1
|
Liu D, Xie LS, Lian S, Li K, Yang Y, Wang WZ, Hu S, Liu SJ, Liu C, He Z. Anaerostipes hadrus, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil. mSphere 2024; 9:e0081623. [PMID: 38470044 PMCID: PMC11036815 DOI: 10.1128/msphere.00816-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Anaerostipes hadrus (A. hadrus) is a dominant species in the human gut microbiota and considered a beneficial bacterium for producing probiotic butyrate. However, recent studies have suggested that A. hadrus may negatively affect the host through synthesizing fatty acid and metabolizing the anticancer drug 5-fluorouracil, indicating that the impact of A. hadrus is complex and unclear. Therefore, comprehensive genomic studies on A. hadrus need to be performed. We integrated 527 high-quality public A. hadrus genomes and five distinct metagenomic cohorts. We analyzed these data using the approaches of comparative genomics, metagenomics, and protein structure prediction. We also performed validations with culture-based in vitro assays. We constructed the first large-scale pan-genome of A. hadrus (n = 527) and identified 5-fluorouracil metabolism genes as ubiquitous in A. hadrus genomes as butyrate-producing genes. Metagenomic analysis revealed the wide and stable distribution of A. hadrus in healthy individuals, patients with inflammatory bowel disease, and patients with colorectal cancer, with healthy individuals carrying more A. hadrus. The predicted high-quality protein structure indicated that A. hadrus might metabolize 5-fluorouracil by producing bacterial dihydropyrimidine dehydrogenase (encoded by the preTA operon). Through in vitro assays, we validated the short-chain fatty acid production and 5-fluorouracil metabolism abilities of A. hadrus. We observed for the first time that A. hadrus can convert 5-fluorouracil to α-fluoro-β-ureidopropionic acid, which may result from the combined action of the preTA operon and adjacent hydA (encoding bacterial dihydropyrimidinase). Our results offer novel understandings of A. hadrus, exceptionally functional features, and potential applications. IMPORTANCE This work provides new insights into the evolutionary relationships, functional characteristics, prevalence, and potential applications of Anaerostipes hadrus.
Collapse
Affiliation(s)
- Danping Liu
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People’s Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| | - Li-Sheng Xie
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shitao Lian
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People’s Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| | - Kexin Li
- Systems Biology and Bioinformatics (SBI), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Yun Yang
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People’s Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| | - Wen-Zhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zilong He
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People’s Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| |
Collapse
|
2
|
Davoudkhani M, Rubino F, Creevey CJ, Ahvenjärvi S, Bayat AR, Tapio I, Belanche A, Muñoz-Tamayo R. Integrating microbial abundance time series with fermentation dynamics of the rumen microbiome via mathematical modelling. PLoS One 2024; 19:e0298930. [PMID: 38507436 PMCID: PMC10954177 DOI: 10.1371/journal.pone.0298930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/02/2024] [Indexed: 03/22/2024] Open
Abstract
The rumen represents a dynamic microbial ecosystem where fermentation metabolites and microbial concentrations change over time in response to dietary changes. The integration of microbial genomic knowledge and dynamic modelling can enhance our system-level understanding of rumen ecosystem's function. However, such an integration between dynamic models and rumen microbiota data is lacking. The objective of this work was to integrate rumen microbiota time series determined by 16S rRNA gene amplicon sequencing into a dynamic modelling framework to link microbial data to the dynamics of the volatile fatty acids (VFA) production during fermentation. For that, we used the theory of state observers to develop a model that estimates the dynamics of VFA from the data of microbial functional proxies associated with the specific production of each VFA. We determined the microbial proxies using CowPi to infer the functional potential of the rumen microbiota and extrapolate their functional modules from KEGG (Kyoto Encyclopedia of Genes and Genomes). The approach was challenged using data from an in vitro RUSITEC experiment and from an in vivo experiment with four cows. The model performance was evaluated by the coefficient of variation of the root mean square error (CRMSE). For the in vitro case study, the mean CVRMSE were 9.8% for acetate, 14% for butyrate and 14.5% for propionate. For the in vivo case study, the mean CVRMSE were 16.4% for acetate, 15.8% for butyrate and 19.8% for propionate. The mean CVRMSE for the VFA molar fractions were 3.1% for acetate, 3.8% for butyrate and 8.9% for propionate. Ours results show the promising application of state observers integrated with microbiota time series data for predicting rumen microbial metabolism.
Collapse
Affiliation(s)
- Mohsen Davoudkhani
- INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, Université Paris-Saclay, Palaiseau, France
| | - Francesco Rubino
- Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Christopher J. Creevey
- Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Seppo Ahvenjärvi
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Ali R. Bayat
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Ilma Tapio
- Genomics and Breeding, Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Alejandro Belanche
- Departamento de Producción Animal y Ciencia de los Alimentos, Universidad de Zaragoza, Zaragoza, Spain
| | - Rafael Muñoz-Tamayo
- INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, Université Paris-Saclay, Palaiseau, France
| |
Collapse
|
3
|
Karim MR, Iqbal S, Mohammad S, Morshed MN, Haque MA, Mathiyalagan R, Yang DC, Kim YJ, Song JH, Yang DU. Butyrate's (a short-chain fatty acid) microbial synthesis, absorption, and preventive roles against colorectal and lung cancer. Arch Microbiol 2024; 206:137. [PMID: 38436734 DOI: 10.1007/s00203-024-03834-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 03/05/2024]
Abstract
Butyrate, a short-chain fatty acid (SCFA) produced by bacterial fermentation of fiber in the colon, is a source of energy for colonocytes. Butyrate is essential for improving gastrointestinal (GI) health since it helps colonocyte function, reduces inflammation, preserves the gut barrier, and fosters a balanced microbiome. Human colonic butyrate producers are Gram-positive firmicutes, which are phylogenetically varied. The two most prevalent subgroups are associated with Eubacterium rectale/Roseburia spp. and Faecalibacterium prausnitzii. Now, the mechanism for the production of butyrate from microbes is a very vital topic to know. In the present study, we discuss the genes encoding the core of the butyrate synthesis pathway and also discuss the butyryl-CoA:acetate CoA-transferase, instead of butyrate kinase, which usually appears to be the enzyme that completes the process. Recently, butyrate-producing microbes have been genetically modified by researchers to increase butyrate synthesis from microbes. The activity of butyrate as a histone deacetylase inhibitor (HDACi) has led to several clinical trials to assess its effectiveness as a potential cancer treatment. Among various significant roles, butyrate is the main energy source for intestinal epithelial cells, which helps maintain colonic homeostasis. Moreover, people with non-small-cell lung cancer (NSCLC) have distinct gut microbiota from healthy adults and frequently have dysbiosis of the butyrate-producing bacteria in their guts. So, with an emphasis on colon and lung cancer, this review also discusses how the microbiome is crucial in preventing the progression of certain cancers through butyrate production. Further studies should be performed to investigate the underlying mechanisms of how these specific butyrate-producing bacteria can control both colon and lung cancer progression and prognosis.
Collapse
Affiliation(s)
- Md Rezaul Karim
- Department of Biopharmaceutical Biotechnology, College of Life Science, Kyung Hee University, Yongin-Si, 17104, Gyeonggi-Do, Korea
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh
| | - Safia Iqbal
- Department of Biopharmaceutical Biotechnology, College of Life Science, Kyung Hee University, Yongin-Si, 17104, Gyeonggi-Do, Korea
- Department of Microbiology, Varendra Institute of Biosciences, Affiliated University of Rajshahi, Natore, 6400, Rajshahi, Bangladesh
| | - Shahnawaz Mohammad
- Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin-Si, 17104, Gyeonggi-Do, Korea
| | - Md Niaj Morshed
- Department of Biopharmaceutical Biotechnology, College of Life Science, Kyung Hee University, Yongin-Si, 17104, Gyeonggi-Do, Korea
| | - Md Anwarul Haque
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh
| | - Ramya Mathiyalagan
- Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin-Si, 17104, Gyeonggi-Do, Korea
| | - Deok Chun Yang
- Department of Biopharmaceutical Biotechnology, College of Life Science, Kyung Hee University, Yongin-Si, 17104, Gyeonggi-Do, Korea
- Hanbangbio Inc., Yongin-Si, 17104, Gyeonggi-Do, Republic of Korea
| | - Yeon Ju Kim
- Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin-Si, 17104, Gyeonggi-Do, Korea
| | - Joong Hyun Song
- Department of Veterinary International Medicine, College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Korea.
| | - Dong Uk Yang
- Department of Biopharmaceutical Biotechnology, College of Life Science, Kyung Hee University, Yongin-Si, 17104, Gyeonggi-Do, Korea.
- AIBIOME, 6, Jeonmin-Ro 30Beon-Gil, Yuseong-Gu, Daejeon, Republic of Korea.
| |
Collapse
|
4
|
Pistol GC, Pertea AM, Taranu I. The Use of Fruit and Vegetable by-Products as Enhancers of Health Status of Piglets after Weaning: The Role of Bioactive Compounds from Apple and Carrot Industrial Wastes. Vet Sci 2023; 11:15. [PMID: 38250921 PMCID: PMC10820549 DOI: 10.3390/vetsci11010015] [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: 11/15/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
At weaning, piglets are exposed to a large variety of stressors, from environmental/behavioral factors to nutritional stress. Weaning transition affects the gastrointestinal tract especially, resulting in specific disturbances at the level of intestinal morphology, barrier function and integrity, mucosal immunity and gut microbiota. All these alterations are associated with intestinal inflammation, oxidative stress and perturbation of intracellular signaling pathways. The nutritional management of the weaning period aims to achieve the reinforcement of intestinal integrity and functioning to positively modulate the intestinal immunity and that of the gut microbiota and to enhance the health status of piglets. That is why the current research is focused on the raw materials rich in phytochemicals which could positively modulate animal health. The composition analysis of fruit, vegetable and their by-products showed that identified phytochemicals could act as bioactive compounds, which can be used as modulators of weaning-induced disturbances in piglets. This review describes nutritional studies which investigated the effects of bioactive compounds derived from fruit (apple) and vegetables (carrot) or their by-products on the intestinal architecture and function, inflammatory processes and oxidative stress at the intestinal level. Data on the associated signaling pathways and on the microbiota modulation by bioactive compounds from these by-products are also presented.
Collapse
Affiliation(s)
- Gina Cecilia Pistol
- Laboratory of Animal Biology, INCDBNA-IBNA, National Research—Development Institute for Animal Biology and Nutrition, 077015 Balotesti, Ilfov, Romania; (A.-M.P.); (I.T.)
| | | | | |
Collapse
|
5
|
Li Z, Selim A, Kuehn S. Statistical prediction of microbial metabolic traits from genomes. PLoS Comput Biol 2023; 19:e1011705. [PMID: 38113208 PMCID: PMC10729968 DOI: 10.1371/journal.pcbi.1011705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
The metabolic activity of microbial communities is central to their role in biogeochemical cycles, human health, and biotechnology. Despite the abundance of sequencing data characterizing these consortia, it remains a serious challenge to predict microbial metabolic traits from sequencing data alone. Here we culture 96 bacterial isolates individually and assay their ability to grow on 10 distinct compounds as a sole carbon source. Using these data as well as two existing datasets, we show that statistical approaches can accurately predict bacterial carbon utilization traits from genomes. First, we show that classifiers trained on gene content can accurately predict bacterial carbon utilization phenotypes by encoding phylogenetic information. These models substantially outperform predictions made by constraint-based metabolic models automatically constructed from genomes. This result solidifies our current knowledge about the strong connection between phylogeny and metabolic traits. However, phylogeny-based predictions fail to predict traits for taxa that are phylogenetically distant from any strains in the training set. To overcome this we train improved models on gene presence/absence to predict carbon utilization traits from gene content. We show that models that predict carbon utilization traits from gene presence/absence can generalize to taxa that are phylogenetically distant from the training set either by exploiting biochemical information for feature selection or by having sufficiently large datasets. In the latter case, we provide evidence that a statistical approach can identify putatively mechanistic genes involved in metabolic traits. Our study demonstrates the potential power for predicting microbial phenotypes from genotypes using statistical approaches.
Collapse
Affiliation(s)
- Zeqian Li
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
- Department of Physics, The University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ahmed Selim
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, Illinois, United States of America
| | - Seppe Kuehn
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| |
Collapse
|
6
|
Zhang Y, Xing H, Bolotnikov G, Krämer M, Gotzmann N, Knippschild U, Kissmann AK, Rosenau F. Enriched Aptamer Libraries in Fluorescence-Based Assays for Rikenella microfusus-Specific Gut Microbiome Analyses. Microorganisms 2023; 11:2266. [PMID: 37764110 PMCID: PMC10535755 DOI: 10.3390/microorganisms11092266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Rikenella microfusus is an essential intestinal probiotic with great potential. The latest research shows that imbalance in the intestinal flora are related to the occurrence of various diseases, such as intestinal diseases, immune diseases, and metabolic diseases. Rikenella may be a target or biomarker for some diseases, providing a new possibility for preventing and treating these diseases by monitoring and optimizing the abundance of Rikenella in the intestine. However, the current monitoring methods have disadvantages, such as long detection times, complicated operations, and high costs, which seriously limit the possibility of clinical application of microbiome-based treatment options. Therefore, the intention of this study was to evolve an enriched aptamer library to be used for specific labeling of R. microfusus, allowing rapid and low-cost detection methods and, ultimately the construction of aptamer-based biosensors. In this study, we used Rikenella as the target bacterium for an in vitro whole Cell-SELEX (Systematic Evolution of Ligands by EXponential Enrichment) to evolve and enrich specific DNA oligonucleotide aptamers. Five other prominent anaerobic gut bacteria were included in this process for counterselection and served as control cells. The aptamer library R.m-R13 was evolved with high specificity and strong affinity (Kd = 9.597 nM after 13 rounds of selection). With this enriched aptamer library, R. microfusus could efficiently be discriminated from the control bacteria in complex mixtures using different analysis techniques, including fluorescence microscopy or fluorometric suspension assays, and even in human stool samples. These preliminary results open new avenues toward the development of aptamer-based microbiome bio-sensing applications for fast and reliable monitoring of R. microfusus.
Collapse
Affiliation(s)
- Yiting Zhang
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Nina Gotzmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
- Max-Planck-Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (Y.Z.); (H.X.); (G.B.); (M.K.); (N.G.); (A.-K.K.)
| |
Collapse
|
7
|
Chaves-Filho AM, Braniff O, Angelova A, Deng Y, Tremblay MÈ. Chronic inflammation, neuroglial dysfunction, and plasmalogen deficiency as a new pathobiological hypothesis addressing the overlap between post-COVID-19 symptoms and myalgic encephalomyelitis/chronic fatigue syndrome. Brain Res Bull 2023; 201:110702. [PMID: 37423295 DOI: 10.1016/j.brainresbull.2023.110702] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/13/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
After five waves of coronavirus disease 2019 (COVID-19) outbreaks, it has been recognized that a significant portion of the affected individuals developed long-term debilitating symptoms marked by chronic fatigue, cognitive difficulties ("brain fog"), post-exertional malaise, and autonomic dysfunction. The onset, progression, and clinical presentation of this condition, generically named post-COVID-19 syndrome, overlap significantly with another enigmatic condition, referred to as myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Several pathobiological mechanisms have been proposed for ME/CFS, including redox imbalance, systemic and central nervous system inflammation, and mitochondrial dysfunction. Chronic inflammation and glial pathological reactivity are common hallmarks of several neurodegenerative and neuropsychiatric disorders and have been consistently associated with reduced central and peripheral levels of plasmalogens, one of the major phospholipid components of cell membranes with several homeostatic functions. Of great interest, recent evidence revealed a significant reduction of plasmalogen contents, biosynthesis, and metabolism in ME/CFS and acute COVID-19, with a strong association to symptom severity and other relevant clinical outcomes. These bioactive lipids have increasingly attracted attention due to their reduced levels representing a common pathophysiological manifestation between several disorders associated with aging and chronic inflammation. However, alterations in plasmalogen levels or their lipidic metabolism have not yet been examined in individuals suffering from post-COVID-19 symptoms. Here, we proposed a pathobiological model for post-COVID-19 and ME/CFS based on their common inflammation and dysfunctional glial reactivity, and highlighted the emerging implications of plasmalogen deficiency in the underlying mechanisms. Along with the promising outcomes of plasmalogen replacement therapy (PRT) for various neurodegenerative/neuropsychiatric disorders, we sought to propose PRT as a simple, effective, and safe strategy for the potential relief of the debilitating symptoms associated with ME/CFS and post-COVID-19 syndrome.
Collapse
Affiliation(s)
| | - Olivia Braniff
- Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Angelina Angelova
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, F-91400 Orsay, France
| | - Yuru Deng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China.
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada; Department of Molecular Medicine, Université Laval, Québec City, Québec, Canada; Neurology and Neurosurgery Department, McGill University, Montréal, Québec, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Advanced Materials and Related Technology (CAMTEC) and Institute on Aging and Lifelong Health (IALH), University of Victoria, Victoria, British Columbia, Canada.
| |
Collapse
|
8
|
Walker AW, Hoyles L. Human microbiome myths and misconceptions. Nat Microbiol 2023; 8:1392-1396. [PMID: 37524974 DOI: 10.1038/s41564-023-01426-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 06/15/2023] [Indexed: 08/02/2023]
Abstract
Over the past two decades, interest in human microbiome research has increased exponentially. Regrettably, this increased activity has brought with it a degree of hype and misinformation, which can undermine progress and public confidence in the research. Here we highlight selected human microbiome myths and misconceptions that lack a solid evidence base. By presenting these examples, we hope to draw increased attention to the implications of inaccurate dogma becoming embedded in the literature, and the importance of acknowledging nuance when describing the complex human microbiome.
Collapse
Affiliation(s)
- Alan W Walker
- Microbiome, Food Innovation and Food Security Research Theme, Rowett Institute, University of Aberdeen, Aberdeen, UK.
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
| |
Collapse
|
9
|
Omotosho AO, Tajudeen YA, Oladipo HJ, Yusuff SI, AbdulKadir M, Muili AO, Egbewande OM, Yusuf RO, Faniran ZO, Afolabi AO, El‐Sherbini MS. Parkinson's disease: Are gut microbes involved? Brain Behav 2023; 13:e3130. [PMID: 37340511 PMCID: PMC10454343 DOI: 10.1002/brb3.3130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023] Open
Abstract
INTRODUCTION Parkinson's disease (PD) is a neurodegenerative disorder that affects more than 10 million individuals worldwide. It is characterized by motor and sensory deficits. Research studies have increasingly demonstrated a correlation between Parkinson's disease and alternations in the composition of the gut microbiota in affected patients. Also, the significant role of prebiotics and probiotics in gastrointestinal and neurological conditions is imperative to understand their relation to Parkinson's disease. METHOD To explore the scientific interaction of the gut-microbiota-brain axis and its association with Parkinson's disease, a comprehensive narrative review of the relevant literature was conducted. Articles were retrieved systematically from reputable sources, including PubMed, Science Direct, World Health Organization (WHO), and Advanced Google Scholar. Key search terms included are "Parkinson's Disease", "Gut Microbiome", "Braak's Theory", "Neurological Disorders", and "Gut-brain axis". Articles included in our review are published in English and they provide detailed information on the relationship between Parkinson's disease and gut microbiota RESULTS: This review highlights the impact of gut microbiota composition and associated factors on the progression of Parkinson's disease. Evidence-based studies highlighting the existing evidence of the relationship between Parkinson's disease and alteration in gut microbiota are discussed. Consequently, the potential mechanisms by which the gut microbiota may affect the composition of the gut microbiota were revealed, with a particular emphasis on the role of the gut-brain axis in this interplay. CONCLUSION Understanding the complex interplay between gut microbiota and Parkinson's disease is a potential implication for the development of novel therapeutics against Parkinson's disease. Following the existing relationship demonstrated by different evidence-based studies on Parkinson's disease and gut microbiota, our review concludes by providing recommendations and suggestions for future research studies with a particular emphasis on the impact of the microbiota-brain axis on Parkinson's disease.
Collapse
Affiliation(s)
- Abass Olawale Omotosho
- Department of Microbiology, Faculty of Pure and Applied SciencesKwara State University, Malete‐IlorinIlorinNigeria
| | - Yusuf Amuda Tajudeen
- Department of Microbiology, Faculty of Life SciencesUniversity of IlorinIlorinNigeria
- Faculty of Pharmaceutical SciencesUniversity of IlorinIlorinNigeria
| | - Habeebullah Jayeola Oladipo
- Department of Microbiology, Faculty of Life SciencesUniversity of IlorinIlorinNigeria
- Department of Epidemiology and Medical Statistics, Faculty of Public Health, College of MedicineUniversity of IbadanIbadanNigeria
| | - Sodiq Inaolaji Yusuff
- Department of Medicine, Faculty of Clinical SciencesObafemi Awolowo UniversityIfeNigeria
| | - Muritala AbdulKadir
- Department of Epidemiology and Medical Statistics, Faculty of Public Health, College of MedicineUniversity of IbadanIbadanNigeria
| | | | - Oluwaseyi Muyiwa Egbewande
- Department of Epidemiology and Medical Statistics, Faculty of Public Health, College of MedicineUniversity of IbadanIbadanNigeria
| | - Rashidat Onyinoyi Yusuf
- Department of Epidemiology and Medical Statistics, Faculty of Public Health, College of MedicineUniversity of IbadanIbadanNigeria
| | | | - Abdullateef Opeyemi Afolabi
- Faculty of Biomedical Sciences, Department of Microbiology and ImmunologyKampala International UniversityBushenyiUganda
| | - Mona Said El‐Sherbini
- Narrative Medicine and Planetary Health, Integrated Program of Kasr Al-Ainy (IPKA), Faculty of MedicineCairo UniversityCairoEgypt
- Invited Facultythe Nova Institute for HealthBaltimoreMDUSA
- Department of Medical Parasitology, Faculty of MedicineCairo UniversityCairoEgypt
| |
Collapse
|
10
|
Rusch JA, Layden BT, Dugas LR. Signalling cognition: the gut microbiota and hypothalamic-pituitary-adrenal axis. Front Endocrinol (Lausanne) 2023; 14:1130689. [PMID: 37404311 PMCID: PMC10316519 DOI: 10.3389/fendo.2023.1130689] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/25/2023] [Indexed: 07/06/2023] Open
Abstract
Cognitive function in humans depends on the complex and interplay between multiple body systems, including the hypothalamic-pituitary-adrenal (HPA) axis. The gut microbiota, which vastly outnumbers human cells and has a genetic potential that exceeds that of the human genome, plays a crucial role in this interplay. The microbiota-gut-brain (MGB) axis is a bidirectional signalling pathway that operates through neural, endocrine, immune, and metabolic pathways. One of the major neuroendocrine systems responding to stress is the HPA axis which produces glucocorticoids such as cortisol in humans and corticosterone in rodents. Appropriate concentrations of cortisol are essential for normal neurodevelopment and function, as well as cognitive processes such as learning and memory, and studies have shown that microbes modulate the HPA axis throughout life. Stress can significantly impact the MGB axis via the HPA axis and other pathways. Animal research has advanced our understanding of these mechanisms and pathways, leading to a paradigm shift in conceptual thinking about the influence of the microbiota on human health and disease. Preclinical and human trials are currently underway to determine how these animal models translate to humans. In this review article, we summarize the current knowledge of the relationship between the gut microbiota, HPA axis, and cognition, and provide an overview of the main findings and conclusions in this broad field.
Collapse
Affiliation(s)
- Jody A. Rusch
- Division of Chemical Pathology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- C17 Chemical Pathology Laboratory, Groote Schuur Hospital, National Health Laboratory Service, Cape Town, South Africa
| | - Brian T. Layden
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States
| | - Lara R. Dugas
- Division of Epidemiology and Biostatistics, School of Public Health, University of Cape Town, Cape Town, South Africa
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States
| |
Collapse
|
11
|
Talapko J, Meštrović T, Dmitrović B, Juzbašić M, Matijević T, Bekić S, Erić S, Flam J, Belić D, Petek Erić A, Milostić Srb A, Škrlec I. A Putative Role of Candida albicans in Promoting Cancer Development: A Current State of Evidence and Proposed Mechanisms. Microorganisms 2023; 11:1476. [PMID: 37374978 DOI: 10.3390/microorganisms11061476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Candida albicans is a commensal fungal species that commonly colonizes the human body, but it is also a pervasive opportunistic pathogen in patients with malignant diseases. A growing body of evidence suggests that this fungus is not only coincidental in oncology patients, but may also play an active role in the development of cancer. More specifically, several studies have investigated the potential association between C. albicans and various types of cancer, including oral, esophageal, and colorectal cancer, with a possible role of this species in skin cancer as well. The proposed mechanisms include the production of carcinogenic metabolites, modulation of the immune response, changes in cell morphology, microbiome alterations, biofilm production, the activation of oncogenic signaling pathways, and the induction of chronic inflammation. These mechanisms may act together or independently to promote cancer development. Although more research is needed to fully grasp the potential role of C. albicans in carcinogenesis, the available evidence suggests that this species may be an active contributor and underscores the importance of considering the impact of the human microbiome on cancer pathogenesis. In this narrative review, we aimed to summarize the current state of evidence and offer some insights into proposed mechanisms.
Collapse
Affiliation(s)
- Jasminka Talapko
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Tomislav Meštrović
- University Centre Varaždin, University North, 42000 Varaždin, Croatia
- Institute for Health Metrics and Evaluation and the Department of Health Metrics Sciences, University of Washington, Seattle, WA 98195, USA
| | - Branko Dmitrović
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Pathology and Forensic Medicine, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Martina Juzbašić
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Tatjana Matijević
- Department of Dermatology and Venereology, University Hospital Center Osijek, 31000 Osijek, Croatia
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Sanja Bekić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Family Medicine Practice, 31000 Osijek, Croatia
| | - Suzana Erić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Radiotherapy and Oncology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Josipa Flam
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Radiotherapy and Oncology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Dino Belić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Radiotherapy and Oncology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Anamarija Petek Erić
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Psychiatry, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Andrea Milostić Srb
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Ivana Škrlec
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| |
Collapse
|
12
|
Duncan SH, Conti E, Ricci L, Walker AW. Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health. Biomedicines 2023; 11:biomedicines11051338. [PMID: 37239009 DOI: 10.3390/biomedicines11051338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe-microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.
Collapse
Affiliation(s)
- Sylvia H Duncan
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Elena Conti
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Liviana Ricci
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Alan W Walker
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| |
Collapse
|
13
|
Ho SFS, Wheeler NE, Millard AD, van Schaik W. Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data. MICROBIOME 2023; 11:84. [PMID: 37085924 PMCID: PMC10120246 DOI: 10.1186/s40168-023-01533-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND The prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A comparative analysis of ten state-of-the-art phage identification tools was performed to inform their usage in microbiome research. METHODS Artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage species, were used to evaluate the precision, recall, and F1 scores of the tools. We also generated a dataset of randomly shuffled sequences to quantify false-positive calls. In addition, a set of previously simulated viromes was used to assess diversity bias in each tool's output. RESULTS VIBRANT and VirSorter2 achieved the highest F1 scores (0.93) in the RefSeq artificial contigs dataset, with several other tools also performing well. Kraken2 had the highest F1 score (0.86) in the mock community benchmark by a large margin (0.3 higher than DeepVirFinder in second place), mainly due to its high precision (0.96). Generally, k-mer-based tools performed better than reference similarity tools and gene-based methods. Several tools, most notably PPR-Meta, called a high number of false positives in the randomly shuffled sequences. When analysing the diversity of the genomes that each tool predicted from a virome set, most tools produced a viral genome set that had similar alpha- and beta-diversity patterns to the original population, with Seeker being a notable exception. CONCLUSIONS This study provides key metrics used to assess performance of phage detection tools, offers a framework for further comparison of additional viral discovery tools, and discusses optimal strategies for using these tools. We highlight that the choice of tool for identification of phages in metagenomic datasets, as well as their parameters, can bias the results and provide pointers for different use case scenarios. We have also made our benchmarking dataset available for download in order to facilitate future comparisons of phage identification tools. Video Abstract.
Collapse
Affiliation(s)
- Siu Fung Stanley Ho
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nicole E. Wheeler
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Andrew D. Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
14
|
Woo AYM, Aguilar Ramos MA, Narayan R, Richards-Corke KC, Wang ML, Sandoval-Espinola WJ, Balskus EP. Targeting the human gut microbiome with small-molecule inhibitors. NATURE REVIEWS. CHEMISTRY 2023; 7:319-339. [PMID: 37117817 DOI: 10.1038/s41570-023-00471-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 04/30/2023]
Abstract
The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.
Collapse
Affiliation(s)
- Amelia Y M Woo
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | | | - Rohan Narayan
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | | | - Michelle L Wang
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | - Walter J Sandoval-Espinola
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
- Universidad Nacional de Asunción, Facultad de Ciencias Exactas y Naturales, Departamento de Biotecnología, Laboratorio de Biotecnología Microbiana, San Lorenzo, Paraguay
| | - Emily P Balskus
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
15
|
Wang H, Wang Q, Liang C, Pan L, Hu H, Fang H. Acupuncture improved hepatic steatosis in HFD-induced NAFLD rats by regulating intestinal microbiota. Front Microbiol 2023; 14:1131092. [PMID: 37007509 PMCID: PMC10061080 DOI: 10.3389/fmicb.2023.1131092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
BackgroundIntestinal dysbiosis has been increasingly implicated in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). Acupuncture has been shown to have beneficial effects on NAFLD, but the mechanism is not yet clear. This study explores the potential beneficial effects of acupuncture on intestinal microbiota in NAFLD.MethodsAn NAFLD model in Sprague Dawley rats was established using a high-fat diet (HFD) for 10 weeks. NAFLD rats were randomly divided into control, model, and acupuncture groups. Following acupuncture treatment over 6 weeks, automated biochemical analysis was used to measure serum lipid metabolism parameters, including levels of alanine transferase, aspartate transferase, alkaline phosphatase, total cholesterol, triglycerides, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol. The level of serum inflammatory factors interleukin (IL)-6, IL-10, and tumor necrosis factor-alpha (TNF-α) were measured by enzyme-linked immunosorbent assay. The characteristics of steatosis were evaluated using quantitative computed tomography, hematoxylin and eosin staining, and Oil Red O staining in the liver, while the intestinal microbiota was determined using 16S rRNA gene sequencing.ResultsAcupuncture decreased the systemic inflammatory response, ameliorated dyslipidemia, and improved liver function indexes in NAFLD model rats. Tomography and staining indicated that acupuncture reduced steatosis and infiltration of inflammatory cells in the liver. 16S rRNA analysis showed that acupuncture reduced the Firmicutes to Bacteroidetes (F/B) ratio, increased the abundance of microbiota, including Bacteroidales_S24-7_group, Prevotellaceae, Bacteroidaceae, Blautia, norank_f_Bacteroidales_S24-7_group, Bacteroides, and Prevotella_9, and decreased the abundance of Ruminococcaceae_UCG-014. Correlation analysis suggested a close correlation between lipid metabolism, inflammation factors, hepatic steatosis, and the changed intestinal microbiota.ConclusionAcupuncture can significantly improve lipid metabolism and the systemic inflammatory response in HFD-induced NAFLD rats, potentially by regulating intestinal microbiota composition.
Collapse
Affiliation(s)
- Haiying Wang
- Department of Cardiology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qiang Wang
- Chinese People’s Liberation Army Center of Disease Control and Prevention, Beijing, China
| | - Cuimei Liang
- Department of Acupuncture, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Liang Pan
- Department of Acupuncture, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Hui Hu
- Department of Acupuncture, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Hui Hu,
| | - Hongjuan Fang
- Department of Endocrinology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Hongjuan Fang,
| |
Collapse
|
16
|
Peripheral Regulation of Central Brain-Derived Neurotrophic Factor Expression through the Vagus Nerve. Int J Mol Sci 2023; 24:ijms24043543. [PMID: 36834953 PMCID: PMC9964523 DOI: 10.3390/ijms24043543] [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: 01/12/2023] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The brain-derived neurotrophic factor (BDNF) is an extensively studied neurotrophin es sential for both developing the brain and maintaining adult brain function. In the adult hippocampus, BDNF is critical for maintaining adult neurogenesis. Adult hippocampal neurogenesis is involved not only in memory formation and learning ability, but also mood regulation and stress responses. Accordingly, decreased levels of BDNF, accompanied by low levels of adult neurogenesis, occurs in brains of older adults with impaired cognitive function and in those of patients with major depression disorder. Therefore, elucidating the mechanisms that maintain hippocampal BDNF levels is biologically and clinically important. It has been revealed that signalling from peripheral tissues contribute to the regulation of BDNF expression in the brain across the blood-brain barrier. Moreover, recent studies indicated evidence that neuronal pathways can also be a mechanism by which peripheral tissues signal to the brain for the regulation of BDNF expression. In this review, we give an overview of the current status in the regulation of central BDNF expression by peripheral signalling, with a special interest in the regulation of hippocampal BDNF levels by signals via the vagus nerve. Finally, we discuss the relationship between signalling from peripheral tissues and age-associated control of central BDNF expression.
Collapse
|
17
|
Wu W, Ouyang Y, Zheng P, Xu X, He C, Xie C, Hong J, Lu N, Zhu Y, Li N. Research trends on the relationship between gut microbiota and colorectal cancer: A bibliometric analysis. Front Cell Infect Microbiol 2023; 12:1027448. [PMID: 36699721 PMCID: PMC9868464 DOI: 10.3389/fcimb.2022.1027448] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023] Open
Abstract
Background Colorectal cancer (CRC)is the third most common cancer in the world and the second leading cause of cancer-related deaths, and over the past two decades, many of these researchers have provided a substantial amount of important information on the role of gut microbes in the development and progression of CRC. A causal relationship between the presence of specific microorganisms and CRC development has also been validated. Although a large number of papers related to this area have been published, no bibliometric study has been conducted to review the current state of research in this area and to highlight the research trends and hotspots in this area. This study aims to analyze the current status and future research trends of gut microbiota and CRC through bibliometric analysis. Methods Publications from 2001 to 2022 were retrieved from the Web of Science Core Collection database and screened according to inclusion criteria. VOSviewer and CiteSpace software were used to visualize the research trends in this field, including the analysis of title, country, institution, author, number of publications, year of publication, number of citations, journal, and H-index. Results A total of 863 studies were eventually identified, and the articles retrieved were cited an average of 44.85 times each. The number of publications on this topic has been increased steadily since 2011. China and the USA have made the largest contribution in the field. FRONTIERS IN MICROBIOLOGY is the top productive journal with 26 papers, and Gut journal has the highest average citation (167.23). Shanghai Jiao Tong University is the most contributive institution. Professor Yu J, Sung, Joseph J. Y and Fang JY are the most productive authors in this field. Keyword co-occurrence analysis showed that the terms of "Gut Microbiota", "Colorectal Cancer", "Inflammation", "Probiotic" and "Fusobacterium Nucleatum" were the most frequent, which revealed the research hotpots and trends in this field. Conclusions There has been a growing number of publications over the past two decades according to the global trends. China and the USA still maintained the leading position in this field. However, collaboration between institutions needs to be strengthened. It's commended to pay attention to the latest hotspots, such as "F. nucleatum" and "probiotics". This bibliometric analysis evaluates the scope and trends of gut microbiota and CRC, providing a useful perspective on current research and future directions for studying the link between the gut microbiota and CRC.
Collapse
Affiliation(s)
- Weigen Wu
- Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yaobin Ouyang
- Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Pan Zheng
- Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xinbo Xu
- Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Cong He
- Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chuan Xie
- Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Junbo Hong
- Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Nonghua Lu
- Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yin Zhu
- Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Nianshuang Li
- Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China,*Correspondence: Nianshuang Li,
| |
Collapse
|
18
|
Esteban-Torres M, Ruiz L, Rossini V, Nally K, van Sinderen D. Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait. Gut Microbes 2023; 15:2235067. [PMID: 37526383 PMCID: PMC10395257 DOI: 10.1080/19490976.2023.2235067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.
Collapse
Affiliation(s)
- Maria Esteban-Torres
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Benefitial Microbes (MicroHealth Group), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Valerio Rossini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
19
|
Peng K, Dong W, Luo T, Tang H, Zhu W, Huang Y, Yang X. Butyrate and obesity: Current research status and future prospect. Front Endocrinol (Lausanne) 2023; 14:1098881. [PMID: 36909336 PMCID: PMC9999029 DOI: 10.3389/fendo.2023.1098881] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/07/2023] [Indexed: 03/14/2023] Open
Abstract
Over the past few decades, increasing prevalence of obesity caused an enormous medical, social, and economic burden. As the sixth most important risk factor contributing to the overall burden of disease worldwide, obesity not only directly harms the human body, but also leads to many chronic diseases such as diabetes, cardiovascular diseases (CVD), nonalcoholic fatty liver disease (NAFLD), and mental illness. Weight loss is still one of the most effective strategies against obesity and related disorders. Recently, the link between intestinal microflora and metabolic health has been constantly established. Butyrate, a four-carbon short-chain fatty acid, is a major metabolite of the gut microbiota that has many beneficial effects on metabolic health. The anti-obesity activity of butyrate has been demonstrated, but its mechanisms of action have not been fully described. This review summarizes current knowledge of butyrate, including its production, absorption, distribution, metabolism, and the effect and mechanisms involved in weight loss and obesity-related diseases. The aim was to contribute to and advance our understanding of butyrate and its role in obesity. Further exploration of butyrate and its pathway may help to identify new anti-obesity.
Collapse
Affiliation(s)
- Ke Peng
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Wenjie Dong
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Taimin Luo
- Department of Pharmacy, Chengdu Seventh People’s Hospital, Chengdu, Sichuan, China
| | - Hui Tang
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Wanlong Zhu
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Yilan Huang
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
- *Correspondence: Yilan Huang, ; Xuping Yang,
| | - Xuping Yang
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
- *Correspondence: Yilan Huang, ; Xuping Yang,
| |
Collapse
|
20
|
D'Auria E, Acunzo M, Salvatore S, Grazi R, Agosti M, Vandenplas Y, Zuccotti G. Biotics in atopic diseases: state of the art and future perspectives. Minerva Pediatr (Torino) 2022; 74:688-702. [PMID: 36149096 DOI: 10.23736/s2724-5276.22.07010-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Prevalence of allergic diseases has growing in recent decades, being a significant burden for patients and their families. Different environmental factors, acting in early life, can significantly affect the timing and diversity of bacterial colonization and the immune system development. Growing evidence points to a correlation between early life microbial perturbation and development of allergic diseases. Besides, changes in the microbiota in one body site may influence other microbiota communities at distance by different mechanisms, including microbial-derived metabolites, mainly the short chain fatty acids (SCFA). Hence, there has been an increasing interest on the role of "biotics" (probiotics, prebiotics, symbiotics and postbiotics) in shaping dysbiosis and modulating allergic risk. Systemic type 2 inflammation is emerging as a common pathogenetic pathway of allergic diseases, intertwining communication with the gut mcirobiota. The aim of this review was to provide an update overview of the current knowledge of biotics in prevention and treatment of allergic diseases, also addressing research gaps which need to be filled.
Collapse
Affiliation(s)
- Enza D'Auria
- Department of Pediatrics, Vittore Buzzi Children's Hospital, University of Milan, Milan, Italy -
| | - Miriam Acunzo
- Department of Pediatrics, Vittore Buzzi Children's Hospital, University of Milan, Milan, Italy
| | - Silvia Salvatore
- Department of Pediatrics, University of Insubria, F. Del Ponte Hospital, Varese, Italy
| | - Roberta Grazi
- Department of Pediatrics, Vittore Buzzi Children's Hospital, University of Milan, Milan, Italy
| | - Massimo Agosti
- Department of Pediatrics, University of Insubria, F. Del Ponte Hospital, Varese, Italy
| | - Yvan Vandenplas
- KidZ Health Castle, Free University of Brussels, Brussels, Belgium
| | - Gianvincenzo Zuccotti
- Department of Pediatrics, Vittore Buzzi Children's Hospital, University of Milan, Milan, Italy
| |
Collapse
|
21
|
Yang J, Qin S, Zhang H. Precise strategies for selecting probiotic bacteria in treatment of intestinal bacterial dysfunctional diseases. Front Immunol 2022; 13:1034727. [PMID: 36341458 PMCID: PMC9632739 DOI: 10.3389/fimmu.2022.1034727] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/07/2022] [Indexed: 11/20/2022] Open
Abstract
Abundant microbiota resides in the organs of the body, which utilize the nutrition and form a reciprocal relationship with the host. The composition of these microbiota changes under different pathological conditions, particularly in response to stress and digestive diseases, making the microbial composition and health of the hosts body interdependent. Probiotics are living microorganisms that have demonstrated beneficial effects on physical health and as such are used as supplements to ameliorate symptoms of various digestive diseases by optimizing microbial composition of the gut and restore digestive balance. However, the supplementary effect does not achieve the expected result. Therefore, a targeted screening strategy on probiotic bacteria is crucial, owing to the presence of several bacterial strains. Core bacteria work effectively in maintaining microbiological homeostasis and stabilization in the gastrointestinal tract. Some of the core bacteria can be inherited and acquired from maternal pregnancy and delivery; others can be acquired from contact with the mother, feces, and the environment. Knowing the genera and functions of the core bacteria could be vital in the isolation and selection of probiotic bacteria for supplementation. In addition, other supporting strains of probiotic bacteria are also needed. A comprehensive strategy for mining both core and supporting bacteria before its clinical use is needed. Using metagenomics or other methods of estimation to discern the typically differentiated strains of bacteria is another important strategy to treat dysbiosis. Hence, these two factors are significant to carry out targeted isolation and selection of the functional strains to compose the resulting probiotic preparation for application in both research and clinical use. In conclusion, precise probiotic supplementation, by screening abundant strains of bacteria and isolating specific probiotic strains, could rapidly establish the core microbiota needed to confer resilience, particularly in bacterial dysfunctional diseases. This approach can help identify distinct bacteria which can be used to improve supplementation therapies.
Collapse
Affiliation(s)
- Jiajun Yang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Shunyi Qin
- Key Laboratory of Agricultural Animal Breeding and Healthy Breeding of Tianjin, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China
| | - Hao Zhang
- College of Animal Science and Technology, Chinese Agricultural University, Beijing, China
- *Correspondence: Hao Zhang,
| |
Collapse
|
22
|
Exploring Bacterial Attributes That Underpin Symbiont Life in the Monogastric Gut. Appl Environ Microbiol 2022; 88:e0112822. [PMID: 36036591 PMCID: PMC9499014 DOI: 10.1128/aem.01128-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The large bowel of monogastric animals, such as that of humans, is home to a microbial community (microbiota) composed of a diversity of mostly bacterial species. Interrelationships between the microbiota as an entity and the host are complex and lifelong and are characteristic of a symbiosis. The relationships may be disrupted in association with disease, resulting in dysbiosis. Modifications to the microbiota to correct dysbiosis require knowledge of the fundamental mechanisms by which symbionts inhabit the gut. This review aims to summarize aspects of niche fitness of bacterial species that inhabit the monogastric gut, especially of humans, and to indicate the research path by which progress can be made in exploring bacterial attributes that underpin symbiont life in the gut.
Collapse
|
23
|
Xing H, Zhang Y, Krämer M, Kissmann AK, Henkel M, Weil T, Knippschild U, Rosenau F. A Polyclonal Selex Aptamer Library Directly Allows Specific Labelling of the Human Gut Bacterium Blautia producta without Isolating Individual Aptamers. Molecules 2022; 27:molecules27175693. [PMID: 36080459 PMCID: PMC9458011 DOI: 10.3390/molecules27175693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
Recent studies have demonstrated that changes in the abundance of the intestinal bacterium Blautia producta, a potential probiotic, are closely associated with the development of various diseases such as obesity, diabetes, some neurodegenerative diseases, and certain cancers. However, there is still a lack of an effective method to detect the abundance of B. producta in the gut rapidly. Especially, DNA aptamers are now widely used as biometric components for medical testing due to their unique characteristics, including high chemical stability, low production cost, ease of chemical modification, low immunogenicity, and fast reproducibility. We successfully obtained a high-affinity nucleic acid aptamer library (B.p-R14) after 14 SELEX rounds, which efficiently discriminates B. producta in different analysis techniques including fluorometric suspension assays or fluorescence microscopy from other major gut bacteria in complex mixtures and even in human stool samples. These preliminary findings will be the basis towards aptamer-based biosensing applications for the fast and reliable monitoring of B. producta in the human gut microbiome.
Collapse
Affiliation(s)
- Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Yiting Zhang
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Max-Planck-Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
- Correspondence: (A.-K.K.); (F.R.)
| | - Marius Henkel
- Cellular Agriculture, TUM School of Life Sciences, Technical University of Munich, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Tanja Weil
- Max-Planck-Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Max-Planck-Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
- Correspondence: (A.-K.K.); (F.R.)
| |
Collapse
|
24
|
A Polyclonal Aptamer Library for the Specific Binding of the Gut Bacterium Roseburia intestinalis in Mixtures with Other Gut Microbiome Bacteria and Human Stool Samples. Int J Mol Sci 2022; 23:ijms23147744. [PMID: 35887092 PMCID: PMC9317077 DOI: 10.3390/ijms23147744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 02/07/2023] Open
Abstract
Roseburia intestinalis has received attention as a potential probiotic bacterium. Recent studies have demonstrated that changes in its intestinal abundance can cause various diseases, such as obesity, enteritis and atherosclerosis. Probiotic administration or fecal transplantation alter the structure of the intestinal flora, offering possibilities for the prevention and treatment of these diseases. However, current monitoring methods, such as 16S rRNA sequencing, are complex and costly and require specialized personnel to perform the tests, making it difficult to continuously monitor patients during treatment. Hence, the rapid and cost-effective quantification of intestinal bacteria has become an urgent problem to be solved. Aptamers are of emerging interest because their stability, low immunogenicity and ease of modification are attractive properties for a variety of applications. We report a FluCell-SELEX polyclonal aptamer library specific for R. intestinalis isolated after seven evolution rounds, that can bind and label this organism for fluorescence microscopy and binding assays. Moreover, R. intestinalis can be distinguished from other major intestinal bacteria in complex defined mixtures and in human stool samples. We believe that this preliminary evidence opens new avenues towards aptamer-based electronic biosensors as new powerful and inexpensive diagnostic tools for the relative quantitative monitoring of R. intestinalis in gut microbiomes.
Collapse
|
25
|
Liu Q, Wu H, Huang C, Lin H, Li W, Zhao X, Li Z, Lv S. Microbial compositions, ecological networks, and metabolomics in sediments of black-odour water in Dongguan, China. ENVIRONMENTAL RESEARCH 2022; 210:112918. [PMID: 35181306 DOI: 10.1016/j.envres.2022.112918] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/29/2022] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
Black-odour water with organic compounds and heavy metals caused by domestic and industrial activities has aroused people's attention in recent years, yet little is known about the ecological effects on aquatic organisms, especially microorganisms in sediments. To explore the response of microbial communities to environmental factors, the community and metabolites of nine river sediments with different pollution in Dongguan city, China were investigated using 16S rRNA gene sequencing and liquid chromatography tandem-mass. The results revealed that the composition and structure of sedimentary microbial communities significantly changed in rivers with varying pollution levels. Cyanobacteria were the most abundant organisms in the sediment of black-odorous rivers, while the relative abundance of Thaumarchaeota was gradually increased with the river quality gets better. The relative abundance of organic acids (including amino acids), alcohols, esters, and ketones associated with microbial metabolism in sediments of polluted rivers was increased. The 16S rRNA gene sequencing-based molecular ecological network analysis indicated that the interactions amongst bacteria were enhanced in severely contaminated communities. Sphingomonadaceae and Cyanobacteria have important roles in bacterial community structures of polluted rivers and those with ongoing treatment. The correlation analysis showed significant metal resistance and/or tolerance of the following bacteria species Thalassiosira weissflogii, Aminicenantes bacterium clone OPB95, 'Candidatus Halomonas phosphatis', and archaeal species Methanolinea and unidentified Thermoplasmata. These results indicated that sedimentary microbial communities may shift in composition and structure, as well as their interaction network, to adapt and resist environmental contamination and promote restoration.
Collapse
Affiliation(s)
- Qian Liu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Haowen Wu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Cong Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Hui Lin
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Wei Li
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - XiuFang Zhao
- Ecological Science Institute, LingNan Eco & Culture-Tourism Co.Ltd., Dongguan, 523125, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Sihao Lv
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China.
| |
Collapse
|
26
|
Rhodes KA, Ma MC, Rendón MA, So M. Neisseria genes required for persistence identified via in vivo screening of a transposon mutant library. PLoS Pathog 2022; 18:e1010497. [PMID: 35580146 PMCID: PMC9140248 DOI: 10.1371/journal.ppat.1010497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/27/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
The mechanisms used by human adapted commensal Neisseria to shape and maintain a niche in their host are poorly defined. These organisms are common members of the mucosal microbiota and share many putative host interaction factors with Neisseria meningitidis and Neisseria gonorrhoeae. Evaluating the role of these shared factors during host carriage may provide insight into bacterial mechanisms driving both commensalism and asymptomatic infection across the genus. We identified host interaction factors required for niche development and maintenance through in vivo screening of a transposon mutant library of Neisseria musculi, a commensal of wild-caught mice which persistently and asymptomatically colonizes the oral cavity and gut of CAST/EiJ and A/J mice. Approximately 500 candidate genes involved in long-term host interaction were identified. These included homologs of putative N. meningitidis and N. gonorrhoeae virulence factors which have been shown to modulate host interactions in vitro. Importantly, many candidate genes have no assigned function, illustrating how much remains to be learned about Neisseria persistence. Many genes of unknown function are conserved in human adapted Neisseria species; they are likely to provide a gateway for understanding the mechanisms allowing pathogenic and commensal Neisseria to establish and maintain a niche in their natural hosts. Validation of a subset of candidate genes confirmed a role for a polysaccharide capsule in N. musculi persistence but not colonization. Our findings highlight the potential utility of the Neisseria musculi-mouse model as a tool for studying the pathogenic Neisseria; our work represents a first step towards the identification of novel host interaction factors conserved across the genus. The Neisseria genus contains many genetically related commensals of animals and humans, and two human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. The mechanisms allowing commensal Neisseria to maintain a niche in their host is little understood. To identify genes required for persistence, we screened a library of transposon mutants of Neisseria musculi, a commensal of wild-caught mice, in CAST/EiJ mice, which persistently and asymptomatically colonizes. Approximately 500 candidate host interaction genes were identified. A subset of these are homologs of N. meningitidis and N. gonorrhoeae genes known to modulate pathogen-host interactions in vitro. Many candidate genes have no known function, demonstrating how much remains to be learned about N. musculi niche maintenance. As many genes of unknown function are conserved in human adapted Neisseria, they provide a gateway for understanding Neisseria persistence mechanisms in general.
Collapse
Affiliation(s)
- Katherine A. Rhodes
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
| | - Man Cheong Ma
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - María A. Rendón
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Magdalene So
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| |
Collapse
|
27
|
Hu H, Xu K, Wang K, Zhang F, Bai X. Dissecting the Effect of Berberine on the Intestinal Microbiome in the Weaned Piglets by Metagenomic Sequencing. Front Microbiol 2022; 13:862882. [PMID: 35464928 PMCID: PMC9021597 DOI: 10.3389/fmicb.2022.862882] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/11/2022] [Indexed: 12/19/2022] Open
Abstract
This study aimed to investigate the microbial structure and function in the rectum of weaned piglets with berberine supplementation. Twelve healthy 21-day-old Duorc × (Landrace × Large White) weaned piglets (similar body weight) were evenly divided into control and berberine groups and were fed a basal diet supplemented with 0 and 0.1% berberine, respectively. After 21 days, metagenomic sequencing analysis was performed to detect microbial composition and function in the rectum of weaned piglets. Results showed that there were 10,597,721,931–14,059,392,900 base pairs (bp) and 10,186,558,171–15,859,563,342 bp of clean data in the control and berberine groups, respectively. The Q20s of the control and berberine groups were 97.15 to 97.7% and 96.26 to 97.68%, respectively. The microorganisms in the berberine group had lower (p < 0.05) Chao1, alternating conditional expectation, Shannon, and Simpson indices at the species levels than those in the control group. Analysis of similarity showed that there were significant differences (p < 0.01) between the control and berberine groups at the genus and species levels of the gut microorganisms. Dietary berberine significantly increased (p < 0.05) the abundance of Subdoligranulum variabile, but decreased (p < 0.05) the abundance of Prevotella copri compared with the control group. Carbohydrate-active enzymes analysis revealed that the levels of polysaccharide lyases and carbohydrate esterases were lower (p < 0.05) in the berberine group than that in the control group. Linear discriminant analysis effect size analysis showed that berberine supplementation could induce various significant Kyoto Encyclopedia of Genes and Genomes pathways, including carbohydrate metabolism, environmental information processing, and microbial metabolism in diverse environments. In conclusion, our findings suggest that berberine could improve the composition, abundance, structure, and function of gut microbiome in the weaned piglets, potentially providing a suitable approach for the application of berberine in human and animal health.
Collapse
Affiliation(s)
- Hong Hu
- College of Animal Science, Anhui Science and Technology University, Chuzhou, China
| | - Kexing Xu
- College of Animal Science, Anhui Science and Technology University, Chuzhou, China
| | - Kunping Wang
- College of Animal Science, Anhui Science and Technology University, Chuzhou, China
| | - Feng Zhang
- College of Animal Science, Anhui Science and Technology University, Chuzhou, China.,Anhui Province Key Laboratory of Animal Nutrition Regulation and Health, Chuzhou, China
| | - Xi Bai
- College of Animal Science, Anhui Science and Technology University, Chuzhou, China
| |
Collapse
|
28
|
Guo T, Chen L. Gut microbiota and inflammation in Parkinson’s disease: Pathogenetic and therapeutic insights. EUR J INFLAMM 2022. [DOI: 10.1177/1721727x221083763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Parkinson’s disease (PD) is a progressive neurodegenerative disease characterized by dopaminergic neuronal loss and α-synuclein (α-syn) aggregation. With the acceleration of population aging process, the incidence of PD is expected to increase, putting a heavy burden on the whole society. Recent studies have found the alterations of gut microbiota (GM) in PD patients and the clinical relevance of these changes, indicating the underlying relationship between GM and PD. Additionally, elevated inflammatory responses originating from the gut play a crucial role in the initiation and progression of PD, which is closely associated with GM. In this review, we will summarize recent studies on the correlation between GM and PD, and discuss the possible pathogenesis of PD mediated by GM and subsequent inflammatory cascades. We will also focus on the promising GM-based therapeutic strategies of PD, including antibiotics, probiotics and/or prebiotics, fecal microbiota transplantation, and dietary interventions, aiming to provide some new therapeutic insights for PD.
Collapse
Affiliation(s)
- Tong Guo
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Li Chen
- Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing, China
| |
Collapse
|
29
|
Ahlinder J, Svedberg AL, Nystedt A, Dryselius R, Jacobsson K, Hägglund M, Brindefalk B, Forsman M, Ottoson J, Troell K. Use of metagenomic microbial source tracking to investigate the source of a foodborne outbreak of cryptosporidiosis. Food Waterborne Parasitol 2022; 26:e00142. [PMID: 35024477 PMCID: PMC8728467 DOI: 10.1016/j.fawpar.2021.e00142] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
Cryptosporidium is a protozoan parasite of global public health importance that causes gastroenteritis in a variety of vertebrate hosts, with many human outbreaks reported yearly, often from ingestion of contaminated water or food. Despite the major public health implications, little is typically known about sources of contamination of disease outbreaks caused by Cryptosporidium. Here, we study a national foodborne outbreak resulted from infection with Cryptosporidium parvum via romaine lettuce, with the main goal to trace the source of the parasite. To do so, we combined traditional outbreak investigation methods with molecular detection and characterization methods (i.e. PCR based typing, amplicon and shotgun sequencing) of romaine lettuce samples collected at the same farm from which the contaminated food was produced. Using 18S rRNA typing, we detected C. parvum in two out of three lettuce samples, which was supported by detections in the metagenome analysis. Microbial source tracking analysis of the lettuce samples suggested sewage water as a likely source of the contamination, albeit with some uncertainty. In addition, the high degree of overlap in bacterial species content with a public human gut microbial database corroborated the source tracking results. The combination of traditional and molecular based methods applied here is a promising tool for future source tracking investigations of food- and waterborne outbreaks of Cryptosporidium spp. and can help to control and mitigate contamination risks.
Collapse
Affiliation(s)
- J. Ahlinder
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | - A.-L. Svedberg
- Department of Infection control, Region Norrbotten, Luleå, Sweden
| | - A. Nystedt
- Department of Infection control, Region Norrbotten, Luleå, Sweden
| | - R. Dryselius
- Department of Biology, National Food Agency, Uppsala, Sweden
| | - K. Jacobsson
- Department of Biology, National Food Agency, Uppsala, Sweden
| | - M. Hägglund
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Stockholm, Sweden
| | - B. Brindefalk
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | - M. Forsman
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden
| | - J. Ottoson
- Department of Risk and benefit assessment, National Food Agency, Uppsala, Sweden
| | - K. Troell
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala university, Uppsala, Sweden
| |
Collapse
|
30
|
Suryani D, Subhan Alfaqih M, Gunadi JW, Sylviana N, Goenawan H, Megantara I, Lesmana R. Type, Intensity, and Duration of Exercise as Regulator of Gut Microbiome Profile. Curr Sports Med Rep 2022; 21:84-91. [PMID: 35245243 DOI: 10.1249/jsr.0000000000000940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
ABSTRACT Gut microbiome profile is related to individual health. In metabolic syndrome, there is a change in the gut microbiome profile, indicated by an increase in the ratio of Firmicutes to Bacteroidetes. Many studies have been conducted to determine the effect of exercise on modifying the gut microbiome profile. The effectiveness of exercise is influenced by its type, intensity, and duration. Aerobic training decreases splanchnic blood flow and shortens intestinal transit time. High-intensity exercise improves mitochondrial function and increases the essential bacteria in lactate metabolism and urease production. Meanwhile, exercise duration affects the hypothalamic-pituitary-adrenal axis. All of these mechanisms are related to each other in producing the effect of exercise on the gut microbiome profile.
Collapse
Affiliation(s)
| | | | - Julia Windi Gunadi
- Department of Physiology, Faculty of Medicine, Universitas Kristen Maranatha, Bandung, INDONESIA
| | | | | | | | | |
Collapse
|
31
|
Xu Z, Jiang W, Huang W, Lin Y, Chan FKL, Ng SC. Gut microbiota in patients with obesity and metabolic disorders - a systematic review. GENES & NUTRITION 2022; 17:2. [PMID: 35093025 PMCID: PMC8903526 DOI: 10.1186/s12263-021-00703-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/23/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Previous observational studies have demonstrated inconsistent and inconclusive results of changes in the intestinal microbiota in patients with obesity and metabolic disorders. We performed a systematic review to explore evidence for this association across different geography and populations. METHODS We performed a systematic search of MEDLINE (OvidSP) and Embase (OvidSP) of articles published from Sept 1, 2010, to July 10, 2021, for case-control studies comparing intestinal microbiome of individuals with obesity and metabolic disorders with the microbiome of non-obese, metabolically healthy individuals (controls). The primary outcome was bacterial taxonomic changes in patients with obesity and metabolic disorders as compared to controls. Taxa were defined as "lean-associated" if they were depleted in patients with obesity and metabolic disorders or negatively associated with abnormal metabolic parameters. Taxa were defined as "obesity-associated" if they were enriched in patients with obesity and metabolic disorders or positively associated with abnormal metabolic parameters. RESULTS Among 2390 reports screened, we identified 110 full-text articles and 60 studies were included. Proteobacteria was the most consistently reported obesity-associated phylum. Thirteen, nine, and ten studies, respectively, reported Faecalibacterium, Akkermansia, and Alistipes as lean-associated genera. Prevotella and Ruminococcus were obesity-associated genera in studies from the West but lean-associated in the East. Roseburia and Bifidobacterium were lean-associated genera only in the East, whereas Lactobacillus was an obesity-associated genus in the West. CONCLUSIONS We identified specific bacteria associated with obesity and metabolic disorders in western and eastern populations. Mechanistic studies are required to determine whether these microbes are a cause or product of obesity and metabolic disorders.
Collapse
Affiliation(s)
- Zhilu Xu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota Innovation Centre (MagIC Centre), Hong Kong, China
| | - Wei Jiang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenli Huang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota Innovation Centre (MagIC Centre), Hong Kong, China
| | - Yu Lin
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota Innovation Centre (MagIC Centre), Hong Kong, China
| | - Francis K L Chan
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Microbiota Innovation Centre (MagIC Centre), Hong Kong, China
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China. .,Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China. .,Microbiota Innovation Centre (MagIC Centre), Hong Kong, China.
| |
Collapse
|
32
|
Rosenberg E, Zilber-Rosenberg I. Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations. Microorganisms 2021; 10:microorganisms10010070. [PMID: 35056519 PMCID: PMC8780831 DOI: 10.3390/microorganisms10010070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.
Collapse
|
33
|
Pagan L, Ederveen RAM, Huisman BW, Schoones JW, Zwittink RD, Schuren FHJ, Rissmann R, Piek JMJ, van Poelgeest MIE. The Human Vulvar Microbiome: A Systematic Review. Microorganisms 2021; 9:2568. [PMID: 34946169 PMCID: PMC8705571 DOI: 10.3390/microorganisms9122568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 02/07/2023] Open
Abstract
The link between cancer and the microbiome is a fast-moving field in research. There is little knowledge on the microbiome in ((pre)malignant) conditions of the vulvar skin. This systematic review aims to provide an overview of the literature regarding the microbiome composition of the healthy vulvar skin and in (pre)malignant vulvar disease. This study was performed according to the PRISMA guidelines. A comprehensive, electronic search strategy was used to identify original research articles (updated September 2021). The inclusion criteria were articles using culture-independent methods for microbiome profiling of the vulvar region. Ten articles were included. The bacterial composition of the vulva consists of several genera including Lactobacillus, Corynebacterium, Staphylococcus and Prevotella, suggesting that the vulvar microbiome composition shows similarities with the corresponding vaginal milieu. However, the vulvar microbiome generally displayed higher diversity with commensals of cutaneous and fecal origin. This is the first systematic review that investigates the relationship between microbiome and vulvar (pre)malignant disease. There are limited data and the level of evidence is low with limitations in study size, population diversity and methodology. Nevertheless, the vulvar microbiome represents a promising field for exploring potential links for disease etiology and targets for therapy.
Collapse
Affiliation(s)
- Lisa Pagan
- Centre for Human Drug Research, 2333 CL Leiden, The Netherlands; (L.P.); (B.W.H.); (M.I.E.v.P.)
- Department of Gynecology and Obstetrics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Roos A. M. Ederveen
- Faculty of Health, Medicine and Life Sciences, Maastricht University Medical Centre, 6229 ER Maastricht, The Netherlands;
- Department of Obstetrics and Gynaecology and Catharina Cancer Institute, Catharina Ziekenhuis, Michelangelolaan 2, 5623 EJ Eindhoven, The Netherlands;
| | - Bertine W. Huisman
- Centre for Human Drug Research, 2333 CL Leiden, The Netherlands; (L.P.); (B.W.H.); (M.I.E.v.P.)
- Department of Gynecology and Obstetrics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Jan W. Schoones
- Directorate of Research Policy (Formerly: Walaeus Library), Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands;
| | - Romy D. Zwittink
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands;
| | - Frank H. J. Schuren
- Netherlands Organisation for Applied Scientific Research, TNO, 3704 HE Zeist, The Netherlands;
- Leiden Skin Institute, 2333 CL Leiden, The Netherlands
| | - Robert Rissmann
- Centre for Human Drug Research, 2333 CL Leiden, The Netherlands; (L.P.); (B.W.H.); (M.I.E.v.P.)
- Leiden Skin Institute, 2333 CL Leiden, The Netherlands
- Leiden Amsterdam Center for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jurgen M. J. Piek
- Department of Obstetrics and Gynaecology and Catharina Cancer Institute, Catharina Ziekenhuis, Michelangelolaan 2, 5623 EJ Eindhoven, The Netherlands;
| | - Mariëtte I. E. van Poelgeest
- Centre for Human Drug Research, 2333 CL Leiden, The Netherlands; (L.P.); (B.W.H.); (M.I.E.v.P.)
- Department of Gynecology and Obstetrics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| |
Collapse
|
34
|
Lee JY, Kang W, Shin NR, Hyun DW, Kim PS, Kim HS, Lee JY, Tak EJ, Sung H, Bae JW. Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn's disease. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870576 DOI: 10.1099/ijsem.0.005129] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cultivation and isolation of gut bacteria are necessary for understanding their role in the intestinal ecosystem. We isolated a novel bacterium, designated strain BG01T, from the faeces of a patient with Crohn's disease. Strain BG01T was a strictly anaerobic, rod-shaped, Gram-variable and endospore-forming bacterium. Strain BG01T possessed C12 : 0, C18 : 0 dimethyl aldehyde (DMA) and C18 : 1 ω9c DMA as predominant cellular fatty acids and meso-diaminopimelic acid as a diagnostic diamino acid. Strain BG01T grew at 15-45 °C (optimum, 37 °C), with 0-4 % (w/v) NaCl (optimum, 0-1 %), at pH 6-10 (optimum, pH 7) and was resistant to bile salt, but not to ampicillin, metronidazole, vancomycin and cefoperazone. Butyrate, propionate, oxalacetate and fumarate were produced as fermentation end products from Gifu anaerobic medium broth. Strain BG01T showed 97.7 % 16S rRNA gene sequence similarity, and 92.0 and 48.5 % of average nucleotide identity and digital DNA-DNA hybridization values, respectively, with Anaerostipes caccae KCTC 15019T. Genomic analysis indicated that strain BG01T had a butyrate-producing pathway. The genomic G+C content of the strain was 43.5 mol%. Results of the phenotypic, phylogenetic and genotypic analyses indicated that strain BG01T represents a novel butyrate-producing species of the genus Anaerostipes, for which the name Anaerostipes hominis sp. nov. is proposed. The type strain is BG01T (=KCTC 15617T=JCM 32275T).
Collapse
Affiliation(s)
- Jae-Yun Lee
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Woorim Kang
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hyun Sik Kim
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Euon Jung Tak
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hojun Sung
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology, Department of Life and Nanopharmaceutical Sciences and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
| |
Collapse
|
35
|
Mirzaei R, Dehkhodaie E, Bouzari B, Rahimi M, Gholestani A, Hosseini-Fard SR, Keyvani H, Teimoori A, Karampoor S. Dual role of microbiota-derived short-chain fatty acids on host and pathogen. Biomed Pharmacother 2021; 145:112352. [PMID: 34840032 DOI: 10.1016/j.biopha.2021.112352] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
A growing body of documents shows microbiota produce metabolites such as short-chain fatty acids (SCFAs) as crucial executors of diet-based microbial influence the host and bacterial pathogens. The production of SCFAs depends on the metabolic activity of intestinal microflora and is also affected by dietary changes. SCFAs play important roles in maintaining colonic health as an energy source, as a regulator of gene expression and cell differentiation, and as an anti-inflammatory agent. Additionally, the regulated expression of virulence genes is critical for successful infection by an intestinal pathogen. Bacteria rely on sensing environmental signals to find preferable niches and reach the infectious state. This review will present data supporting the diverse functional roles of microbiota-derived butyrate, propionate, and acetate on host cellular activities such as immune modulation, energy metabolism, nervous system, inflammation, cellular differentiation, and anti-tumor effects, among others. On the other hand, we will discuss and summarize data about the role of these SCFAs on the virulence factor of bacterial pathogens. In this regard, receptors and signaling routes for SCFAs metabolites in host and pathogens will be introduced.
Collapse
Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Elahe Dehkhodaie
- Department of Biology, Science and Research Branch, Islamic Azad University Tehran, Iran
| | - Behnaz Bouzari
- Department of Pathology, Firouzgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mandana Rahimi
- Department of Pathology, School of Medicine, Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Gholestani
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Hosseini-Fard
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Ali Teimoori
- Department of Virology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
36
|
Goelz H, Wetzel S, Mehrbarzin N, Utzolino S, Häcker G, Badr MT. Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients. Cells 2021; 10:3226. [PMID: 34831447 PMCID: PMC8617993 DOI: 10.3390/cells10113226] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Infections of the ascitic fluid are serious conditions that require rapid diagnosis and treatment. Ascites is often accompanied by other critical pathologies such as gastrointestinal bleeding and bowel perforation, and infection increases the risk of mortality in intensive care patients. Owing to a relatively low success rate of conventional culture methods in identifying the responsible pathogens, new methods may be helpful to guide antimicrobial therapy and to refine empirical regimens. Here, we aim to assess outcomes and to identify responsible pathogens in ascitic fluid infections, in order to improve patients' care and to guide empirical therapy. METHODS Between October 2019 and March 2021, we prospectively collected 50 ascitic fluid samples from ICU patients with suspected infection. Beside standard culture-based microbiology methods, excess fluid underwent DNA isolation and was analyzed by next- and third-generation sequencing (NGS) methods. RESULTS NGS-based methods had higher sensitivity in detecting additional pathogenic bacteria such as E. faecalis and Klebsiella in 33 out of 50 (66%) ascitic fluid samples compared with culture-based methods (26%). Anaerobic bacteria were especially identified by sequencing-based methods in 28 samples (56%), in comparison with only three samples in culture. Analysis of clinical data showed a correlation between sequencing results and various clinical parameters such as peritonitis and hospitalization outcomes. CONCLUSIONS Our results show that, in ascitic fluid infections, NGS-based methods have a higher sensitivity for the identification of clinically relevant pathogens than standard microbiological culture diagnostics, especially in detecting hard-to-culture anaerobic bacteria. Patients with such infections may benefit from the use of NGS methods by the possibility of earlier and better targeted antimicrobial therapy, which has the potential to lower the high morbidity and mortality in critically ill patients with ascitic bacterial infection.
Collapse
Affiliation(s)
- Hanna Goelz
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
| | - Simon Wetzel
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
| | - Negin Mehrbarzin
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
| | - Stefan Utzolino
- Center of Surgery, Department of General and Visceral Surgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany;
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (H.G.); (S.W.); (N.M.); (G.H.)
- IMM-PACT-Program, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
37
|
Feng Y, Wang Y, Zhu B, Gao GF, Guo Y, Hu Y. Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes. Commun Biol 2021; 4:1305. [PMID: 34795385 PMCID: PMC8602611 DOI: 10.1038/s42003-021-02827-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
Abstract
Gut microbial reference genomes and gene catalogs are necessary for understanding the chicken gut microbiome. Here, we assembled 12,339 microbial genomes and constructed a gene catalog consisting of ~16.6 million genes by integrating 799 public chicken gut microbiome samples from ten countries. We found that 893 and 38 metagenome-assembled genomes (MAGs) in our dataset were putative novel species and genera, respectively. In the chicken gut, Lactobacillus aviarius and Lactobacillus crispatus were the most common lactic acid bacteria, and glycoside hydrolases were the most abundant carbohydrate-active enzymes (CAZymes). Antibiotic resistome profiling results indicated that Chinese chicken samples harbored a higher relative abundance but less diversity of antimicrobial resistance genes (ARGs) than European samples. We also proposed the effects of geography and host species on the gut resistome. Our study provides the largest integrated metagenomic dataset from the chicken gut to date and demonstrates its value in exploring chicken gut microbial genes. Feng et al. include genome recovery and data analysis of large number of chicken gut metagenomic datasets which significantly expands the reference genomes available from the chicken gut microbial communities, and catalog the genes prevalent in the gut systems. They further depict the countryspecific chicken gut antibiotic resistomes and the effects of geography and host species on the gut resistome.
Collapse
Affiliation(s)
- Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Yanan Wang
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
| |
Collapse
|
38
|
Jayatunga DPW, Hone E, Khaira H, Lunelli T, Singh H, Guillemin GJ, Fernando B, Garg ML, Verdile G, Martins RN. Therapeutic Potential of Mitophagy-Inducing Microflora Metabolite, Urolithin A for Alzheimer's Disease. Nutrients 2021; 13:nu13113744. [PMID: 34836000 PMCID: PMC8617978 DOI: 10.3390/nu13113744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/28/2021] [Accepted: 10/12/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial dysfunction including deficits of mitophagy is seen in aging and neurodegenerative disorders including Alzheimer’s disease (AD). Apart from traditionally targeting amyloid beta (Aβ), the main culprit in AD brains, other approaches include investigating impaired mitochondrial pathways for potential therapeutic benefits against AD. Thus, a future therapy for AD may focus on novel candidates that enhance optimal mitochondrial integrity and turnover. Bioactive food components, known as nutraceuticals, may serve as such agents to combat AD. Urolithin A is an intestinal microbe-derived metabolite of a class of polyphenols, ellagitannins (ETs). Urolithin A is known to exert many health benefits. Its antioxidant, anti-inflammatory, anti-atherogenic, anti-Aβ, and pro-mitophagy properties are increasingly recognized. However, the underlying mechanisms of urolithin A in inducing mitophagy is poorly understood. This review discusses the mitophagy deficits in AD and examines potential molecular mechanisms of its activation. Moreover, the current knowledge of urolithin A is discussed, focusing on its neuroprotective properties and its potential to induce mitophagy. Specifically, this review proposes potential mechanisms by which urolithin A may activate and promote mitophagy.
Collapse
Affiliation(s)
- Dona Pamoda W. Jayatunga
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027, Australia; (D.P.W.J.); (E.H.); (B.F.); (G.V.)
| | - Eugene Hone
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027, Australia; (D.P.W.J.); (E.H.); (B.F.); (G.V.)
- Cooperative Research Centre for Mental Health, Carlton, VIC 3053, Australia
| | - Harjot Khaira
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand; (H.K.); (T.L.); (H.S.); (M.L.G.)
| | - Taciana Lunelli
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand; (H.K.); (T.L.); (H.S.); (M.L.G.)
| | - Harjinder Singh
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand; (H.K.); (T.L.); (H.S.); (M.L.G.)
| | - Gilles J. Guillemin
- Department of Pharmacology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia;
- St. Vincent’s Centre for Applied Medical Research, Sydney, NSW 2011, Australia
| | - Binosha Fernando
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027, Australia; (D.P.W.J.); (E.H.); (B.F.); (G.V.)
| | - Manohar L. Garg
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand; (H.K.); (T.L.); (H.S.); (M.L.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Giuseppe Verdile
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027, Australia; (D.P.W.J.); (E.H.); (B.F.); (G.V.)
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Ralph N. Martins
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027, Australia; (D.P.W.J.); (E.H.); (B.F.); (G.V.)
- Australian Alzheimer’s Research Foundation, Ralph and Patricia Sarich Neuroscience Research Institute, 8 Verdun Street., Nedlands, WA 6009, Australia
- Department of Biomedical Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Correspondence: ; Tel.: +61-8-9347-4200
| |
Collapse
|
39
|
Mining the Microbiome and Microbiota-Derived Molecules in Inflammatory Bowel Disease. Int J Mol Sci 2021; 22:ijms222011243. [PMID: 34681902 PMCID: PMC8540913 DOI: 10.3390/ijms222011243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal microbiota is a complex community that consists of an ecosystem with a dynamic interplay between bacteria, fungi, archaea, and viruses. Recent advances in model systems have revealed that the gut microbiome is critical for maintaining homeostasis through metabolic digestive function, immune regulation, and intestinal barrier integrity. Taxonomic shifts in the intestinal microbiota are strongly correlated with a multitude of human diseases, including inflammatory bowel disease (IBD). However, many of these studies have been descriptive, and thus the understanding of the cause and effect relationship often remains unclear. Using non-human experimental model systems such as gnotobiotic mice, probiotic mono-colonization, or prebiotic supplementation, researchers have defined numerous species-level functions of the intestinal microbiota that have produced therapeutic candidates for IBD. Despite these advances, the molecular mechanisms responsible for the function of much of the microbiota and the interplay with host cellular processes remain areas of tremendous research potential. In particular, future research will need to unlock the functional molecular units of the microbiota in order to utilize this untapped resource of bioactive molecules for therapy. This review will highlight the advances and remaining challenges of microbiota-based functional studies and therapeutic discovery, specifically in IBD. One of the limiting factors for reviewing this topic is the nascent development of this area with information on some drug candidates still under early commercial development. We will also highlight the current and evolving strategies, including in the biotech industry, used for the discovery of microbiota-derived bioactive molecules in health and disease.
Collapse
|
40
|
Montoliu-Nerin M, Sánchez-García M, Bergin C, Kutschera VE, Johannesson H, Bever JD, Rosling A. In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:716385. [PMID: 37744125 PMCID: PMC10512289 DOI: 10.3389/ffunb.2021.716385] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/06/2021] [Indexed: 09/26/2023]
Abstract
Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.
Collapse
Affiliation(s)
- Merce Montoliu-Nerin
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Marisol Sánchez-García
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden
- Department of Forest Mycology and Plant Pathology, Uppsala Biocentre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Claudia Bergin
- Microbial Single Cell Genomics Facility, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Verena Esther Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden
| | - James D. Bever
- Department of Ecology and Evolutionary Biology, and Kansas Biological Survey, University of Kansas, Lawrence, KS, United States
| | - Anna Rosling
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
41
|
Piscotta FJ, Whitfield ST, Nakashige TG, Estrela AB, Ali T, Brady SF. Multiplexed functional metagenomic analysis of the infant microbiome identifies effectors of NF-κB, autophagy, and cellular redox state. Cell Rep 2021; 36:109746. [PMID: 34551287 PMCID: PMC8480279 DOI: 10.1016/j.celrep.2021.109746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/19/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
The human microbiota plays a critical role in host health. Proper development of the infant microbiome is particularly important. Its dysbiosis leads to both short-term health issues and long-term disorders lasting into adulthood. A central way in which the microbiome interacts with the host is through the production of effector molecules, such as proteins and small molecules. Here, a metagenomic library constructed from 14 infant stool microbiomes is analyzed for the production of effectors that modulate three distinct host pathways: immune response (nuclear factor κB [NF-κB] activation), autophagy (LC3-B puncta formation), and redox potential (NADH:NAD ratio). We identify microbiome-encoded bioactive metabolites, including commendamide and hydrogen sulfide and their associated biosynthetic genes, as well as a previously uncharacterized autophagy-inducing operon from Klebsiella spp. This work extends our understanding of microbial effector molecules that are known to influence host pathways. Parallel functional screening of metagenomic libraries can be easily expanded to investigate additional host processes. Construction of a metagenomic library from stool of infants A multiplexed screen for bacterial effectors of host cellular processes Identification of microbiome-encoded effectors hydrogen sulfide and commendamide The products of a Klebsiella pneumoniae operon induce autophagy
Collapse
Affiliation(s)
- Frank J Piscotta
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Shawn T Whitfield
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Toshiki G Nakashige
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Andreia B Estrela
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Thahmina Ali
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
42
|
Yen S, Johnson JS. Metagenomics: a path to understanding the gut microbiome. Mamm Genome 2021; 32:282-296. [PMID: 34259891 PMCID: PMC8295064 DOI: 10.1007/s00335-021-09889-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/28/2021] [Indexed: 12/16/2022]
Abstract
The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded by their collective metagenome. This revolution in understanding is being driven by continued development of sequencing technologies and in consequence necessitates reciprocal development of computational approaches that can adapt to the evolving nature of sequence datasets. In this review, we provide an overview of current bioinformatic strategies for handling metagenomic sequence data and discuss their strengths and limitations. We then go on to discuss key technological developments that have the potential to once again revolutionise the way we are able to view and hence understand the microbiome.
Collapse
Affiliation(s)
- Sandi Yen
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, UK
| | - Jethro S Johnson
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, UK.
| |
Collapse
|
43
|
Zhang F, Xu N, Wang W, Yu Y, Wu S. The gut microbiome of the Sunda pangolin ( Manis javanica) reveals its adaptation to specialized myrmecophagy. PeerJ 2021; 9:e11490. [PMID: 34141474 PMCID: PMC8179220 DOI: 10.7717/peerj.11490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022] Open
Abstract
Background The gut microbiomes of mammals are closely related to the diets of their hosts. The Sunda pangolin (Manis javanica) is a specialized myrmecophage, but its gut microbiome has rarely been studied. Methods Using high-throughput Illumina barcoded 16S rRNA amplicons of nine fecal samples from nine captive Sunda pangolins, we investigated their gut microbiomes. Results The detected bacteria were classified into 14 phyla, 24 classes, 48 orders, 97 families, and 271 genera. The main bacterial phyla were Firmicutes (73.71%), Proteobacteria (18.42%), Actinobacteria (3.44%), and Bacteroidetes (0.51%). In the PCoA and neighbor-net network (PERMANOVA: pangolins vs. other diets, weighted UniFrac distance p < 0.01, unweighted UniFrac distance p < 0.001), the gut microbiomes of the Sunda pangolins were distinct from those of mammals with different diets, but were much closer to other myrmecophages, and to carnivores, while distant from herbivores. We identified some gut microbiomes related to the digestion of chitin, including Lactococcus, Bacteroides, Bacillus, and Staphylococcus species, which confirms that the gut microbiome of pangolins may help them to digest chitin. Significance The results will aid studies of extreme dietary adaption and the mechanisms of diet differentiation in mammals, as well as metagenomic studies, captive breeding, and ex situ conservation of pangolins.
Collapse
Affiliation(s)
- Fuhua Zhang
- School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| | - Na Xu
- School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| | - Wenhua Wang
- School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| | - Yishuang Yu
- School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| | - Shibao Wu
- School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| |
Collapse
|
44
|
Fang Q, Liu N, Zheng B, Guo F, Zeng X, Huang X, Ouyang D. Roles of Gut Microbial Metabolites in Diabetic Kidney Disease. Front Endocrinol (Lausanne) 2021; 12:636175. [PMID: 34093430 PMCID: PMC8173181 DOI: 10.3389/fendo.2021.636175] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Diabetes is a highly prevalent metabolic disease that has emerged as a global challenge due to its increasing prevalence and lack of sustainable treatment. Diabetic kidney disease (DKD), which is one of the most frequent and severe microvascular complications of diabetes, is difficult to treat with contemporary glucose-lowering medications. The gut microbiota plays an important role in human health and disease, and its metabolites have both beneficial and harmful effects on vital physiological processes. In this review, we summarize the current findings regarding the role of gut microbial metabolites in the development and progression of DKD, which will help us better understand the possible mechanisms of DKD and explore potential therapeutic approaches for DKD.
Collapse
Affiliation(s)
- Qing Fang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Na Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Binjie Zheng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Fei Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Xiangchang Zeng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Xinyi Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Dongsheng Ouyang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| |
Collapse
|
45
|
Li X, Zhang X, Yang W, Guo L, Huang L, Li X, Gao W. Preparation and characterization of native and autoclaving-cooling treated Pinellia ternate starch and its impact on gut microbiota. Int J Biol Macromol 2021; 182:1351-1361. [PMID: 34000312 DOI: 10.1016/j.ijbiomac.2021.05.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 12/30/2022]
Abstract
The aim of this study was to investigate and compare the structural and physicochemical properties of native Banxia starch (BXS) and autoclaving-cooling treated Banxia starch (CTBXS) and its related impacts on production of short chain fatty acids (SCFAs) and human gut microbiota by in vitro fecal fermentation. BXS had semicircle to spherical granules, whereas CTBXS exhibited block-shape. According to XRD and TGA, BXS had a C-type crystalline pattern, while CTBXS had a B-type crystalline pattern. CTBXS had better thermal stability than BXS. In addition, BXS exhibited significantly higher solubility and swelling power than CTBXS, and CTBXS had higher content of SDS than BXS. Moreover, BXS and CTBXS could change the composition and abundance of gut microbiota, could also promote the production of SCFAs. This study is beneficial to well understand the in vitro digestion and fecal fermentation behaviors of BXS and CTBXS, and can be developed as a potential functional food with the aim of improving colonic health.
Collapse
Affiliation(s)
- Xinyang Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300193, China
| | - Xueqian Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300193, China
| | - Wenna Yang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300193, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Xia Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300193, China.
| | - Wenyuan Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300193, China.
| |
Collapse
|
46
|
Al Othaim A, Marasini D, Carbonero F. Impact of cranberry juice consumption on gut and vaginal microbiota in postmenopausal women. FOOD FRONTIERS 2021. [DOI: 10.1002/fft2.76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Ayoub Al Othaim
- Cell and Molecular Biology Program University of Arkansas Fayetteville Arkansas USA
- Department of Medical Laboratories College of Applied Medical Sciences Majmaah University Al‐Majmaah Saudi Arabia
| | - Daya Marasini
- Department of Food Science University of Arkansas Fayetteville Arkansas USA
| | - Franck Carbonero
- Cell and Molecular Biology Program University of Arkansas Fayetteville Arkansas USA
- Department of Food Science University of Arkansas Fayetteville Arkansas USA
- Department of Food Science Washington State University Spokane Washington USA
- Department of Nutrition and Exercise Physiology Elson Floyd School of Medicine Washington State University Spokane Spokane Washington USA
| |
Collapse
|
47
|
d'Enfert C, Kaune AK, Alaban LR, Chakraborty S, Cole N, Delavy M, Kosmala D, Marsaux B, Fróis-Martins R, Morelli M, Rosati D, Valentine M, Xie Z, Emritloll Y, Warn PA, Bequet F, Bougnoux ME, Bornes S, Gresnigt MS, Hube B, Jacobsen ID, Legrand M, Leibundgut-Landmann S, Manichanh C, Munro CA, Netea MG, Queiroz K, Roget K, Thomas V, Thoral C, Van den Abbeele P, Walker AW, Brown AJP. The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives. FEMS Microbiol Rev 2021; 45:fuaa060. [PMID: 33232448 PMCID: PMC8100220 DOI: 10.1093/femsre/fuaa060] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.
Collapse
Affiliation(s)
- Christophe d'Enfert
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Ann-Kristin Kaune
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Leovigildo-Rey Alaban
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Sayoni Chakraborty
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Neugasse 25, 07743 Jena, Germany
| | - Nathaniel Cole
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Margot Delavy
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Daria Kosmala
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Benoît Marsaux
- ProDigest BV, Technologiepark 94, B-9052 Gent, Belgium
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links, 9000 Ghent, Belgium
| | - Ricardo Fróis-Martins
- Immunology Section, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Moran Morelli
- Mimetas, Biopartner Building 2, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Diletta Rosati
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Marisa Valentine
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Zixuan Xie
- Gut Microbiome Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119–129, 08035 Barcelona, Spain
| | - Yoan Emritloll
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Peter A Warn
- Magic Bullet Consulting, Biddlecombe House, Ugbrook, Chudleigh Devon, TQ130AD, UK
| | - Frédéric Bequet
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
| | - Marie-Elisabeth Bougnoux
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Stephanie Bornes
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF0545, 20 Côte de Reyne, 15000 Aurillac, France
| | - Mark S Gresnigt
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Bernhard Hube
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Ilse D Jacobsen
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Mélanie Legrand
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Salomé Leibundgut-Landmann
- Immunology Section, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Chaysavanh Manichanh
- Gut Microbiome Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119–129, 08035 Barcelona, Spain
| | - Carol A Munro
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Karla Queiroz
- Mimetas, Biopartner Building 2, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Karine Roget
- NEXBIOME Therapeutics, 22 allée Alan Turing, 63000 Clermont-Ferrand, France
| | - Vincent Thomas
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
| | - Claudia Thoral
- NEXBIOME Therapeutics, 22 allée Alan Turing, 63000 Clermont-Ferrand, France
| | | | - Alan W Walker
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Alistair J P Brown
- MRC Centre for Medical Mycology, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| |
Collapse
|
48
|
Míguez B, Gullón P, Cotos-Yáñez T, Massot-Cladera M, Pérez-Cano FJ, Vila C, Alonso JL. Manufacture and Prebiotic Potential of Xylooligosaccharides Derived From Eucalyptus nitens Wood. FRONTIERS IN CHEMICAL ENGINEERING 2021. [DOI: 10.3389/fceng.2021.670440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Mixtures of xylooligosaccharides (XOS) were manufactured from Eucalyptus nitens samples by hydrothermal processing. In order to obtain a product suitable to be used as a prebiotic, the liquors obtained were subjected to a refining sequence consisting of a two-step membrane filtration followed by anion exchange and freeze-drying. The process proposed allowed to obtain a highly refined product mainly made up of a mixture of substituted XOS with a degree of polymerization, DP3–10, which was evaluated for its prebiotic potential by in vitro fermentation assays. Their effects on the microbiota composition and the metabolic activity were assessed along the fermentation time and compared to fructooligosaccharides (FOS, a gold standard prebiotic), using fecal inocula from donors belonging to two age-groups (young and elderly). Significant and similar increases were observed in most of the bacterial groups considered (including Bifidobacterium spp. or several butyrate-producers) in both XOS and FOS in vitro interventions, although XOS resulted in significantly higher increases in total bacteria and lower rises in Clostridium clusters I and II than FOS. Regarding the metabolic activity, higher amounts of total organic acid (TOA; 150 vs. 110 mM) and higher total short-chain fatty acid (SCFA)/TOA ratio (0.88 vs. 0.70 mol/mol) were achieved at 28 h using XOS as a carbon source in comparison with FOS. Moreover, both substrates resulted in different metabolite profiles. Higher percentages of acetate and propionate were achieved when XOS were used as substrates, whereas FOS resulted in slightly higher concentrations of butyrate. No differences were found between both age-groups. Taking together these results, it can be concluded that XOS produced from E. nitens by a biorefinery-based approach led to, at least, similar prebiotic activity as that observed with FOS.
Collapse
|
49
|
Beck LC, Granger CL, Masi AC, Stewart CJ. Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside. Expert Rev Proteomics 2021; 18:247-259. [PMID: 33896313 DOI: 10.1080/14789450.2021.1922278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: At birth, the gastrointestinal (GI) tract is colonized by a complex community of microorganisms, forming the basis of the gut microbiome. The gut microbiome plays a fundamental role in host health, disorders of which can lead to an array of GI diseases, both short and long term. Pediatric GI diseases are responsible for significant morbidity and mortality, but many remain poorly understood. Recent advancements in high-throughput technologies have enabled deeper profiling of GI morbidities. Technologies, such as metagenomics, transcriptomics, proteomics and metabolomics, have already been used to identify associations with specific pathologies, and highlight an exciting area of research. However, since these diseases are often complex and multifactorial by nature, reliance on a single experimental approach may not capture the true biological complexity. Therefore, multi-omics aims to integrate singular omic data to further enhance our understanding of disease.Areas covered: This review will discuss and provide an overview of the main omic technologies that are used to study complex GI pathologies in early life.Expert opinion: Multi-omic technologies can help to unravel the complexities of several diseases during early life, aiding in biomarker discovery and enabling the development of novel therapeutics and augment predictive models.
Collapse
Affiliation(s)
- Lauren C Beck
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Claire L Granger
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.,Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| |
Collapse
|
50
|
Bayer G, Ganobis CM, Allen-Vercoe E, Philpott DJ. Defined gut microbial communities: promising tools to understand and combat disease. Microbes Infect 2021; 23:104816. [PMID: 33785422 DOI: 10.1016/j.micinf.2021.104816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022]
Abstract
Defined gut microbial communities are emerging tools that allow detailed studies of microbial ecosystems and their interactions with the host. In this article, we review strategies underlying the design of defined consortia and summarize the efforts to introduce simplified communities into in vitro and in vivo models. We conclude by highlighting the potential of defined microbial ecosystems as effective modulation strategies for health benefits.
Collapse
Affiliation(s)
- Giuliano Bayer
- Department of Immunology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Caroline M Ganobis
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Dana J Philpott
- Department of Immunology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.
| |
Collapse
|