were transplanted into Apoe−/− mice fed with high choline/TMA supplemented diet. Similar to C57BL/6 mice, following initial provision of the MA, there was progressive attrition of MA within fecal microbial communities post-transplantation during the initial 3 weeks of the study. In general, plasma TMAO concentrations decreased significantly in proportion to the level of MA colonization. In a subsequent experiment, use of antibiotics and repeated transplantation of Apoe−/− mice with M. smithii, led to high engraftment levels during the 9 weeks of the study, resulting in a sustained and significantly lower average plasma TMAO concentrations (18.2 ± 19.6 μM) compared to that in mock-transplanted control mice (120.8 ± 13.0 μM, p < 0.001). Compared to control Apoe−/− mice, M. smithii-colonized mice also had a 44% decrease in aortic plaque area (8,570 μm [95% CI 19587–151821] vs. 15,369 μm [95% CI [70058–237321], p = 0.34), and 52% reduction in the fat content in the atherosclerotic plaques (14,283 μm [95% CI 4,957–23,608] vs. 29,870 μm [95% CI 18,074–41,666], p = 0.10), although these differences did not reach significance. Gut colonization with M. smithii leads to a significant reduction in plasma TMAO levels, with a tendency for attenuation of atherosclerosis burden in Apoe−/− mice. The anti-atherogenic potential of MA should be further tested in adequately powered experiments.
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Affiliation(s)
- Ali Ramezani
- Division of Renal Diseases and Hypertension, The George Washington University School of Medicine, Washington, DC, USA
| | - Thomas D Nolin
- Department of Pharmacy and Therapeutics, Center for Clinical Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Medicine, Renal-Electrolyte Division, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ian R Barrows
- Department of Medicine Georgetown University School of Medicine, Washington, DC, USA
| | - Myrna G Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
| | - Gregory A Buck
- Department of Microbiology and Immunology, Medical College of Virginia Campus of Virginia Commonwealth University, Richmond, VA, USA
| | - Renu Regunathan-Shenk
- Division of Renal Diseases and Hypertension, The George Washington University School of Medicine, Washington, DC, USA
| | - Raymond E West
- Department of Pharmacy and Therapeutics, Center for Clinical Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patricia S Latham
- Departments of Pathology and Medicine, The George Washington University, Washington, DC, USA
| | - Richard Amdur
- Medical Faculty Associates, Department of Surgery, George Washington University School of Medicine & Health Sciences, Washington, DC, USA
| | - Dominic S Raj
- Division of Renal Diseases and Hypertension, The George Washington University School of Medicine, Washington, DC, USA.
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20
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Alterations of the human gut Methanobrevibacter smithii as a biomarker for inflammatory bowel diseases. Microb Pathog 2018; 117:285-289. [DOI: 10.1016/j.micpath.2018.01.029] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 01/17/2018] [Accepted: 01/19/2018] [Indexed: 12/17/2022]
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21
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Malik SS, Azem-E-Zahra S, Kim KM, Caetano-Anollés G, Nasir A. Do Viruses Exchange Genes across Superkingdoms of Life? Front Microbiol 2017; 8:2110. [PMID: 29163404 PMCID: PMC5671483 DOI: 10.3389/fmicb.2017.02110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/16/2017] [Indexed: 12/13/2022] Open
Abstract
Viruses can be classified into archaeoviruses, bacterioviruses, and eukaryoviruses according to the taxonomy of the infected host. The host-constrained perception of viruses implies preference of genetic exchange between viruses and cellular organisms of their host superkingdoms and viral origins from host cells either via escape or reduction. However, viruses frequently establish non-lytic interactions with organisms and endogenize into the genomes of bacterial endosymbionts that reside in eukaryotic cells. Such interactions create opportunities for genetic exchange between viruses and organisms of non-host superkingdoms. Here, we take an atypical approach to revisit virus-cell interactions by first identifying protein fold structures in the proteomes of archaeoviruses, bacterioviruses, and eukaryoviruses and second by tracing their spread in the proteomes of superkingdoms Archaea, Bacteria, and Eukarya. The exercise quantified protein structural homologies between viruses and organisms of their host and non-host superkingdoms and revealed likely candidates for virus-to-cell and cell-to-virus gene transfers. Unexpected lifestyle-driven genetic affiliations between bacterioviruses and Eukarya and eukaryoviruses and Bacteria were also predicted in addition to a large cohort of protein folds that were universally shared by viral and cellular proteomes and virus-specific protein folds not detected in cellular proteomes. These protein folds provide unique insights into viral origins and evolution that are generally difficult to recover with traditional sequence alignment-dependent evolutionary analyses owing to the fast mutation rates of viral gene sequences.
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Affiliation(s)
- Shahana S Malik
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Syeda Azem-E-Zahra
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Arshan Nasir
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan.,Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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22
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Ryan PM, London LEE, Bjorndahl TC, Mandal R, Murphy K, Fitzgerald GF, Shanahan F, Ross RP, Wishart DS, Caplice NM, Stanton C. Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E -/- mice. MICROBIOME 2017; 5:30. [PMID: 28285599 PMCID: PMC5346842 DOI: 10.1186/s40168-017-0246-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 02/23/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND There is strong evidence indicating that gut microbiota have the potential to modify, or be modified by the drugs and nutritional interventions that we rely upon. This study aims to characterize the compositional and functional effects of several nutritional, neutraceutical, and pharmaceutical cardiovascular disease interventions on the gut microbiome, through metagenomic and metabolomic approaches. Apolipoprotein-E-deficient mice were fed for 24 weeks either high-fat/cholesterol diet alone (control, HFC) or high-fat/cholesterol in conjunction with one of three dietary interventions, as follows: plant sterol ester (PSE), oat β-glucan (OBG) and bile salt hydrolase-active Lactobacillus reuteri APC 2587 (BSH), or the drug atorvastatin (STAT). The gut microbiome composition was then investigated, in addition to the host fecal and serum metabolome. RESULTS We observed major shifts in the composition of the gut microbiome of PSE mice, while OBG and BSH mice displayed more modest fluctuations, and STAT showed relatively few alterations. Interestingly, these compositional effects imparted by PSE were coupled with an increase in acetate and reduction in isovalerate (p < 0.05), while OBG promoted n-butyrate synthesis (p < 0.01). In addition, PSE significantly dampened the microbial production of the proatherogenic precursor compound, trimethylamine (p < 0.05), attenuated cholesterol accumulation, and nearly abolished atherogenesis in the model (p < 0.05). However, PSE supplementation produced the heaviest mice with the greatest degree of adiposity (p < 0.05). Finally, PSE, OBG, and STAT all appeared to have considerable impact on the host serum metabolome, including alterations in several acylcarnitines previously associated with a state of metabolic dysfunction (p < 0.05). CONCLUSIONS We observed functional alterations in microbial and host-derived metabolites, which may have important implications for systemic metabolic health, suggesting that cardiovascular disease interventions may have a significant impact on the microbiome composition and functionality. This study indicates that the gut microbiome-modifying effects of novel therapeutics should be considered, in addition to the direct host effects.
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Affiliation(s)
- Paul M. Ryan
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- School of Microbiology, University College Cork, Co. Cork, Ireland
| | - Lis E. E. London
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Trent C. Bjorndahl
- Department of Biological Sciences, University of Alberta, Edmonton, AB Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, AB Canada
| | - Kiera Murphy
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Gerald F. Fitzgerald
- School of Microbiology, University College Cork, Co. Cork, Ireland
- APC Microbiome Institute, Biosciences Institute, University College Cork, Co. Cork, Ireland
| | - Fergus Shanahan
- Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
- APC Microbiome Institute, Biosciences Institute, University College Cork, Co. Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Institute, Biosciences Institute, University College Cork, Co. Cork, Ireland
- College of Science, Engineering & Food Science, University College Cork, Co. Cork, Ireland
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB Canada
- Department of Computing Science, University of Alberta, Edmonton, AB Canada
- National Institute for Nanotechnology, Edmonton, AB Canada
| | - Noel M. Caplice
- Centre for Research in Vascular Biology, University College Cork, Co. Cork, Ireland
| | - Catherine Stanton
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, Biosciences Institute, University College Cork, Co. Cork, Ireland
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Lyu Z, Whitman WB. Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease. Cell Mol Life Sci 2017; 74:183-212. [PMID: 27261368 PMCID: PMC11107668 DOI: 10.1007/s00018-016-2286-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/05/2016] [Accepted: 05/27/2016] [Indexed: 12/22/2022]
Abstract
Current evolutionary models suggest that Eukaryotes originated from within Archaea instead of being a sister lineage. To test this model of ancient evolution, we review recent studies and compare the three major information processing subsystems of replication, transcription and translation in the Archaea and Eukaryotes. Our hypothesis is that if the Eukaryotes arose within the archaeal radiation, their information processing systems will appear to be one of kind and not wholly original. Within the Eukaryotes, the mammalian or human systems are emphasized because of their importance in understanding health. Biochemical as well as genetic studies provide strong evidence for the functional similarity of archaeal homologs to the mammalian information processing system and their dissimilarity to the bacterial systems. In many independent instances, a simple archaeal system is functionally equivalent to more elaborate eukaryotic homologs, suggesting that evolution of complexity is likely an central feature of the eukaryotic information processing system. Because fewer components are often involved, biochemical characterizations of the archaeal systems are often easier to interpret. Similarly, the archaeal cell provides a genetically and metabolically simpler background, enabling convenient studies on the complex information processing system. Therefore, Archaea could serve as a parsimonious and tractable host for studying human diseases that arise in the information processing systems.
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Affiliation(s)
- Zhe Lyu
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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Budhram A, Parvathy S, Kremenchutzky M, Silverman M. Breaking down the gut microbiome composition in multiple sclerosis. Mult Scler 2016; 23:628-636. [PMID: 27956557 DOI: 10.1177/1352458516682105] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND The gut microbiome, which consists of a highly diverse ecologic community of micro-organisms, has increasingly been studied regarding its role in multiple sclerosis (MS) immunopathogenesis. This review critically examines the literature investigating the gut microbiome in MS. METHODS A comprehensive search was performed of PubMed databases and ECTRIMS meeting abstracts for literature relating to the gut microbiome in MS. Controlled studies examining the gut microbiome in patients with MS were included for review. RESULTS Identified studies were predominantly case-control in their design and consistently found differences in the gut microbiome of MS patients compared to controls. We examine plausible mechanistic links between these differences and MS immunopathogenesis, and discuss the therapeutic implications of these findings. CONCLUSIONS Review of the available literature reveals potential immunopathogenic links between the gut microbiome and MS, identifies avenues for therapeutic advancement, and emphasizes the need for further systematic study in this emerging field.
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Affiliation(s)
- Adrian Budhram
- Department of Clinical Neurological Sciences, Division of Neurology, University Hospital, London, ON, Canada
| | - Seema Parvathy
- Division of Infectious Diseases, St. Joseph's Health Care, London, ON, Canada
| | - Marcelo Kremenchutzky
- Department of Clinical Neurological Sciences, Division of Neurology, University Hospital, London, ON, Canada
| | - Michael Silverman
- Division of Infectious Diseases, St. Joseph's Health Care, London, ON, Canada
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25
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Thombre RS, Shinde V, Thaiparambil E, Zende S, Mehta S. Antimicrobial Activity and Mechanism of Inhibition of Silver Nanoparticles against Extreme Halophilic Archaea. Front Microbiol 2016; 7:1424. [PMID: 27679615 PMCID: PMC5020055 DOI: 10.3389/fmicb.2016.01424] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 08/29/2016] [Indexed: 01/31/2023] Open
Abstract
Haloarchaea are salt-loving halophilic microorganisms that inhabit marine environments, sea water, salterns, and lakes. The resistance of haloarchaea to physical extremities that challenge organismic survival is ubiquitous. Metal and antibiotic resistance of haloarchaea has been on an upsurge due to the exposure of these organisms to metal sinks and drug resistance genes augmented in their natural habitats due to anthropogenic activities and environmental pollution. The efficacy of silver nanoparticles (SNPs) as a potent and broad spectrum inhibitory agent is known, however, there are no reports on the inhibitory activity of SNPs against haloarchaea. In the present study, we have investigated the antimicrobial potentials of SNPs synthesized using aqueous leaf extract of Cinnamomum tamala against antibiotic resistant haloarchaeal isolates Haloferax prahovense RR8, Haloferax lucentense RR15, Haloarcula argentinensis RR10 and Haloarcula tradensis RR13. The synthesized SNPs were characterized by UV-Vis spectroscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy, dynamic light scattering, X-ray diffraction and Fourier transform infrared spectroscopy. The SNPs demonstrated potent antimicrobial activity against the haloarchaea with a minimum inhibitory concentration of 300-400 μg/ml. Growth kinetics of haloarchaea in the presence of SNPs was studied by employing the Baranyi mathematical model for microbial growth using the DMFit curve fitting program. The C. tamala SNPs also demonstrated cytotoxic activity against human lung adenocarcinoma epithelial cell line (A540) and human breast adenocarcinoma cell line (MCF-7). The mechanism of inhibition of haloarchaea by the SNPs was investigated. The plausible mechanism proposed is the alterations and disruption of haloarchaeal membrane permeability by turbulence, inhibition of respiratory dehydrogenases and lipid peroxidation causing cellular and DNA damage resulting in cell death.
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Affiliation(s)
- Rebecca S. Thombre
- Department of Biotechnology, Modern College of Arts, Science and CommercePune, India
| | - Vinaya Shinde
- Department of Biotechnology, Modern College of Arts, Science and CommercePune, India
| | - Elvina Thaiparambil
- Department of Biotechnology, Modern College of Arts, Science and CommercePune, India
| | - Samruddhi Zende
- Department of Biotechnology, Modern College of Arts, Science and CommercePune, India
| | - Sourabh Mehta
- National Center for Nanosciences and Nanotechnology, University of MumbaiMumbai, India
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Carey DE, Zitomer DH, Kappell AD, Choi MJ, Hristova KR, McNamara PJ. Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2016; 18:1060-1067. [PMID: 27291499 DOI: 10.1039/c6em00282j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Triclosan, an antimicrobial chemical found in consumer personal care products, has been shown to stimulate antibiotic resistance in pathogenic bacteria. Although many studies focus on antibiotic resistance pertinent to medical scenarios, resistance developed in natural and engineered environments is less studied and has become an emerging concern for human health. In this study, the impacts of chronic triclosan (TCS) exposure on antibiotic resistance genes (ARGs) and microbial community structure were assessed in lab-scale anaerobic digesters. TCS concentrations from below detection to 2500 mg kg(-1) dry solids were amended into anaerobic digesters over 110 days and acclimated for >3 solid retention time values. Four steady state TCS concentrations were chosen (30-2500 mg kg(-1)). Relative abundance of mexB, a gene coding for a component of a multidrug efflux pump, was significantly higher in all TCS-amended digesters (30 mg kg(-1) or higher) relative to the control. TCS selected for bacteria carrying tet(L) and against those carrying erm(F) at concentrations which inhibited digester function; the pH decrease associated with digester failure was suspected to cause this selection. Little to no impact of TCS was observed on intI1 relative abundance. Microbial communities were also surveyed by high-throughput 16S rRNA gene sequencing. Compared to the control digesters, significant shifts in community structure towards clades containing commensal and pathogenic bacteria were observed in digesters containing TCS. Based on these results, TCS should be included in studies and risk assessments that attempt to elucidate relationships between chemical stressors (e.g. antibiotics), antibiotic resistance genes, and public health.
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Affiliation(s)
- Daniel E Carey
- Department of Civil, Construction and Environmental Engineering, Marquette University, P.O. Box 1881, Milwaukee, WI, USA.
| | - Daniel H Zitomer
- Department of Civil, Construction and Environmental Engineering, Marquette University, P.O. Box 1881, Milwaukee, WI, USA.
| | - Anthony D Kappell
- Department of Biological Sciences, Marquette University, 530 N. 15th Street, Milwaukee, WI, USA
| | - Melinda J Choi
- Department of Civil, Construction and Environmental Engineering, Marquette University, P.O. Box 1881, Milwaukee, WI, USA.
| | - Krassimira R Hristova
- Department of Biological Sciences, Marquette University, 530 N. 15th Street, Milwaukee, WI, USA
| | - Patrick J McNamara
- Department of Civil, Construction and Environmental Engineering, Marquette University, P.O. Box 1881, Milwaukee, WI, USA.
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Ryan PM, Ross RP, Fitzgerald GF, Caplice NM, Stanton C. Functional food addressing heart health: do we have to target the gut microbiota? Curr Opin Clin Nutr Metab Care 2015; 18:566-71. [PMID: 26406391 DOI: 10.1097/mco.0000000000000224] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Health promoting functional food ingredients for cardiovascular health are generally aimed at modulating lipid metabolism in consumers. However, significant advances have furthered our understanding of the mechanisms involved in development, progression, and treatment of cardiovascular disease. In parallel, a central role of the gut microbiota, both in accelerating and attenuating cardiovascular disease, has emerged. RECENT FINDINGS Modulation of the gut microbiota, by use of prebiotics and probiotics, has recently shown promise in cardiovascular disease prevention. Certain prebiotics can promote a short chain fatty acid profile that alters hormone secretion and attenuates cholesterol synthesis, whereas bile salt hydrolase and exopolysaccharide-producing probiotics have been shown to actively correct hypercholesterolemia. Furthermore, specific microbial genera have been identified as potential cardiovascular disease risk factors. This effect is attributed to the ability of certain members of the gut microbiota to convert dietary quaternary amines to trimethylamine, the primary substrate of the putatively atherosclerosis-promoting compound trimethylamine-N-oxide. In this respect, current research is indicating trimethylamine-depleting Achaea - termed Archeabiotics as a potential novel dietary strategy for promoting heart health. SUMMARY The microbiota offers a modifiable target, which has the potential to progress or prevent cardiovascular disease development. Whereas host-targeted interventions remain the standard, current research implicates microbiota-mediated therapies as an effective means of modulating cardiovascular health.
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Affiliation(s)
- Paul M Ryan
- aFood Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy bSchool of Microbiology cAPC Microbiome Institute, Biosciences Institute dCollege of Science, Engineering and Food Science eCentre for Research in Vascular Biology, University College Cork, Cork, Ireland
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Bang C, Schmitz RA. Archaea associated with human surfaces: not to be underestimated. FEMS Microbiol Rev 2015; 39:631-48. [DOI: 10.1093/femsre/fuv010] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 12/18/2022] Open
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