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Zugman M, Wong M, Jaime-Casas S, Pal SK. The gut microbiome and dietary metabolites in the treatment of renal cell carcinoma. Urol Oncol 2024:S1078-1439(24)00540-4. [PMID: 39095306 DOI: 10.1016/j.urolonc.2024.07.003] [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: 04/10/2024] [Revised: 06/13/2024] [Accepted: 07/02/2024] [Indexed: 08/04/2024]
Abstract
The gut microbiome is interlinked with renal cell carcinoma (RCC) and its response to systemic treatment. Mounting data suggests that certain elements of the gut microbiome may correlate with improved outcomes. New generation sequencing techniques and advanced bioinformatic data curation are accelerating the investigation of specific markers and metabolites that could predict treatment response. A variety of new therapeutic strategies, such as fecal microbiota transplantation, probiotic supplements, and dietary interventions, are currently being developed to modify the gut microbiome and improve anticancer therapies in patients with RCC. This review discusses the preliminary evidence indicating the role of the microbiome in cancer treatment, the techniques and tools necessary for its proper study and some of the current forms with which the microbiome can be modulated to improve patient outcomes.
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Affiliation(s)
- Miguel Zugman
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA; Centro de Oncologia e Hematologia Família Dayan-Daycoval Einstein, Hospital Israelita Albert, São Paulo, São Paulo, Brazil
| | - Megan Wong
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Salvador Jaime-Casas
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Sumanta K Pal
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA.
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Aziz-Zadeh L, Mayer E, Labus J, Ringold S, Jayashankar A, Kilroy E, Butera C, Jacobs J, Tanartkit S, Joshi S, Dapretto M. Relationships between tryptophan-related gut metabolites, brain activity, and autism symptomatology. RESEARCH SQUARE 2024:rs.3.rs-4559624. [PMID: 39108481 PMCID: PMC11302680 DOI: 10.21203/rs.3.rs-4559624/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
Abstract
Gut microbial metabolites have been theorized to play a causative role in the pathophysiology of autism spectrum disorder (ASD). This hypothesis is based on results from mechanistic preclinical studies and several correlational studies showing differences in gut microbial composition between ASD subjects and neurotypical (NT) controls. However, alterations in how the human brain interacts with the gut microbiome in ASD have not been examined. In this cross-sectional, case-control observational study, fecal metabolomics, task-based functional magnetic resonance imaging (fMRI), and behavioral assessments were obtained from 43 ASD and 41 NT children aged 8-17. The fMRI tasks were based on socio-emotional and sensory paradigms that commonly show strong evoked brain differences in ASD participants. General linear models and mediational modeling were applied to examine the links between tryptophan metabolism and evoked brain activity and behavior. Results indicated that fecal levels of specific tryptophan-related metabolites were associated with: 1) brain activity atypicalities in regions previously implicated in ASD (i.e., insula and cingulate); and 2) ASD severity and symptomatology (i.e., ADOS scores, disgust propensity, and sensory sensitivities). Importantly, activity in the mid-insula and mid-cingulate significantly mediated relationships between the microbial tryptophan metabolites, indolelactate and tryptophan betaine, and ASD severity and disgust sensitivity. To our knowledge, this is the first study to elucidate how interactions between gut metabolites and brain activity may impact autism symptomatology, particularly in functional brain pathways associated with vagal and interoceptive/emotion processing.
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Xiong J, Ma YJ, Liao XS, Li LQ, Bao L. Gut microbiota in infants with food protein enterocolitis. Pediatr Res 2024:10.1038/s41390-024-03424-9. [PMID: 39033251 DOI: 10.1038/s41390-024-03424-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/07/2024] [Indexed: 07/23/2024]
Abstract
BACKGROUND We explored the effects of two formulas, extensively hydrolyzed formula (EHF) and amino acid-based formula (AAF), on the gut microbiota and short-chain fatty acids (SCFAs) in infants with food protein-induced enterocolitis syndrome (FPIES). METHODS Fecal samples of thirty infants with bloody diarrhea receiving EHF or AAF feeding were collected at enrollment, diagnosis of FPIES, and four weeks after diagnosis. The gut microbiota and SCFAs were analyzed using 16 S rRNA gene sequencing and gas chromatography-mass spectrometry, respectively. RESULTS Microbial diversity of FPIES infants was significantly different from that of the controls. FPIES infants had a significantly lower abundance of Bifidobacterium and a higher level of hexanoic acid compared with controls. In EHF-fed FPIES infants, microbial richness was significantly decreased over time; while the microbial diversity and richness in AAF-fed FPIES infants exhibited no differences at the three time points. By four weeks after diagnosis, EHF-fed FPIES infants contained a decreased abundance of Acinetobacter, whereas AAF-fed FPIES infants contained an increased abundance of Escherichia-Shigella. EHF-fed infants experienced significantly decreased levels of butyric acid and hexanoic acid at four weeks after diagnosis. CONCLUSIONS Infants with FPIES had intestinal dysbiosis and different formulas differentially affected gut microbiota and SCFAs in FPIES infants. IMPACT We firstly report the impacts of two different nutritional milk formulas on the gut microbial composition and SCFAs levels in infants with FPIES. We show that infants with FPIES have obvious intestinal dysbiosis and different formulas differentially affect gut microbiota and SCFAs in FPIES infants. Understanding the effects of different types of formulas on gut microbial colonization and composition, as well as the related metabolites in infants with FPIES could help provide valuable insights for making choices about feeding practices.
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Affiliation(s)
- Jing Xiong
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- China International Science and Technology Cooperation base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatric Metabolism and Inflammatory Diseases, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yu-Jue Ma
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- China International Science and Technology Cooperation base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatric Metabolism and Inflammatory Diseases, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xing-Sheng Liao
- Department of Neonatology, The first People's Hospital of Jiulongpo District, Chongqing, China
| | - Lu-Quan Li
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- China International Science and Technology Cooperation base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Pediatric Metabolism and Inflammatory Diseases, Children's Hospital of Chongqing Medical University, Chongqing, China.
| | - Lei Bao
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- China International Science and Technology Cooperation base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Pediatric Metabolism and Inflammatory Diseases, Children's Hospital of Chongqing Medical University, Chongqing, China.
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Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M, Villaseñor A. Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach. Nat Commun 2024; 15:3004. [PMID: 38589361 PMCID: PMC11001937 DOI: 10.1038/s41467-024-47182-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.
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Affiliation(s)
- Tomás Clive Barker-Tejeda
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Elisa Zubeldia-Varela
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Andrea Macías-Camero
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Lola Alonso
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Isabel Adoración Martín-Antoniano
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Instituto de Estudios de las Adicciones IEA-CEU, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - María Fernanda Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Leticia Mera-Berriatua
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Raphaëlle Bazire
- Department of Allergy, Hospital Infantil Niño Jesús, Fib-HNJ, Madrid, Spain
- Instituto de Investigación Sanitaria-La Princesa, Madrid, Spain
| | - Paula Cabrera-Freitag
- Pedriatic Allergy Unit, Allergy Service, Hospital General Universitario Gregorio Marañón, and Gregorio Marañón Health Research Institute, Madrid, Spain
| | - Meera Shanmuganathan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Carles Ubeda
- Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO), Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - M Pilar Francino
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
- Joint Research Unit in Genomics and Health, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO) and Institut de Biologia Integrativa de Sistemes (Universitat de València / Consejo Superior de Investigaciones Científicas), València, Spain
| | - Domingo Barber
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - María Dolores Ibáñez-Sandín
- Department of Allergy, Hospital Infantil Niño Jesús, Fib-HNJ, Madrid, Spain
- Instituto de Investigación Sanitaria-La Princesa, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Marina Pérez-Gordo
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
| | - Alma Villaseñor
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
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Yan Z, He X, Ayala J, Xu Q, Yu X, Hou R, Yao Y, Huang H, Wang H. The Impact of Bamboo Consumption on the Spread of Antibiotic Resistance Genes in Giant Pandas. Vet Sci 2023; 10:630. [PMID: 37999453 PMCID: PMC10675626 DOI: 10.3390/vetsci10110630] [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: 09/01/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/25/2023] Open
Abstract
The spread of antibiotic resistance genes (ARGs) in the environment exacerbates the contamination of these genes; therefore, the role plants play in the transmission of resistance genes in the food chain requires further research. Giant pandas consume different bamboo parts at different times, which provides the possibility of investigating how a single food source can affect the variation in the spread of ARGs. In this study, metagenomic analysis and the Comprehensive Antibiotic Resistance Database (CARD) database were used to annotate ARGs and the differences in gut microbiota ARGs during the consumption of bamboo shoots, leaves, and culms by captive giant pandas. These ARGs were then compared to investigate the impact of bamboo part consumption on the spread of ARGs. The results showed that the number of ARGs in the gut microbiota of the subjects was highest during the consumption of bamboo leaves, while the variety of ARGs was highest during the consumption of shoots. Escherichia coli, which poses a higher risk of ARG dissemination, was significantly higher in the leaf group, while Klebsiella, Enterobacter, and Raoultella were significantly higher in the shoot group. The ARG risk brought by bamboo shoots and leaves may originate from soil and environmental pollution. It is recommended to handle the feces of giant pandas properly and regularly monitor the antimicrobial and virulence genes in their gut microbiota to mitigate the threat of antibiotic resistance.
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Affiliation(s)
- Zheng Yan
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (Z.Y.); (J.A.); (Q.X.); (X.Y.); (R.H.); (Y.Y.); (H.H.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
- Key Laboratory for Biodiversity and Ecological Engineering of Ministry of Education, Department of Ecology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xin He
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (Z.Y.); (J.A.); (Q.X.); (X.Y.); (R.H.); (Y.Y.); (H.H.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - James Ayala
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (Z.Y.); (J.A.); (Q.X.); (X.Y.); (R.H.); (Y.Y.); (H.H.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Qin Xu
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (Z.Y.); (J.A.); (Q.X.); (X.Y.); (R.H.); (Y.Y.); (H.H.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Xiaoqiang Yu
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (Z.Y.); (J.A.); (Q.X.); (X.Y.); (R.H.); (Y.Y.); (H.H.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (Z.Y.); (J.A.); (Q.X.); (X.Y.); (R.H.); (Y.Y.); (H.H.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Ying Yao
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (Z.Y.); (J.A.); (Q.X.); (X.Y.); (R.H.); (Y.Y.); (H.H.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - He Huang
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (Z.Y.); (J.A.); (Q.X.); (X.Y.); (R.H.); (Y.Y.); (H.H.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (Z.Y.); (J.A.); (Q.X.); (X.Y.); (R.H.); (Y.Y.); (H.H.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
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Creus-Martí I, Marín-Miret J, Moya A, Santonja FJ. Evidence of the cooperative response of Blattella germanica gut microbiota to antibiotic treatment. Math Biosci 2023; 364:109057. [PMID: 37562583 DOI: 10.1016/j.mbs.2023.109057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023]
Abstract
Gut microbiota plays a key role in host health under normal conditions. However, bacterial composition can be altered by external factors such as antibiotic (AB) intake. While there are many descriptive publications about the effects of AB on gut microbiota composition after treatment, the dynamics and interactions among the bacterial taxa are still poorly understood. In this work, we performed a longitudinal study of gut microbiome dynamics in B. germanica treated with kanamycin. The AB was supplied in three separate periods, giving the microbiota time to recover between each antibiotic intake. We applied two new statistical models, not focusing on pair-wise interactions, to more realistically study the interactions between groups of bacterial taxa and how some groups affect a single taxon. The first model provides information on the importance of a given genus, and the rest of the community, to define the abundance of that genus. The second model, on the other hand, provides details about the relationship between groups of bacteria, focusing on which community groups affect the taxa. These models help us to identify which bacteria are community-dependent in stress conditions, which taxa might be better adapted than the rest of the community, and which bacteria might be working together within the community to overcome the antibiotic. In addition, these models enable us to identify different bacterial groups that were separated in control conditions but were found together in treated conditions, suggesting that when the environment is more hostile (as it is under antibiotic treatment), the whole community tends to work together.
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Affiliation(s)
- Irene Creus-Martí
- Institute for Integrative Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain; Department of Statistics and Operation Research, Universitat de València, Valencia, Spain
| | - Jesús Marín-Miret
- Institute for Integrative Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain; The Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Francisco J Santonja
- Department of Statistics and Operation Research, Universitat de València, Valencia, Spain.
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Yang Q, Wu Z. Gut Probiotics and Health of Dogs and Cats: Benefits, Applications, and Underlying Mechanisms. Microorganisms 2023; 11:2452. [PMID: 37894110 PMCID: PMC10609632 DOI: 10.3390/microorganisms11102452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Pets (mostly domestic dogs and cats) play an important role in the daily lives of humans and their health has attracted growing attention from pet owners. The intestinal microbiota, a complex microbial community with barrier-protective, nutritional, metabolic, and immunological functions, is integral to host health. Dysbiosis has been related to a variety of diseases in humans and animals. Probiotics have been used in functional foods and dietary supplements to modulate intestinal microbiota and promote host health, which has been introduced in pet dogs and cats in recent years. Various canine- and feline-derived probiotic strains have been isolated and characterized. The administration of probiotics has shown positive effects on the gut health and can alleviate some intestinal diseases and disorders in dogs and cats, although the underlying mechanisms are largely unresolved. In this review, we summarize the current knowledge on the benefits of probiotics and discuss their possible mechanisms in dogs and cats in order to provide new insights for the further development and application of probiotics in pets.
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Affiliation(s)
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition, Department of Companion Animal Science, China Agricultural University, Beijing 100193, China;
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Zaidi S, Ali K, Khan AU. It's all relative: analyzing microbiome compositions, its significance, pathogenesis and microbiota derived biofilms: Challenges and opportunities for disease intervention. Arch Microbiol 2023; 205:257. [PMID: 37280443 DOI: 10.1007/s00203-023-03589-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/06/2023] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
Concept of microorganisms has largely been perceived from their pathogenic view point. Nevertheless, it is being gradually revisited in terms of its significance to human health and now appears to be the most dominant force that shapes the immune system of the human body and also determines an individual's predisposition to diseases. Human inhabits bacterial diversity (which is predominant among all microbial communities in human body) occupying 0.3% of body mass, known as microbiota. On birth, a part of microbiota that child obtains is essentially a mother's legacy. So, the review was initiated with this critical topic of microbiotal inheritance. Since, each body site has distinct physiological specifications; therefore, they contain discrete microbiome composition that has been separately discussed along with dysbiosis-induced pathologies originating in different body organs. Factors affecting microbiome composition and may cause dysbiosis like antibiotics, delivery, feeding method etc. as well as the strategies that immune system adopts to prevent dysbiosis have been highlighted. We also tried to bring into attention the topic of dysbiosis induced biofilms, that enables cohort to survive stresses, evolve, disseminate and infection resurgence that is still in dormancy. Eventually, we put spotlight on microbiome significance in medical therapeutics. We didn't merely confine article to gut microbiota, that is being studied more extensively. Numerous community forms at diverse body sites are inter-related, and being exposed to awfully variable perturbations appear to be challenging to evaluate perturbation risks holistically. All aspects have been elaborately discussed to achieve a global depiction of human microbiota in order to meet urgent necessity for protocol standardisation. Demonstrates that environmental challenges (antibiotic use, alterations in diet, stress, smoking etc.) might cause dysbiosis i.e. transition of healthy microbiome composition to the one in which pathogenic microorganisms become more abundant, and eventually results in an infected state.
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Affiliation(s)
- Sahar Zaidi
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Khursheed Ali
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Santarossa S, Sitarik AR, Cassidy-Bushrow AE, Comstock SS. Prenatal physical activity and the gut microbiota of pregnant women: results from a preliminary investigation. Phys Act Nutr 2023; 27:1-7. [PMID: 37583065 PMCID: PMC10440177 DOI: 10.20463/pan.2023.0011] [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: 03/14/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 08/17/2023] Open
Abstract
PURPOSE To determine whether physical activity (PA), specifically meeting the recommended 150 minutes of moderate-intensity PA per week, is associated with gut microbiota composition in pregnant women. METHODS In an ongoing birth cohort study, questions from the Behavioral Risk Factor Surveillance System, which provides data on PA variables, were used to determine whether pregnant women met or exceeded the PA recommendations. To profile the composition of gut bacterial microbiota, 16S rRNA sequencing was performed on stool samples obtained from pregnant women. Differences in alpha diversity metrics (richness, Pielou's evenness, and Shannon's diversity) according to PA were determined using linear regression, whereas beta diversity relationships (Canberra and Bray-Curtis) were assessed using Permutational multivariate analysis of variance (PERMANOVA). Differences in relative taxon abundance were determined using DESeq2. RESULTS The complete analytical sample included 23 women that were evaluated for both PA and 16S rRNA sequencing data (median age [Q1; Q3] = 30.5 [26.6; 34.0] years; 17.4% Black), and 11 (47.8%) met or exceeded the PA recommendations. Meeting or exceeding the PA recommendations during pregnancy was not associated with gut microbiota richness, evenness, or diversity, but it was related to distinct bacterial composition using both Canberra (p = 0.005) and Bray-Curtis (p = 0.022) distances. Significantly lower abundances of Bacteroidales, Bifidobacteriaceae, Lactobacillaceae, and Streptococcaceae were observed in women who met or exceeded the PA recommendations (all false discovery rates adjusted, p < 0.02). CONCLUSION Pregnant women who met or exceeded the PA recommendations showed altered gut microbiota composition. This study forms the basis for future studies on the impact of PA on gut microbiota during pregnancy.
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Affiliation(s)
- Sara Santarossa
- Department of Public Health Sciences, Henry Ford Health System, Michigan, USA
| | | | | | - Sarah S. Comstock
- Department of Food Science and Human Nutrition, Michigan State University, Michigan, USA
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10
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Cassidy-Bushrow AE, Sitarik AR, Johnson CC, Johnson-Hooper TM, Kassem Z, Levin AM, Lynch SV, Ownby DR, Phillips JM, Yong GJM, Wegienka G, Straughen JK. Early-life gut microbiota and attention deficit hyperactivity disorder in preadolescents. Pediatr Res 2023; 93:2051-2060. [PMID: 35440767 PMCID: PMC9582043 DOI: 10.1038/s41390-022-02051-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 12/13/2021] [Accepted: 12/31/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND Gut microbiota maturation coincides with nervous system development. Cross-sectional data suggest gut microbiota of individuals with and without attention deficit hyperactivity disorder (ADHD) differs. We hypothesized that infant gut microbiota composition is associated with later ADHD development in our on-going birth cohort study, WHEALS. METHODS Gut microbiota was profiled using 16S ribosomal RNA and the internal transcribed spacer region 2 (ITS2) sequencing in stool samples from 1 month and 6 months of age. ADHD was defined by parent-reported or medical record doctor diagnosis at age 10. RESULTS A total of 314 children had gut microbiota and ADHD data; 59 (18.8%) had ADHD. After covariate adjustment, bacterial phylogenetic diversity (p = 0.017) and bacterial composition (unweighted UniFrac p = 0.006, R2 = 0.9%) at age 6 months were associated with development of ADHD. At 1 month of age, 18 bacterial and 3 fungal OTUs were associated with ADHD development. At 6 months of age, 51 bacterial OTUs were associated with ADHD; 14 of the order Lactobacillales. Three fungal OTUs at 6 months of age were associated with ADHD development. CONCLUSIONS Infant gut microbiota is associated with ADHD development in pre-adolescents. Further studies replicating these findings and evaluating potential mechanisms of the association are needed. IMPACT Cross-sectional studies suggest that the gut microbiota of individuals with and without ADHD differs. We found evidence that the bacterial gut microbiota of infants at 1 month and 6 months of age is associated with ADHD at age 10 years. We also found novel evidence that the fungal gut microbiota in infancy (ages 1 month and 6 months) is associated with ADHD at age 10 years. This study addresses a gap in the literature in providing longitudinal evidence for an association of the infant gut microbiota with later ADHD development.
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Affiliation(s)
- Andrea E Cassidy-Bushrow
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA.
- Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI, USA.
| | | | - Christine Cole Johnson
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
- Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI, USA
| | - Tisa M Johnson-Hooper
- Department of Pediatrics, Henry Ford Hospital, Detroit, MI, USA
- Center for Autism and Developmental Disabilities, Henry Ford Hospital, Detroit, MI, USA
| | - Zeinab Kassem
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Dennis R Ownby
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Augusta University, Augusta, GA, USA
| | - Jannel M Phillips
- Center for Autism and Developmental Disabilities, Henry Ford Hospital, Detroit, MI, USA
- Department of Psychiatry and Behavioral Health Services, Division of Neuropsychology, Henry Ford Hospital, Detroit, MI, USA
| | - Germaine J M Yong
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Ganesa Wegienka
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
- Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI, USA
| | - Jennifer K Straughen
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
- Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI, USA
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Fardi F, Bahari Khasraghi L, Shahbakhti N, Salami Naseriyan A, Najafi S, Sanaaee S, Alipourfard I, Zamany M, Karamipour S, Jahani M, Majidpoor J, Kalhor K, Talebi M, Mohsen Aghaei-Zarch S. An interplay between non-coding RNAs and gut microbiota in human health. Diabetes Res Clin Pract 2023:110739. [PMID: 37270071 DOI: 10.1016/j.diabres.2023.110739] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 04/22/2023] [Accepted: 05/30/2023] [Indexed: 06/05/2023]
Abstract
Humans have a complicated symbiotic relationship with their gut microbiome, which is postulated to impact host health and disease broadly. Epigenetic alterations allow host cells to regulate gene expression without altering the DNA sequence. The gut microbiome, offering environmental hints, can influence responses to stimuli by host cells with modifications on their epigenome and gene expression. Recent increasing data suggest that regulatory non-coding RNAs (miRNAs, circular RNAs, and long lncRNA) may affect host-microbe interactions. These RNAs have been suggested as potential host response biomarkers in microbiome-associated disorders, including diabetes and cancer. This article reviews the current understanding of the interplay between gut microbiota and non-coding RNA, including lncRNA, miRNA, and circular RNA. This can lead to a profound understanding of human disease and influence therapy. Furthermore, microbiome engineering as a mainstream strategy for improving human health has been discussed and confirms the hypothesis about a direct cross-talk between microbiome composition and non-coding RNA.
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Affiliation(s)
- Fatemeh Fardi
- Department of Microbiology, Faculty of Biological Sciences, Islamic Azad University, Kish international, Kish, Iran
| | - Leila Bahari Khasraghi
- 15 Khordad Educational Hospital, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Negin Shahbakhti
- Department of biology, Faculty of Zoology, University of Razi, Kermanshah, Iran
| | - Amir Salami Naseriyan
- Department of Microbial Biotechnology, Islamic Azad University, Varamin-Pishva Branch, Tabriz, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saameh Sanaaee
- Department of New Science, Faculty of Cellular and Molecular biology, Islamic Azad University, Tehran Medical Branch, Tehran, Iran
| | - Iraj Alipourfard
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Marzieh Zamany
- Shahid Akbarabadi Clinical Research Development Unit, Iran University of medical Science, Tehran, Iran
| | - Saman Karamipour
- Department of Genetics and Molecular biology, Faculty of Medicine, Iran University of Medical science, Tehran, Iran
| | - Mehdi Jahani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Kambiz Kalhor
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, USA.
| | - Mehrdad Talebi
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Seyed Mohsen Aghaei-Zarch
- Department of Genetics and Molecular biology, Faculty of Medicine, Iran University of Medical science, Tehran, Iran.
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12
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Ranjbar Z, Lavaee F, Karandish M, Peiravian F, Zarei F. Vitamin D serum level in participants with positive history of recurrent herpes labialis. BMC Oral Health 2023; 23:230. [PMID: 37081493 PMCID: PMC10116727 DOI: 10.1186/s12903-023-02924-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/29/2023] [Indexed: 04/22/2023] Open
Abstract
AIM Vitamin D plays an important role in immune system regulation, also its deficiency is assumed to affect the patients' predisposition to viral diseases such as recurrent herpes labialis. In this cross-sectional study, we tried to compare the mean serum level of vitamin D in participants with a positive history of recurrent herpes labial lesions and healthy controls. MATERIALS AND METHODS The vitamin D serum level of 43 participants with a positive history of recurrent herpes labial lesions who were referred to the Motahhari laboratory in Shiraz during 2020-2022, was compared with 42 healthy controls. It was assessed by an Elisa kit. An Independent T-test was used to compare the vitamin D serum level between two genders. In order to assess the mean age value and gender distribution, an independent T-test and Pearson Chi-Square were used, respectively for the two groups. The serum vitamin D level was compared between both control and test groups. RESULTS There was no significant difference between vitamin D mean serum levels in the two evaluated groups (p.value = 0.72). Although the age (p.value = 0.09) and recurrence (p.value = 0.13) of herpes labialis had no statistically significant relation to the vitamin D serum level, the healing duration of herpes labialis was inversely related (p.value = 0.01). Lower-level of serum vitamin D were accompanied by a longer healing duration of the lesions. CONCLUSION Although the vitamin D serum level of participants with a history of recurrent herpes labialis had no relation with age and herpes virus recurrence frequency, a longer healing duration of lesions had been reported in patients with lower serum levels of vitamin D.
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Affiliation(s)
- Zahra Ranjbar
- Oral and Dental Disease Research center, Oral and Maxillofacial Disease Department, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Lavaee
- Oral and Dental Disease Research center, Oral and Maxillofacial Disease Department, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Maryam Karandish
- Department of Orthodontics, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farnaz Peiravian
- Student research committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fateme Zarei
- Student research committee, Shiraz University of Medical Sciences, Shiraz, Iran
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Monticolo M, Mucha K, Foroncewicz B. Lupus Nephritis and Dysbiosis. Biomedicines 2023; 11:biomedicines11041165. [PMID: 37189783 DOI: 10.3390/biomedicines11041165] [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: 02/26/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 05/17/2023] Open
Abstract
Lupus nephritis (LN) is one of the most common and serious complications of systemic lupus erythematosus (SLE). The risk factors for developing LN by SLE patients are not fully understood. They are considered to be a mix of genetic and environmental variables, one of them being dysbiosis, proposed recently to interfere with autoimmunity. As of yet, the relations between the human microbiome, its genetic determinants, individual variability and clinical consequences remain to be established. One of the major obstacles in studying them is the magnitude of confounders, such as diet, drugs, infections or antibiotics use. They also make comparison between the studies extremely complicated. We reviewed the available evidence for the interplay between microbiome, dysbiosis and mechanisms triggering the autoimmune responses and potentially contributing to LN development. One such mechanism is the stimulation of autoimmune responses by bacterial metabolites that can mimic autoantigens and cause antibody production. These mimicking microbial antigens seem to be a promising target for future interventions.
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Affiliation(s)
- Marta Monticolo
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, 02-006 Warsaw, Poland
| | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, 02-006 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Bartosz Foroncewicz
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, 02-006 Warsaw, Poland
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Lama Tamang R, Juritsch AF, Ahmad R, Salomon JD, Dhawan P, Ramer-Tait AE, Singh AB. The diet-microbiota axis: a key regulator of intestinal permeability in human health and disease. Tissue Barriers 2023; 11:2077069. [PMID: 35603609 PMCID: PMC10161950 DOI: 10.1080/21688370.2022.2077069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/07/2022] [Indexed: 01/21/2023] Open
Abstract
The intestinal barrier orchestrates selective permeability to nutrients and metabolites while excluding noxious stimuli. Recent scientific advances establishing a causal role for the gut microbiota in human health outcomes have generated a resurgent interest toward intestinal permeability. Considering the well-established role of the gut barrier in protection against foreign antigens, there is mounting evidence for a causal link between gut permeability and the microbiome in regulating human health. However, an understanding of the dynamic host-microbiota interactions that govern intestinal barrier functions remains poorly defined. Furthermore, the system-level mechanisms by which microbiome-targeted therapies, such as probiotics and prebiotics, simultaneously promote intestinal barrier function and host health remain an area of active investigation. This review summarizes the recent advances in understanding the dynamics of intestinal permeability in human health and its integration with gut microbiota. We further summarize mechanisms by which probiotics/prebiotics influence the gut microbiota and intestinal barrier functions.
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Affiliation(s)
- Raju Lama Tamang
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Anthony F. Juritsch
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Rizwan Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jeffrey D. Salomon
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Punita Dhawan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, Nebraska, USA
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Amar B. Singh
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, Nebraska, USA
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15
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The gut microbiota and depressive symptoms across ethnic groups. Nat Commun 2022; 13:7129. [PMID: 36473853 PMCID: PMC9726934 DOI: 10.1038/s41467-022-34504-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/27/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome is thought to play a role in depressive disorders, which makes it an attractive target for interventions. Both the microbiome and depressive symptom levels vary substantially across ethnic groups. Thus, any intervention for depression targeting the microbiome requires understanding of microbiome-depression associations across ethnicities. Analysing data from the HELIUS cohort, we characterize the gut microbiota and its associations with depressive symptoms in 6 ethnic groups (Dutch, South-Asian Surinamese, African Surinamese, Ghanaian, Turkish, Moroccan; N = 3211), living in the same urban area. Diversity of the gut microbiota, both within (α-diversity) and between individuals (β-diversity), predicts depressive symptom levels, taking into account demographic, behavioural, and medical differences. These associations do not differ between ethnic groups. Further, β-diversity explains 29%-18% of the ethnic differences in depressive symptoms. Bacterial genera associated with depressive symptoms belong to mulitple families, prominently including the families Christensenellaceae, Lachnospiraceae, and Ruminococcaceae. In summary, the results show that the gut microbiota are linked to depressive symptom levels and that this association generalizes across ethnic groups. Moreover, the results suggest that ethnic differences in the gut microbiota may partly explain parallel disparities in depression.
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16
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Yadav A, Pandey R. Viral infectious diseases severity: co-presence of transcriptionally active microbes (TAMs) can play an integral role for disease severity. Front Immunol 2022; 13:1056036. [PMID: 36532032 PMCID: PMC9755851 DOI: 10.3389/fimmu.2022.1056036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022] Open
Abstract
Humans have been challenged by infectious diseases for all of their recorded history, and are continually being affected even today. Next-generation sequencing (NGS) has enabled identification of, i) culture independent microbes, ii) emerging disease-causing pathogens, and iii) understanding of the genome architecture. This, in turn, has highlighted that pathogen/s are not a monolith, and thereby allowing for the differentiation of the wide-ranging disease symptoms, albeit infected by a primary pathogen. The conventional 'one disease - one pathogen' paradigm has been positively revisited by considering limited yet important evidence of the co-presence of multiple transcriptionally active microbes (TAMs), potential pathogens, in various infectious diseases, including the COVID-19 pandemic. The ubiquitous microbiota presence inside humans gives reason to hypothesize that the microbiome, especially TAMs, contributes to disease etiology. Herein, we discuss current evidence and inferences on the co-infecting microbes particularly in the diseases caused by the RNA viruses - Influenza, Dengue, and the SARS-CoV-2. We have highlighted that the specific alterations in the microbial taxonomic abundances (dysbiosis) is functionally connected to the exposure of primary infecting pathogen/s. The microbial presence is intertwined with the differential host immune response modulating differential disease trajectories. The microbiota-host interactions have been shown to modulate the host immune responses to Influenza and SARS-CoV-2 infection, wherein the active commensal microbes are involved in the generation of virus-specific CD4 and CD8 T-cells following the influenza virus infection. Furthermore, COVID-19 dysbiosis causes an increase in inflammatory cytokines such as IL-6, TNF-α, and IL-1β, which might be one of the important predisposing factors for severe infection. Through this article, we aim to provide a comprehensive view of functional microbiomes that can have a significant regulatory impact on predicting disease severity (mild, moderate and severe), as well as clinical outcome (survival and mortality). This can offer fresh perspectives on the novel microbial biomarkers for stratifying patients for severe disease symptoms, disease prevention and augmenting treatment regimens.
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Affiliation(s)
- Aanchal Yadav
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,*Correspondence: Rajesh Pandey, ;
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Unlocking the Potential of the Human Microbiome for Identifying Disease Diagnostic Biomarkers. Diagnostics (Basel) 2022; 12:diagnostics12071742. [PMID: 35885645 PMCID: PMC9315466 DOI: 10.3390/diagnostics12071742] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 02/07/2023] Open
Abstract
The human microbiome encodes more than three million genes, outnumbering human genes by more than 100 times, while microbial cells in the human microbiota outnumber human cells by 10 times. Thus, the human microbiota and related microbiome constitute a vast source for identifying disease biomarkers and therapeutic drug targets. Herein, we review the evidence backing the exploitation of the human microbiome for identifying diagnostic biomarkers for human disease. We describe the importance of the human microbiome in health and disease and detail the use of the human microbiome and microbiota metabolites as potential diagnostic biomarkers for multiple diseases, including cancer, as well as inflammatory, neurological, and metabolic diseases. Thus, the human microbiota has enormous potential to pave the road for a new era in biomarker research for diagnostic and therapeutic purposes. The scientific community needs to collaborate to overcome current challenges in microbiome research concerning the lack of standardization of research methods and the lack of understanding of causal relationships between microbiota and human disease.
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Xing S, Chen S, Zhao Y, Luo Y, Yu B, He J, Huang Z, Zheng P, Mao X, Luo J, Yan H, Yu J. Effects of High Ambient Temperature on Small Intestinal Morphology and Colonic Microbiota in Weaned Piglets. Animals (Basel) 2022; 12:ani12141743. [PMID: 35883290 PMCID: PMC9312015 DOI: 10.3390/ani12141743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022] Open
Abstract
A total of 16 crossbred (Duroc × Landrace × Yorkshire) barrows, with an average initial body weight of 8.61 ± 0.24 kg (28 days of age), were randomly allotted into the control group (CON group) and high ambient temperature group (HT group) with 8 replicates per group, 1 pig per replicate. The ambient temperature of the CON group was controlled at 26 ± 1 °C, and the HT group was controlled at 35 ± 1 °C. The study lasted for 21 days. Our results showed that high ambient temperature significantly decreased the average daily feed intake (ADFI) and average daily gain (ADG) of piglets (p < 0.05), and the feed-to-gain ratio was significantly increased (p < 0.05). The liver index, spleen index, and thymus index of piglets in the HT group were significantly decreased (p < 0.05). The villous height (VH) of the duodenum, jejunum, and ileum of piglets in the HT group was significantly decreased (p < 0.05), whereas the crypt depth (CD) of the duodenum was significantly increased (p < 0.05), and the VH-to-CD ratio of the duodenum and ileum was significantly decreased (p < 0.05). The piglets in the HT group showed a higher (p < 0.05) observed-species index, PD whole tree index, and Shannon index, indicating that there was a significant difference in species richness and diversity between the two groups. At the genus level, the piglets in the HT group showed a greater (p < 0.05) percent of Desulfovibrio, Occillibater, and Catenisphaera. HT reduced glycan biosynthesis and metabolism, transport and catabolism, lipid metabolism, amino acids metabolism, secondary metabolites biosynthesis, aging, endocrine system, signaling molecules, and interaction of colon microbiota (p < 0.05), and increased signal transduction, cell motility, transcription, and genetic information processing (p < 0.05).
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Affiliation(s)
- Shuaibing Xing
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
| | - Shuai Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
| | - Ying Zhao
- Sichuan Tequ Agriculture and Animal Husbandry Technology Group Co., Ltd., Chengdu 610207, China;
| | - Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
| | - Xiangbing Mao
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
| | - Junqiu Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
| | - Hui Yan
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.X.); (S.C.); (Y.L.); (B.Y.); (J.H.); (Z.H.); (P.Z.); (X.M.); (J.L.); (H.Y.)
- Sichuan Tequ Agriculture and Animal Husbandry Technology Group Co., Ltd., Chengdu 610207, China;
- Correspondence: ; Tel.: +86-28-82690922
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Wang X, Zhang Y, Li C, Li G, Wu D, Li T, Qu Y, Deng W, He Y, Penttinen P, Zhang H, Huang Y, Zhao K, Zou L. Antimicrobial resistance of Escherichia coli, Enterobacter spp., Klebsiella pneumoniae and Enterococcus spp. isolated from the feces of giant panda. BMC Microbiol 2022; 22:102. [PMID: 35421931 PMCID: PMC9008915 DOI: 10.1186/s12866-022-02514-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/01/2022] [Indexed: 11/26/2022] Open
Abstract
Background Escherichia coli, Enterobacter spp., Klebsiella pneumoniae and Enterococcus spp., common gut bacteria in giant pandas, include opportunistic pathogens. The giant panda is an endangered species, classified as vulnerable by the World Wildlife Foundation. Continuous monitoring for the emergence of antimicrobial resistance (AMR) among bacterial isolates from giant pandas is vital not only for their protection but also for public health. Results A total of 166 E. coli, 68 Enterobacter spp., 116 K. pneumoniae and 117 Enterococcus spp. isolates were collected from fecal samples of 166 giant pandas. In the antimicrobial susceptibility tests, 144 E. coli isolates, 66 Enterobacter spp. isolates, 110 K. pneumoniae isolates and 43 Enterococcus spp. isolates were resistant to at least one antimicrobial. The resistant isolates carried antimicrobial resistance genes (ARGs), including sul3, blaTEM, blaSHV and tetA. The differences in the prevalence of the bla types implied that the genetic basis for β-lactam resistance among the E. coli, Enterobacter spp. and K. pneumoniae isolates was different. The strain K. pneumoniae K85 that was resistant to sixteen antimicrobials was selected for whole genome sequencing. The genome contained Col440I, IncFIBK and IncFIIK plasmids and altogether 258 ARGs were predicted in the genome; 179 of the predicted ARGs were efflux pump genes. The genetic environment of the β-lactamase genes blaCTX-M-3 and blaTEM-1 in the K. pneumoniae K85 genome was relatively similar to those in other sequenced K. pneumoniae genomes. In comparing the giant panda age groups, the differences in the resistance rates among E. coli, K. pneumoniae and Enterobacter spp. isolates suggested that the infections in giant pandas of different age should be treated differently. Conclusions Antimicrobial resistance was prevalent in the bacterial isolates from the giant pandas, implying that the gut bacteria may pose serious health risks for captive giant pandas. The resistance genes in the genome of K. pneumoniae K85 were associated with insertion sequences and integron-integrase genes, implying a potential for the further spread of the antimicrobial resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02514-0.
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20
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Gheorghe AS, Negru ȘM, Preda M, Mihăilă RI, Komporaly IA, Dumitrescu EA, Lungulescu CV, Kajanto LA, Georgescu B, Radu EA, Stănculeanu DL. Biochemical and Metabolical Pathways Associated with Microbiota-Derived Butyrate in Colorectal Cancer and Omega-3 Fatty Acids Implications: A Narrative Review. Nutrients 2022; 14:nu14061152. [PMID: 35334808 PMCID: PMC8950877 DOI: 10.3390/nu14061152] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 02/01/2023] Open
Abstract
Knowledge regarding the influence of the microbial community in cancer promotion or protection has expanded even more through the study of bacterial metabolic products and how they can modulate cancer risk, which represents an extremely challenging approach for the relationship between intestinal microbiota and colorectal cancer (CRC). This review discusses research progress on the effect of bacterial dysbiosis from a metabolic point of view, particularly on the biochemical mechanisms of butyrate, one of the main short chain fatty acids (SCFAs) with anti-inflammatory and anti-tumor properties in CRC. Increased daily intake of omega-3 polyunsaturated fatty acids (PUFAs) significantly increases the density of bacteria that are known to produce butyrate. Omega-3 PUFAs have been proposed as a treatment to prevent gut microbiota dysregulation and lower the risk or progression of CRC.
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Affiliation(s)
- Adelina Silvana Gheorghe
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (A.S.G.); (R.I.M.); (I.A.K.); (E.A.D.); (L.A.K.); (B.G.); (E.A.R.); (D.L.S.)
| | - Șerban Mircea Negru
- Department of Oncology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timisoara, Romania
- Correspondence: (Ș.M.N.); (M.P.)
| | - Mădălina Preda
- Department of Microbiology, Parasitology and Virology, Faculty of Midwives and Nursing, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Correspondence: (Ș.M.N.); (M.P.)
| | - Raluca Ioana Mihăilă
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (A.S.G.); (R.I.M.); (I.A.K.); (E.A.D.); (L.A.K.); (B.G.); (E.A.R.); (D.L.S.)
| | - Isabela Anda Komporaly
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (A.S.G.); (R.I.M.); (I.A.K.); (E.A.D.); (L.A.K.); (B.G.); (E.A.R.); (D.L.S.)
| | - Elena Adriana Dumitrescu
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (A.S.G.); (R.I.M.); (I.A.K.); (E.A.D.); (L.A.K.); (B.G.); (E.A.R.); (D.L.S.)
| | | | - Lidia Anca Kajanto
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (A.S.G.); (R.I.M.); (I.A.K.); (E.A.D.); (L.A.K.); (B.G.); (E.A.R.); (D.L.S.)
| | - Bogdan Georgescu
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (A.S.G.); (R.I.M.); (I.A.K.); (E.A.D.); (L.A.K.); (B.G.); (E.A.R.); (D.L.S.)
| | - Emanuel Alin Radu
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (A.S.G.); (R.I.M.); (I.A.K.); (E.A.D.); (L.A.K.); (B.G.); (E.A.R.); (D.L.S.)
| | - Dana Lucia Stănculeanu
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (A.S.G.); (R.I.M.); (I.A.K.); (E.A.D.); (L.A.K.); (B.G.); (E.A.R.); (D.L.S.)
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21
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Alharthi A, Alhazmi S, Alburae N, Bahieldin A. The Human Gut Microbiome as a Potential Factor in Autism Spectrum Disorder. Int J Mol Sci 2022; 23:ijms23031363. [PMID: 35163286 PMCID: PMC8835713 DOI: 10.3390/ijms23031363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 11/16/2022] Open
Abstract
The high prevalence of gastrointestinal (GI) disorders among autism spectrum disorder (ASD) patients has prompted scientists to look into the gut microbiota as a putative trigger in ASD pathogenesis. Thus, many studies have linked the gut microbial dysbiosis that is frequently observed in ASD patients with the modulation of brain function and social behavior, but little is known about this connection and its contribution to the etiology of ASD. This present review highlights the potential role of the microbiota–gut–brain axis in autism. In particular, it focuses on how gut microbiota dysbiosis may impact gut permeability, immune function, and the microbial metabolites in autistic people. We further discuss recent findings supporting the possible role of the gut microbiome in initiating epigenetic modifications and consider the potential role of this pathway in influencing the severity of ASD. Lastly, we summarize recent updates in microbiota-targeted therapies such as probiotics, prebiotics, dietary supplements, fecal microbiota transplantation, and microbiota transfer therapy. The findings of this paper reveal new insights into possible therapeutic interventions that may be used to reduce and cure ASD-related symptoms. However, well-designed research studies using large sample sizes are still required in this area of study.
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Affiliation(s)
- Amani Alharthi
- Department of Biology, Faculty of Science, Majmaah University, Al Zulfi 11932, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.); (N.A.)
- Correspondence: (A.A.); (A.B.)
| | - Safiah Alhazmi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.); (N.A.)
| | - Najla Alburae
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.); (N.A.)
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.); (N.A.)
- Correspondence: (A.A.); (A.B.)
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22
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Anklam E, Bahl MI, Ball R, Beger RD, Cohen J, Fitzpatrick S, Girard P, Halamoda-Kenzaoui B, Hinton D, Hirose A, Hoeveler A, Honma M, Hugas M, Ishida S, Kass GEN, Kojima H, Krefting I, Liachenko S, Liu Y, Masters S, Marx U, McCarthy T, Mercer T, Patri A, Pelaez C, Pirmohamed M, Platz S, Ribeiro AJS, Rodricks JV, Rusyn I, Salek RM, Schoonjans R, Silva P, Svendsen CN, Sumner S, Sung K, Tagle D, Tong L, Tong W, van den Eijnden-van-Raaij J, Vary N, Wang T, Waterton J, Wang M, Wen H, Wishart D, Yuan Y, Slikker Jr. W. Emerging technologies and their impact on regulatory science. Exp Biol Med (Maywood) 2022; 247:1-75. [PMID: 34783606 PMCID: PMC8749227 DOI: 10.1177/15353702211052280] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There is an evolution and increasing need for the utilization of emerging cellular, molecular and in silico technologies and novel approaches for safety assessment of food, drugs, and personal care products. Convergence of these emerging technologies is also enabling rapid advances and approaches that may impact regulatory decisions and approvals. Although the development of emerging technologies may allow rapid advances in regulatory decision making, there is concern that these new technologies have not been thoroughly evaluated to determine if they are ready for regulatory application, singularly or in combinations. The magnitude of these combined technical advances may outpace the ability to assess fit for purpose and to allow routine application of these new methods for regulatory purposes. There is a need to develop strategies to evaluate the new technologies to determine which ones are ready for regulatory use. The opportunity to apply these potentially faster, more accurate, and cost-effective approaches remains an important goal to facilitate their incorporation into regulatory use. However, without a clear strategy to evaluate emerging technologies rapidly and appropriately, the value of these efforts may go unrecognized or may take longer. It is important for the regulatory science field to keep up with the research in these technically advanced areas and to understand the science behind these new approaches. The regulatory field must understand the critical quality attributes of these novel approaches and learn from each other's experience so that workforces can be trained to prepare for emerging global regulatory challenges. Moreover, it is essential that the regulatory community must work with the technology developers to harness collective capabilities towards developing a strategy for evaluation of these new and novel assessment tools.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Reza M Salek
- International Agency for Research on Cancer, France
| | | | | | | | | | | | | | - Li Tong
- Universities of Georgia Tech and Emory, USA
| | | | | | - Neil Vary
- Canadian Food Inspection Agency, Canada
| | - Tao Wang
- National Medical Products Administration, China
| | | | - May Wang
- Universities of Georgia Tech and Emory, USA
| | - Hairuo Wen
- National Institutes for Food and Drug Control, China
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23
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Exploring the universal healthy human gut microbiota around the World. Comput Struct Biotechnol J 2022; 20:421-433. [PMID: 35035791 PMCID: PMC8749183 DOI: 10.1016/j.csbj.2021.12.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 02/08/2023] Open
Abstract
The human gut holds a special place in the study of different microbial environments due to growing evidence that the gut microbiota is related to host health. However, despite extensive research, there is still a lack of knowledge about the core taxa forming the gut microbiota and, moreover, available information is biased towards western microbiomes in both genome databases and most core taxa studies. To tackle these limitations, we tested a database enrichment strategy and analyzed public datasets of whole-genome shotgun data, generated from 545 fecal samples, comprising three gradients of westernization. The NT database was selected as a baseline of biological diversity, subsequently being combined with various studies of interest related to the human microbiota. This enrichment strategy made it possible to improve classification capacity, compared to the original unenriched database, regarding the various lifestyles and populations studied. The effects of incomplete-taxonomy metagenome-assembled genomes on genome database enrichment were also examined, revealing that, while they are helpful, they should be used with caution depending on the taxonomic level of interest. Moreover, in terms of high prevalence, the core analysis revealed a conserved set of bacterial taxa in the healthy human gut microbiota worldwide, despite apparent lifestyle differences. Such taxa show a set of traits, metabolic roles, and ancestral status, making them suitable candidates for a hypothetical phylogenetic core of mutualistic microorganisms co-evolving with the human species.
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24
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Wu L, Xie X, Liang T, Ma J, Yang L, Yang J, Li L, Xi Y, Li H, Zhang J, Chen X, Ding Y, Wu Q. Integrated Multi-Omics for Novel Aging Biomarkers and Antiaging Targets. Biomolecules 2021; 12:39. [PMID: 35053186 PMCID: PMC8773837 DOI: 10.3390/biom12010039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 12/12/2022] Open
Abstract
Aging is closely related to the occurrence of human diseases; however, its exact biological mechanism is unclear. Advancements in high-throughput technology provide new opportunities for omics research to understand the pathological process of various complex human diseases. However, single-omics technologies only provide limited insights into the biological mechanisms of diseases. DNA, RNA, protein, metabolites, and microorganisms usually play complementary roles and perform certain biological functions together. In this review, we summarize multi-omics methods based on the most relevant biomarkers in single-omics to better understand molecular functions and disease causes. The integration of multi-omics technologies can systematically reveal the interactions among aging molecules from a multidimensional perspective. Our review provides new insights regarding the discovery of aging biomarkers, mechanism of aging, and identification of novel antiaging targets. Overall, data from genomics, transcriptomics, proteomics, metabolomics, integromics, microbiomics, and systems biology contribute to the identification of new candidate biomarkers for aging and novel targets for antiaging interventions.
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Affiliation(s)
- Lei Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Xinqiang Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Tingting Liang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Jun Ma
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Lingshuang Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Juan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Longyan Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Yu Xi
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Haixin Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Xuefeng Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (J.M.); (X.C.)
| | - Yu Ding
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (L.W.); (X.X.); (T.L.); (L.Y.); (J.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
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25
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Zubeldia-Varela E, Barker-Tejeda TC, Blanco-Pérez F, Infante S, Zubeldia JM, Pérez-Gordo M. Non-IgE-Mediated Gastrointestinal Food Protein-Induced Allergic Disorders. Clinical Perspectives and Analytical Approaches. Foods 2021; 10:foods10112662. [PMID: 34828942 PMCID: PMC8623505 DOI: 10.3390/foods10112662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 10/27/2021] [Indexed: 12/21/2022] Open
Abstract
Non-IgE-mediated gastrointestinal food allergy (non-IgE-GI-FA) is the name given to a series of pathologies whose main entities are food protein-induced allergic proctocolitis (FPIAP), food protein-induced enteropathy (FPE), and food protein-induced enterocolitis syndrome (FPIES). These are more uncommon than IgE-mediated food allergies, their mechanisms remain largely unknown, and their diagnosis is mainly done by clinical history, due to the lack of specific biomarkers. In this review, we present the latest advances found in the literature about clinical aspects, the current diagnosis, and treatment options of non-IgE-GI-FAs. We discuss the use of animal models, the analysis of gut microbiota, omics techniques, and fecal proteins with a focus on understanding the pathophysiological mechanisms of these pathologies and obtaining possible diagnostic and/or prognostic biomarkers. Finally, we discuss the unmet needs that researchers should tackle to advance in the knowledge of these barely explored pathologies.
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Affiliation(s)
- Elisa Zubeldia-Varela
- Department of Basic Medical Sciences, Facultad de Medicina, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo-CEU, CEU Universities, ARADyAL, 28660 Madrid, Spain; (E.Z.-V.); (T.C.B.-T.)
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, 28660 Madrid, Spain
| | - Tomás Clive Barker-Tejeda
- Department of Basic Medical Sciences, Facultad de Medicina, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo-CEU, CEU Universities, ARADyAL, 28660 Madrid, Spain; (E.Z.-V.); (T.C.B.-T.)
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, 28660 Madrid, Spain
| | - Frank Blanco-Pérez
- VPr1 Research Group “Molecular Allergology”, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, 63225 Langen, Germany;
| | - Sonsoles Infante
- Allergy Paediatric Unit, Allergy Service, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain; (S.I.); (J.M.Z.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain
| | - José M. Zubeldia
- Allergy Paediatric Unit, Allergy Service, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain; (S.I.); (J.M.Z.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain
- Rare Diseases Networking Biomedical Research Centre (CIBERER, U-761), Carlos III Institute of Health, 28029 Madrid, Spain
| | - Marina Pérez-Gordo
- Department of Basic Medical Sciences, Facultad de Medicina, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo-CEU, CEU Universities, ARADyAL, 28660 Madrid, Spain; (E.Z.-V.); (T.C.B.-T.)
- Correspondence: ; Tel.: +34-91-372-4700 (ext. 14675)
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26
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Di Rienzi SC, Johnson EL, Waters JL, Kennedy EA, Jacobson J, Lawrence P, Wang DH, Worgall TS, Brenna JT, Ley RE. The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil. J Nutr Biochem 2021; 97:108808. [PMID: 34186211 PMCID: PMC8585862 DOI: 10.1016/j.jnutbio.2021.108808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 10/21/2022]
Abstract
Studies in mice using germfree animals as controls for microbial colonization have shown that the gut microbiome mediates diet-induced obesity. Such studies use diets rich in saturated fat, however, Western diets in the United States America are enriched in soybean oil, composed of unsaturated fatty acids, either linoleic or oleic acid. Here, we addressed whether the microbiome is a variable in fat metabolism in mice on a soybean oil diet. We used conventionally-raised, low-germ, and germfree mice fed for 10 weeks diets either high or low in high-linoleic-acid soybean oil as the sole source of fat. Conventional and germfree mice gained relative fat weight and all mice consumed more calories on the high fat vs. low fat soybean oil diet. Plasma fatty acid levels were generally dependent on diet, with microbial colonization status affecting iso-C18:0, C20:3n-6, C14:0, and C15:0 levels. Colonization status, but not diet, impacted levels of liver sphingolipids including ceramides, sphingomyelins, and sphinganine. Our results confirm that absorbed fatty acids are mainly a reflection of the diet and that microbial colonization influences liver sphingolipid pools regardless of diet.
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Affiliation(s)
- Sara C Di Rienzi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | | | - Jillian L Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elizabeth A Kennedy
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Juliet Jacobson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Peter Lawrence
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Dong Hao Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Tilla S Worgall
- Department of Pathology and Cell Biology and Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - J Thomas Brenna
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA; Dell Pediatric Research Institute, Dell Medical School, University of Texas at Austin, Austin, Texas, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA; Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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27
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Park H, Arellano K, Lee Y, Yeo S, Ji Y, Ko J, Holzapfel W. Pilot Study on the Forehead Skin Microbiome and Short Chain Fatty Acids Depending on the SC Functional Index in Korean Cohorts. Microorganisms 2021; 9:microorganisms9112216. [PMID: 34835341 PMCID: PMC8617931 DOI: 10.3390/microorganisms9112216] [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: 09/25/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 01/05/2023] Open
Abstract
Dry skin is one of the indicators of a compromised skin barrier. An intact skin barrier is not only important to reserve the hydration within the epidermal tissue but also to protect our skin from environmental stressors and inhibit pathogen invasion; damage to the skin barrier may lead to inflammatory skin diseases. Some microbial metabolites such as short chain fatty acids may inhibit or destroy harmful bacteria and regulate the host immune system. The impact of the skin microbiome and short chain fatty acids on skin barrier function was studied in two groups of 75 participants each. The cohort was equally divided in dry and moist skin types, based on stratum corneum (SC) functionality index (SCFI), reflecting the ratio of transepidermal water loss (TEWL). A dry group represents a low SCFI and a moist group a high SCFI. Compared with the dry skin group, propionate and Cutibacterium levels (previously known as Propionibacterium acnes) were significantly higher (p < 0.001) in the moist group. Levels of Cutibacterium were negatively correlated with those of Staphylococcus (p < 0.0001) in both dry and moist groups. The moist group also had a significantly higher propionate concentration (p < 0.001). This study showed that the microbial community and short chain fatty acid concentration may be considered as significant determinants of the SCFI of the skin.
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Affiliation(s)
- Haryung Park
- Department of Advanced Convergence, Handong Global University, Pohang 37554, Korea; (H.P.); (K.A.); (Y.L.); (Y.J.)
- HEM Pharma Inc., Start-Up Incubator, Handong Global University, Pohang 37554, Korea;
| | - Karina Arellano
- Department of Advanced Convergence, Handong Global University, Pohang 37554, Korea; (H.P.); (K.A.); (Y.L.); (Y.J.)
| | - Yuri Lee
- Department of Advanced Convergence, Handong Global University, Pohang 37554, Korea; (H.P.); (K.A.); (Y.L.); (Y.J.)
| | - Subin Yeo
- HEM Pharma Inc., Start-Up Incubator, Handong Global University, Pohang 37554, Korea;
| | - Yosep Ji
- Department of Advanced Convergence, Handong Global University, Pohang 37554, Korea; (H.P.); (K.A.); (Y.L.); (Y.J.)
- HEM Pharma Inc., Start-Up Incubator, Handong Global University, Pohang 37554, Korea;
| | - Joontae Ko
- Boaz Medical Hospital, Handong Global University, Pohang 37554, Korea;
| | - Wilhelm Holzapfel
- Department of Advanced Convergence, Handong Global University, Pohang 37554, Korea; (H.P.); (K.A.); (Y.L.); (Y.J.)
- HEM Pharma Inc., Start-Up Incubator, Handong Global University, Pohang 37554, Korea;
- Correspondence:
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Abstract
Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.
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Pinart M, Nimptsch K, Forslund SK, Schlicht K, Gueimonde M, Brigidi P, Turroni S, Ahrens W, Hebestreit A, Wolters M, Dötsch A, Nöthlings U, Oluwagbemigun K, Cuadrat RRC, Schulze MB, Standl M, Schloter M, De Angelis M, Iozzo P, Guzzardi MA, Vlaemynck G, Penders J, Jonkers DMAE, Stemmer M, Chiesa G, Cavalieri D, De Filippo C, Ercolini D, De Filippis F, Ribet D, Achamrah N, Tavolacci MP, Déchelotte P, Bouwman J, Laudes M, Pischon T. Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis. Nutrients 2021; 13:nu13093292. [PMID: 34579168 PMCID: PMC8466729 DOI: 10.3390/nu13093292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 01/16/2023] Open
Abstract
In any research field, data access and data integration are major challenges that even large, well-established consortia face. Although data sharing initiatives are increasing, joint data analyses on nutrition and microbiomics in health and disease are still scarce. We aimed to identify observational studies with data on nutrition and gut microbiome composition from the Intestinal Microbiomics (INTIMIC) Knowledge Platform following the findable, accessible, interoperable, and reusable (FAIR) principles. An adapted template from the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) consortium was used to collect microbiome-specific information and other related factors. In total, 23 studies (17 longitudinal and 6 cross-sectional) were identified from Italy (7), Germany (6), Netherlands (3), Spain (2), Belgium (1), and France (1) or multiple countries (3). Of these, 21 studies collected information on both dietary intake (24 h dietary recall, food frequency questionnaire (FFQ), or Food Records) and gut microbiome. All studies collected stool samples. The most often used sequencing platform was Illumina MiSeq, and the preferred hypervariable regions of the 16S rRNA gene were V3–V4 or V4. The combination of datasets will allow for sufficiently powered investigations to increase the knowledge and understanding of the relationship between food and gut microbiome in health and disease.
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Affiliation(s)
- Mariona Pinart
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (M.P.); (T.P.)
| | - Katharina Nimptsch
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (M.P.); (T.P.)
- Correspondence: ; Tel.: +49-30-9046-4573
| | - Sofia K. Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany;
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117 Berlin, Germany
- Host-Microbiome Factors in Cardiovascular Disease Lab, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kristina Schlicht
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, 24105 Kiel, Germany; (K.S.); (M.L.)
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain;
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy;
| | - Wolfgang Ahrens
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany; (W.A.); (A.H.); (M.W.)
- Institute of Statistics, Bremen University, 28359 Bremen, Germany
| | - Antje Hebestreit
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany; (W.A.); (A.H.); (M.W.)
| | - Maike Wolters
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany; (W.A.); (A.H.); (M.W.)
| | - Andreas Dötsch
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany;
| | - Ute Nöthlings
- Nutritional Epidemiology Unit, Institute of Nutrition and Food Sciences, University of Bonn, 53115 Bonn, Germany; (U.N.); (K.O.)
| | - Kolade Oluwagbemigun
- Nutritional Epidemiology Unit, Institute of Nutrition and Food Sciences, University of Bonn, 53115 Bonn, Germany; (U.N.); (K.O.)
| | - Rafael R. C. Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (R.R.C.C.); (M.B.S.)
| | - Matthias B. Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (R.R.C.C.); (M.B.S.)
- Institute of Nutritional Science, University of Potsdam, 14558 Potsdam, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy;
| | - Patricia Iozzo
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy; (P.I.); (M.A.G.)
| | - Maria Angela Guzzardi
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy; (P.I.); (M.A.G.)
| | - Geertrui Vlaemynck
- Department Technology and Food, Flanders Research Institute for Agriculture, Fisheries and Food, 9090 Melle, Belgium;
| | - John Penders
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands;
| | - Daisy M. A. E. Jonkers
- Department of Internal Medicine, Division Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands;
| | - Maya Stemmer
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva P.O. Box 653, Israel;
| | - Giulia Chiesa
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy;
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Florence, Italy;
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology National Research Council, Via Moruzzi 1, 56124 Pisa, Italy;
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (D.E.); (F.D.F.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (D.E.); (F.D.F.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - David Ribet
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
| | - Najate Achamrah
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
- Department of Nutrition, CHU Rouen, 76000 Rouen, France
| | - Marie-Pierre Tavolacci
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
- INSERM CIC-CRB 1404, CHU Rouen, 76000 Rouen, France
| | - Pierre Déchelotte
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
- Department of Nutrition, CHU Rouen, 76000 Rouen, France
| | - Jildau Bouwman
- Microbiology and Systems Biology Group, TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands;
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, 24105 Kiel, Germany; (K.S.); (M.L.)
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (M.P.); (T.P.)
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany
- Biobank Technology Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Biobank Core Facility, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10178 Berlin, Germany
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Ahannach S, Spacova I, Decorte R, Jehaes E, Lebeer S. At the Interface of Life and Death: Post-mortem and Other Applications of Vaginal, Skin, and Salivary Microbiome Analysis in Forensics. Front Microbiol 2021; 12:694447. [PMID: 34394033 PMCID: PMC8355522 DOI: 10.3389/fmicb.2021.694447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022] Open
Abstract
Microbial forensics represents a promising tool to strengthen traditional forensic investigative methods and fill related knowledge gaps. Large-scale microbiome studies indicate that microbial fingerprinting can assist forensics in areas such as trace evidence, source tracking, geolocation, and circumstances of death. Nevertheless, the majority of forensic microbiome studies focus on soil and internal organ samples, whereas the microbiome of skin, mouth, and especially vaginal samples that are routinely collected in sexual assault and femicide cases remain underexplored. This review discusses the current and emerging insights into vaginal, skin, and salivary microbiome-modulating factors during life (e.g., lifestyle and health status) and after death (e.g., environmental influences and post-mortem interval) based on next-generation sequencing. We specifically highlight the key aspects of female reproductive tract, skin, and mouth microbiome samples relevant in forensics. To fill the current knowledge gaps, future research should focus on the degree to which the post-mortem succession rate and profiles of vaginal, skin, and saliva microbiota are sensitive to abiotic and biotic factors, presence or absence of oxygen and other gases, and the nutrient richness of the environment. Application of this microbiome-related knowledge could provide valuable complementary data to strengthen forensic cases, for example, to shed light on the circumstances surrounding death with (post-mortem) microbial fingerprinting. Overall, this review synthesizes the present knowledge and aims to provide a framework to adequately comprehend the hurdles and potential application of vaginal, skin, and salivary post-mortem microbiomes in forensic investigations.
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Affiliation(s)
- Sarah Ahannach
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Ronny Decorte
- Laboratory of Forensic Genetics, Department of Forensic Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium
| | - Els Jehaes
- Forensic DNA Laboratory, Department of Forensic Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
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De la Fuente M. The Role of the Microbiota-Gut-Brain Axis in the Health and Illness Condition: A Focus on Alzheimer's Disease. J Alzheimers Dis 2021; 81:1345-1360. [PMID: 33935086 DOI: 10.3233/jad-201587] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Trillions of commensal microbes live in our body, the majority in the gut. This gut microbiota is in constant interaction with the homeostatic systems, the nervous, immune and endocrine systems, being fundamental for their appropriate development and function as well as for the neuroimmunoendocrine communication. The health state of an individual is understood in the frame of this communication, in which the microbiota-gut-brain axis is a relevant example. This bidirectional axis is constituted in early age and is affected by many environmental and lifestyle factors such as diet and stress, among others, being involved in the adequate maintenance of homeostasis and consequently in the health of each subject and in his/her rate of aging. For this, an alteration of gut microbiota, as occurs in a dysbiosis, and the associated gut barrier deterioration and the inflammatory state, affecting the function of immune, endocrine and nervous systems, in gut and in all the locations, is in the base of a great number of pathologies as those that involve alterations in the brain functions. There is an age-related deterioration of microbiota and the homeostatic systems due to oxi-inflamm-aging, and thus the risk of aging associated pathologies such as the neurodegenerative illness. Currently, this microbiota-gut-brain axis has been considered to have a relevant role in the pathogenesis of Alzheimer's disease and represents an important target in the prevention and slowdown of the development of this pathology. In this context, the use of probiotics seems to be a promising help.
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Affiliation(s)
- Mónica De la Fuente
- Department of Genetics, Physiology and Microbiology (Animal Physiology Unit), School of Biology, Complutense University of Madrid. Institute of Investigation of Hospital 12 de Octubre (i+12), Madrid, Spain
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C Campbell B, Gong S, Greenfield P, J Midgley D, T Paulsen I, C George S. Aromatic compound-degrading taxa in an anoxic coal seam microbiome from the Surat Basin, Australia. FEMS Microbiol Ecol 2021; 97:6206826. [PMID: 33791788 DOI: 10.1093/femsec/fiab053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Methane is an important energy resource internationally, and a large proportion of this methane is produced by microbial communities living in coal seams. Despite the value of this resource for human energy security, our understanding of the metabolic roles played by specific taxa during the biodegradation of coal to methane in situ is quite limited. In order to develop a greater understanding of microbial catabolism on coal, a community from a coal seam in the Surat Basin, Australia, was incubated on 10 different aromatic organic compounds: coronene, benzo[a]pyrene, pyrene, phenanthrene, naphthalene, ethylbenzene, phenol, benzoate, vanillate and syringate. Each of these aromatic compounds either occurs in coal or is a possible product of the coal biodegradation process. 16S rRNA sequencing revealed substantial changes to each community in response to each aromatic carbon substrate provided. Abundant taxa from these substrate-specific communities were identified and their probable catabolic roles proposed based on literature searches of related taxa. This study is the first to link specific coal seam taxa to aromatic substrates available in coal seam environments. Two conceptual models of the putative degradation pathways and key taxa responsible are proposed.
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Affiliation(s)
- Bronwyn C Campbell
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia.,Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Se Gong
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Paul Greenfield
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - David J Midgley
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Simon C George
- Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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Kim JH, Kim K, Kim W. Gut microbiota restoration through fecal microbiota transplantation: a new atopic dermatitis therapy. Exp Mol Med 2021; 53:907-916. [PMID: 34017060 PMCID: PMC8178377 DOI: 10.1038/s12276-021-00627-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
The pathogenesis of atopic dermatitis (AD) involves complex factors, including gut microbiota and immune modulation, which remain poorly understood. The aim of this study was to restore gut microbiota via fecal microbiota transplantation (FMT) to ameliorate AD in mice. FMT was performed using stool from donor mice. The gut microbiota was characterized via 16S rRNA sequencing and analyzed using Quantitative Insights into Microbial Ecology 2 with the DADA2 plugin. Gut metabolite levels were determined by measuring fecal short-chain fatty acid (SCFA) contents. AD-induced allergic responses were evaluated by analyzing blood parameters (IgE levels and eosinophil percentage, eosinophil count, basophil percentage, and monocyte percentage), the levels of Th1 and Th2 cytokines, dermatitis score, and the number of mast cells in the ileum and skin tissues. Calprotectin level was measured to assess gut inflammation after FMT. FMT resulted in the restoration of gut microbiota to the donor state and increases in the levels of SCFAs as gut metabolites. In addition, FMT restored the Th1/Th2 balance, modulated Tregs through gut microbiota, and reduced IgE levels and the numbers of mast cells, eosinophils, and basophils. FMT is associated with restoration of gut microbiota and immunologic balance (Th1/Th2) along with suppression of AD-induced allergic responses and is thus a potential new therapy for AD.
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Affiliation(s)
- Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Kiyoung Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea.
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Zilber-Rosenberg I, Rosenberg E. Microbial driven genetic variation in holobionts. FEMS Microbiol Rev 2021; 45:6261188. [PMID: 33930136 DOI: 10.1093/femsre/fuab022] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic variation in holobionts, (host and microbiome), occurring by changes in both host and microbiome genomes, can be observed from two perspectives: observable variations and the processes that bring about the variation. The observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotic organisms. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa, and a more diverse non-core enabling considerable genetic variation. The result being that, the human gut microbiome, for example, contains 1,000 times more unique genes than are present in the human genome. Microbial driven genetic variation processes in holobionts include: (1) Acquisition of novel microbes from the environment, which bring in multiple genes in one step, (2) amplification/reduction of certain microbes in the microbiome, that contribute to holobiont` s adaptation to changing conditions, (3) horizontal gene transfer between microbes and between microbes and host, (4) mutation, which plays an important role in optimizing interactions between different microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, thus a greater chance of vertical transmission and a greater effect of microbiome on evolution of host than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.
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Affiliation(s)
- Ilana Zilber-Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv Israel
| | - Eugene Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv Israel
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Effect of arabinogalactan on the gut microbiome: A randomized, double-blind, placebo-controlled, crossover trial in healthy adults. Nutrition 2021; 90:111273. [PMID: 34004416 DOI: 10.1016/j.nut.2021.111273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/22/2021] [Accepted: 04/03/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Promising evidence suggests beneficial health effects of arabinogalactan, but little is known about the effect of this non-digestible carbohydrate on the gut microbiota, a crucial mediator of human health. The objective of this study was to investigate the effect of an arabinogalactan product (ResistAid) on the fecal microbiome and short-chain fatty acids and gastrointestinal tolerance in healthy adults in a randomized, double-blind, crossover trial. METHODS Thirty adults were randomly assigned to consume 15 g/d maltodextrin (control) or ResistAid for 6 wk. RESULTS At week 6, compared to placebo, ResistAid supplementation led to a significant decrease in the ratio of fecal Firmicutes to Bacteroidetes, driven by an increase in Bacteroidetes and a decrease in Firmicutes. Moreover, the relative abundance of Bifidobacterium tended to increase with ResistAid supplementation. Additionally, ResistAid significantly decreased the α-diversity of the fecal microbiome. Predicted functional abundances based on 16S rRNA sequences showed that ResistAid supplementation increased the gene abundance of the gut microbiome for α-l-rhamnosidase, β-fructosidase, and levanase, as well as tricarboxylic acid and vitamin B6 biosynthesis pathways. Fecal isovaleric, valeric, and hexanoic acids were significantly lower after ResistAid consumption. There were no statistically significant changes in bowel habit, stool consistency, gastrointestinal tolerance symptoms, chemistry profile, metabolic panel, or vitals, suggesting that consumption of 15 g daily ResistAid over 6 wk is safe. CONCLUSION These results demonstrate that the gut microbiome composition and predicted functions can be modulated by ResistAid consumption, perhaps suggesting a mechanistic explanation on its reported benefits in metabolic parameters and the immune system.
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Requena T, Velasco M. The human microbiome in sickness and in health. Rev Clin Esp 2021; 221:233-240. [PMID: 31522775 DOI: 10.1016/j.rce.2019.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022]
Abstract
The study of the human microbiome has led to an exceptional increase in the current understanding of the importance of microbiota for health throughout all stages of life. Human microbial colonization occurs in the skin, genitourinary system and, mainly, in the oral cavity and intestinal tract. In these locations, the human microbiota establishes a symbiotic relationship with the host and helps maintain the physiological homeostasis. Lifestyle, age, diet and use of antibiotics are the main regulators of the composition and functionality of human microbiota. Recent studies have indicated the reduction in microbial diversity as one of the contributors to the development of diseases. In addition to phylogenetic diversity studies, further metagenomic studies are needed at the functional level of the human microbiome to improve our understanding of its involvement in human health.
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Affiliation(s)
- T Requena
- Departamento de Biotecnología y Microbiología de Alimentos, Instituto de Investigación en Ciencias de la Alimentación (CIAL-CSIC), Madrid, España.
| | - M Velasco
- Sección de Enfermedades Infecciosas, Medicina Interna, Hospital Universitario Fundación Alcorcón, Alcorcón, España
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Singh KS, Singh BP, Rokana N, Singh N, Kaur J, Singh A, Panwar H. Bio-therapeutics from human milk: prospects and perspectives. J Appl Microbiol 2021; 131:2669-2687. [PMID: 33740837 DOI: 10.1111/jam.15078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/10/2021] [Accepted: 03/06/2021] [Indexed: 12/12/2022]
Abstract
Human milk is elixir for neonates and is a rich source of nutrients and beneficial microbiota required for infant growth and development. Its benefits prompted research into probing the milk components and their use as prophylactic or therapeutic agents. Culture-independent estimation of milk microbiome and high-resolution identification of milk components provide information, but a holistic purview of these research domains is lacking. Here, we review the current research on bio-therapeutic components of milk and simplified future directions for its efficient usage. Publicly available databases such as PubMed and Google scholar were searched for keywords such as probiotics and prebiotics related to human milk, microbiome and milk oligosaccharides. This was further manually curated for inclusion and exclusion criteria relevant to human milk and clinical efficacy. The literature was classified into subgroups and then discussed in detail to facilitate understanding. Although milk research is still in infancy, it is clear that human milk has many functions including protection of infants by passive immunization through secreted antibodies, and transfer of immune regulators, cytokines and bioactive peptides. Unbiased estimates show that the human milk carries a complex community of microbiota which serves as the initial inoculum for establishment of infant gut. Our search effectively screened for evidence that shows that milk also harbours many types of prebiotics such as human milk oligosaccharides which encourage growth of beneficial probiotics. The milk also trains the naive immune system of the infant by supplying immune cells and stimulatory factors, thereby strengthening mucosal and systemic immune system. Our systematic review would improve understanding of human milk and the inherent complexity and diversity of human milk. The interrelated functional role of human milk components especially the oligosaccharides and microbiome has been discussed which plays important role in human health.
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Affiliation(s)
- K S Singh
- National Centre for Microbial Resource - National Centre for Cell Science, Pune, Maharashtra, India.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - B P Singh
- Department of Microbiology, School of Science, RK University, Rajkot, Gujarat, India
| | - N Rokana
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India
| | - N Singh
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Uttar Pradesh, Kanpur, India
| | - J Kaur
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India
| | - A Singh
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India
| | - H Panwar
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India
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38
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A body weight loss- and health-promoting gut microbiota is established after bariatric surgery in individuals with severe obesity. J Pharm Biomed Anal 2021; 193:113747. [DOI: 10.1016/j.jpba.2020.113747] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/24/2020] [Accepted: 10/31/2020] [Indexed: 02/07/2023]
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39
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Oerlemans MM, Akkerman R, Ferrari M, Walvoort MT, de Vos P. Benefits of bacteria-derived exopolysaccharides on gastrointestinal microbiota, immunity and health. J Funct Foods 2021. [DOI: 10.1016/j.jff.2020.104289] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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40
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Williams GM, Tapsell LC, O'Brien CL, Tosh SM, Barrett EM, Beck EJ. Gut microbiome responses to dietary intake of grain-based fibers with the potential to modulate markers of metabolic disease: a systematic literature review. Nutr Rev 2020; 79:1274-1292. [PMID: 33369654 DOI: 10.1093/nutrit/nuaa128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
CONTEXT Cereal fiber modulates the gut microbiome and benefits metabolic health. The potential link between these effects is of interest.0. OBJECTIVE The aim for this systematic review was to assess evidence surrounding the influence of cereal fiber intake on microbiome composition, microbiome diversity, short-chain fatty acid production, and risk factors for metabolic syndrome. DATA SOURCES AND EXTRACTION The MEDLINE, PubMed, CINAHL, and Cochrane Library databases were searched systematically, and quality of studies was assessed using the Cochrane Risk of Bias 2.0 tool. Evidence relating to study design, dietary data collection, and outcomes was qualitatively synthesized on the basis of fiber type. DATA ANALYSIS Forty-six primary publications and 2 secondary analyses were included. Cereal fiber modulated the microbiome in most studies; however, taxonomic changes indicated high heterogeneity. Short-chain fatty acid production, microbiome diversity, and metabolic-related outcomes varied and did not always occur in parallel with microbiome changes. Poor dietary data were a further limitation. CONCLUSIONS Cereal fiber may modulate the gut microbiome; however, evidence of the link between this and metabolic outcomes is limited. Additional research is required with a focus on robust and consistent methodology. SYSTEMATIC REVIEW REGISTRATION PROSPERO registration no. CRD42018107117.
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Affiliation(s)
- Georgina M Williams
- School of Medicine, Science, Medicine and Health, University of Wollongong, and the Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Linda C Tapsell
- School of Medicine, Science, Medicine and Health, University of Wollongong, and the Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Claire L O'Brien
- Australian National University, Canberra, Australian Capital Territory, Australia
| | - Susan M Tosh
- Faculty of Health Sciences, University of Ottawa, Ottawa, Canada
| | - Eden M Barrett
- School of Medicine, Science, Medicine and Health, University of Wollongong, and the Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Eleanor J Beck
- School of Medicine, Science, Medicine and Health, University of Wollongong, and the Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
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41
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Rivero-Segura NA, Bello-Chavolla OY, Barrera-Vázquez OS, Gutierrez-Robledo LM, Gomez-Verjan JC. Promising biomarkers of human aging: In search of a multi-omics panel to understand the aging process from a multidimensional perspective. Ageing Res Rev 2020; 64:101164. [PMID: 32977058 DOI: 10.1016/j.arr.2020.101164] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022]
Abstract
The aging process has been linked to the occurrence of chronic diseases and functional impairments, including cancer, sarcopenia, frailty, metabolic, cardiovascular, and neurodegenerative diseases. Nonetheless, aging is highly variable and heterogeneous and represents a challenge for its characterization. In this sense, intrinsic capacity (IC) stands as a novel perspective by the World Health Organization, which integrates the individual wellbeing, environment, and risk factors to understand aging. However, there is a lack of quantitative and qualitative attributes to define it objectively. Therefore, in this review we attempt to summarize the most relevant and promising biomarkers described in clinical studies at date over different molecular levels, including epigenomics, transcriptomics, proteomics, metabolomics, and the microbiome. To aid gerontologists, geriatricians, and biomedical researchers to understand the aging process through the IC. Aging biomarkers reflect the physiological state of individuals and the underlying mechanisms related to homeostatic changes throughout an individual lifespan; they demonstrated that aging could be measured independently of time (that may explain its heterogeneity) and to be helpful to predict age-related syndromes and mortality. In summary, we highlight the areas of opportunity and gaps of knowledge that must be addressed to fully integrate biomedical findings into clinically useful tools and interventions.
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Affiliation(s)
| | - O Y Bello-Chavolla
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico; Department of Physiology, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - O S Barrera-Vázquez
- Departamento de Famacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - J C Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico.
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Zubeldia-Varela E, Barber D, Barbas C, Perez-Gordo M, Rojo D. Sample pre-treatment procedures for the omics analysis of human gut microbiota: Turning points, tips and tricks for gene sequencing and metabolomics. J Pharm Biomed Anal 2020; 191:113592. [PMID: 32947167 DOI: 10.1016/j.jpba.2020.113592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/29/2020] [Accepted: 08/23/2020] [Indexed: 02/06/2023]
Abstract
The connection between gut microbiota and human health is becoming increasingly relevant and the number of groups working in this field is constantly growing. In this context, from high-throughput gene sequencing to metabolomics analysis, the omics technologies have contributed enormously to unveil the secret crosstalk between us and our microbes. All the omics technologies produce a great amount of information, and processing this information is time-consuming and expensive. For this reason, a correct experimental design and a careful pre-analytical planning are crucial. To study the human gut microbiota, faeces are the sample of choice. Faecal material is complex, and procedures for collecting and preserving faeces are not well-established. Furthermore, increasing evidence suggests that multiple confounding factors, such as antibiotics consumption, mode of delivery, diet, aging and several diseases and disorders can alter the composition and functionality of the microbiota. This review is focused on the discussion of critical general issues during the pre-analytical planning, from patient handling to faeces sampling, including collection procedures, transport, storage conditions and possible pre-treatments, which are critical for a successful research in omics with a special attention to metabolomics and gene sequencing. We also point out that the adoption of standard operating procedures in the field is needed to guarantee accuracy and reproducibility of results.
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Affiliation(s)
- Elisa Zubeldia-Varela
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Domingo Barber
- Institute of Applied and Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Marina Perez-Gordo
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Institute of Applied and Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - David Rojo
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain.
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43
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Metabolomics analysis of microbiota-gut-brain axis in neurodegenerative and psychiatric diseases. J Pharm Biomed Anal 2020; 194:113681. [PMID: 33279302 DOI: 10.1016/j.jpba.2020.113681] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/30/2020] [Accepted: 10/06/2020] [Indexed: 12/19/2022]
Abstract
Gut microbiota represents a complex physiological ecosystem that influences the host health. Alterations in the microbiome metabolism affect the body homeostasis and they have been associated with the development of different human neurodegenerative and neuropsychiatric disorders, such as Alzheimer's disease, autism spectrum disorder, bipolar disorder, depression, Huntington's disease, Parkinson's disease, posttraumatic stress disorder and schizophrenia. The development of these complex diseases is influenced by various factors, including genetic predisposition and environmental triggers. Gut microbiota has recently emerged as an important actor in their physiopathology that has been shown to play a role in inflammation, oxidative stress, and gut permeability. Therefore, targeting the metabolites that are produced by or associated with the gut microbiota may help us understand how imbalance in the gut-brain axis affects human health. This review offers a comprehensive overview of the literature on this matter, offering the readers an insight in the state-of-art metabolic measurements of the gut-brain axis in various brain-related diseases.
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44
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Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes. Microorganisms 2020; 8:microorganisms8101592. [PMID: 33081076 PMCID: PMC7602701 DOI: 10.3390/microorganisms8101592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
The human gut microbiome is an important component that defines host health. Childhood is a particularly important period for the establishment and development of gut microbiota (GM). We sequenced the 16S rRNA gene from fecal samples of children between 5 and 10 years old, in two Mexican communities with contrasting lifestyles, i.e., “Westernized” (México City, n = 13) and “non-Westernized” (Me’phaa indigenous group, n = 29), in order to characterize and compare their GM. The main differences between these two communities were in bacteria associated with different types of diets (high animal protein and refined sugars vs. high fiber food, respectively). In addition, the GM of Me’phaa children showed higher total diversity and the presence of exclusive phyla, such as Deinococcus-Thermus, Chloroflexi, Elusimicrobia, Acidobacteria, and Fibrobacteres. In contrast, the children from México City showed less diversity and the presence of Saccharibacteria phylum, which was associated with the degradation of sugar compounds and was not present in the samples from Me’phaa children. This comparison provided further knowledge of the selective pressures affecting microbial ecosystemic composition over the course of human evolution and the potential consequences of pathophysiological states correlated with Westernization lifestyles.
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45
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Nettles R, Ricks KD, Koide RT. The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics. MICROBIAL ECOLOGY 2020; 80:573-592. [PMID: 32451559 DOI: 10.1007/s00248-020-01525-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/05/2020] [Indexed: 05/25/2023]
Abstract
We tested two hypotheses concerning the dynamics of intestinal microbial communities of young mice following antibiotic-induced disturbance. The first is that disturbance of the bacterial community causes disturbance of the fungal community. Our results were consistent with that hypothesis. Antibiotics significantly altered bacterial community structure. Antibiotics also altered fungal community structure, significantly increasing the relative abundance of Candida lusitaniae, a known pathogen, while simultaneously significantly decreasing the relative abundances of several other common fungal species. The result was a temporary decrease in fungal diversity. Moreover, bacterial load was negatively correlated with the relative abundances of Candida lusitaniae and Candida parapsilosis, while it was positively correlated with the relative abundances of many other fungal species. Our second hypothesis is that control mice serve as a source of probiotics capable of invading intestines of mice with disturbed microbial communities and restoring pre-antibiotic bacterial and fungal communities. However, we found that control mice did not restore disturbed microbial communities. Instead, mice with disturbed microbial communities induced disturbance in control mice, consistent with the hypothesis that antibiotic-induced disturbance represents an alternate stable state that is easier to achieve than to correct. Our results indicate the occurrence of significant interactions among intestinal bacteria and fungi and suggest that the stimulation of certain bacterial groups may potentially be useful in countering the dominance of fungal pathogens such as Candida spp. However, the stability of disturbed microbial communities could complicate recovery.
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Affiliation(s)
- Rachel Nettles
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Currently: Kintai Therapeutics, 26 Landsdowne Street, Boston, MA, 02139, USA
| | - Kevin D Ricks
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Currently: Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA.
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46
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Ocáriz-Díez M, Cruellas M, Gascón M, Lastra R, Martínez-Lostao L, Ramírez-Labrada A, Paño JR, Sesma A, Torres I, Yubero A, Pardo J, Isla D, Gálvez EM. Microbiota and Lung Cancer. Opportunities and Challenges for Improving Immunotherapy Efficacy. Front Oncol 2020; 10:568939. [PMID: 33117698 PMCID: PMC7552963 DOI: 10.3389/fonc.2020.568939] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022] Open
Abstract
The advances in molecular biology and the emergence of Next Generation Sequencing (NGS) have revealed that microbiome composition is closely related with health and disease, including cancer. This relationship affects different levels of cancer such as development, progression, and response to treatment including immunotherapy. The efficacy of immune checkpoint inhibitors (ICIs) may be influenced by the concomitant use of antibiotics before, during or shortly after treatment with ICIs. Nevertheless, the linking mechanism between microbiote, host immunity and cancer is not clear and the role of microbiota manipulation and analyses in cancer management has not been clinically validated yet. Regarding the use of microbiome as biomarker to predict ICI efficacy it has been recently shown that the use of biochemical serum markers to monitor intestinal permeability and loss of barrier integrity, like citrulline, could be useful to monitor microbiota changes and predict ICI efficacy. There are still many unknowns about the role of these components, their relationship with the microbiota, with the use of antibiotics and the response to immunotherapy. The next challenge in microbiome research will be to identify individual microbial species that causally affect lung cancer phenotypes and response to ICI and disentangle the underlying mechanisms. Thus, further analyses in patients with lung cancer receiving treatment with ICIs and its correlation with the composition of the microbiota in different organs including the respiratory tract, peripheral blood and intestinal tract could be useful to predict the efficacy of ICIs and its modulation with antibiotic use.
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Affiliation(s)
- Maitane Ocáriz-Díez
- Medical Oncology Department, Lozano Blesa University Clinical Hospital, Zaragoza, Spain.,Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - Mara Cruellas
- Medical Oncology Department, Lozano Blesa University Clinical Hospital, Zaragoza, Spain.,Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - Marta Gascón
- Medical Oncology Department, Lozano Blesa University Clinical Hospital, Zaragoza, Spain.,Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - Rodrigo Lastra
- Medical Oncology Department, Lozano Blesa University Clinical Hospital, Zaragoza, Spain.,Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - Luis Martínez-Lostao
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain.,Inmunology Department, Lozano Blesa University Clinical Hospital, Zaragoza, Spain.,Department of Microbiology, Pediatrics, Radiology and Public Health, University of Zaragoza, Zaragoza, Spain.,Aragon Nanoscience Institute, Zaragoza, Spain.,Aragon Materials Science Institute, Zaragoza, Spain
| | - Ariel Ramírez-Labrada
- Unidad de Nanotoxicología e Inmunotoxicología (UNATI), Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
| | - José Ramón Paño
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain.,Infectious Diseases Department, Lozano Blesa University Clinical Hospital, Zaragoza, Spain
| | - Andrea Sesma
- Medical Oncology Department, Lozano Blesa University Clinical Hospital, Zaragoza, Spain.,Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - Irene Torres
- Medical Oncology Department, Lozano Blesa University Clinical Hospital, Zaragoza, Spain.,Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - Alfonso Yubero
- Medical Oncology Department, Lozano Blesa University Clinical Hospital, Zaragoza, Spain.,Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - Julián Pardo
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain.,ARAID Foundation (IIS Aragón), Zaragoza, Spain.,Microbiology, Preventive Medicine and Public Health Department, Medicine, University of Zaragoza, Zaragoza, Spain.,Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine Network (CIBER-BBN), Madrid, Spain
| | - Dolores Isla
- Medical Oncology Department, Lozano Blesa University Clinical Hospital, Zaragoza, Spain.,Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - Eva M Gálvez
- Instituto de Carboquimica (ICB-Consejo Superior de Investigaciones Cientificas), Zaragoza, Spain
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47
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The Human Microbiome and Its Impacts on Health. Int J Microbiol 2020; 2020:8045646. [PMID: 32612660 PMCID: PMC7306068 DOI: 10.1155/2020/8045646] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/22/2020] [Indexed: 01/10/2023] Open
Abstract
The human microbiome comprises bacteria, archaea, viruses, and eukaryotes which reside within and outside our bodies. These organisms impact human physiology, both in health and in disease, contributing to the enhancement or impairment of metabolic and immune functions. Micro-organisms colonise various sites on and in the human body, where they adapt to specific features of each niche. Facultative anaerobes are more dominant in the gastrointestinal tract, whereas strict aerobes inhabit the respiratory tract, nasal cavity, and skin surface. The indigenous organisms in the human body are well adapted to the immune system, due to the biological interaction of the organisms with the immune system over time. An alteration in the intestinal microbial community plays a major role in human health and disease pathogenesis. These alterations result from lifestyle and the presence of an underlying disease. Dysbiosis increases host susceptibility to infection, and the nature of which depends on the anatomical site involved. The unique diversity of the human microbiota accounts for the specific metabolic activities and functions of these micro-organisms within each body site. It is therefore important to understand the microbial composition and activities of the human microbiome as they contribute to health and disease.
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48
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Klimina KM, Voroshilova VN, Poluektova EU, Veselovsky VA, Yunes RA, Kovtun AS, Kudryavtseva AV, Kasianov AS, Danilenko VN. Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota. Toxins (Basel) 2020; 12:toxins12060388. [PMID: 32545455 PMCID: PMC7354421 DOI: 10.3390/toxins12060388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 01/14/2023] Open
Abstract
The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM.
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Affiliation(s)
- Ksenia M. Klimina
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
- Correspondence:
| | - Viktoriya N. Voroshilova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Elena U. Poluektova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
| | - Vladimir A. Veselovsky
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
| | - Roman A. Yunes
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
| | - Aleksey S. Kovtun
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Artem S. Kasianov
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Valery N. Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
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49
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Merten C, Schoonjans R, Di Gioia D, Peláez C, Sanz Y, Maurici D, Robinson T. Editorial: Exploring the need to include microbiomes into EFSA's scientific assessments. EFSA J 2020; 18:e18061. [PMID: 32874347 PMCID: PMC7448006 DOI: 10.2903/j.efsa.2020.e18061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The communities of microorganisms and their genomes in a defined environment are collectively referred to as microbiomes (Marchesi and Ravel, 2015). They include representatives from the Bacteria, Archaea, lower and higher Eukarya, and viruses, and are found in most environments such as soils, aquatic habitats, surfaces and specific lumen of plants, animals and humans. According to ongoing studies, microbiome structures and dynamics across the food system can have both direct and indirect effects on human and animal health, in addition to their impact on food quality, safety and sustainability (CNBBSV concept paper, 2019). Moreover, recent research projects have offered new insights into the associations between microbiomes and a wide range of human diseases as well as their possible impact in modulating the exposure to environmental chemicals. As one of the core tasks of EFSA is to assess risks to human and animal health and/or the environment from substances linked to food and feed production, the increasing understanding of the role of microbiomes in health calls for a prospective mapping of their roles into regulatory scientific assessment processes with a view to understanding their potential health impact.
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Szőke H, Kovács Z, Bókkon I, Vagedes J, Szabó AE, Hegyi G, Sterner MG, Kiss Á, Kapócs G. Gut dysbiosis and serotonin: intestinal 5-HT as a ubiquitous membrane permeability regulator in host tissues, organs, and the brain. Rev Neurosci 2020; 31:415-425. [DOI: 10.1515/revneuro-2019-0095] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022]
Abstract
AbstractThe microbiota and microbiome and disruption of the gut-brain axis were linked to various metabolic, immunological, physiological, neurodevelopmental, and neuropsychiatric diseases. After a brief review of the relevant literature, we present our hypothesis that intestinal serotonin, produced by intestinal enterochromaffin cells, picked up and stored by circulating platelets, participates and has an important role in the regulation of membrane permeability in the intestine, brain, and other organs. In addition, intestinal serotonin may act as a hormone-like continuous regulatory signal for the whole body, including the brain. This regulatory signal function is mediated by platelets and is primarily dependent on and reflects the intestine’s actual health condition. This hypothesis may partially explain why gut dysbiosis could be linked to various human pathological conditions as well as neurodevelopmental and neuropsychiatric disorders.
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Affiliation(s)
- Henrik Szőke
- Department of CAM, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
- Doctorate School, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - Zoltán Kovács
- Doctorate School, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - István Bókkon
- Vision Research Institute, Neuroscience and Consciousness Research Department, Lowell, MA, USA
- Psychosomatic Outpatient Clinics, Budapest, Hungary
| | - Jan Vagedes
- University of Tübingen, Children’s Hospital, Tübingen, Germany
- ARCIM Institute (Academic Research in Complementary and Integrative Medicine), Filderstadt, Germany
| | | | - Gabriella Hegyi
- Department of CAM, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
- Doctorate School, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | | | - Ágnes Kiss
- Doctorate School, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - Gábor Kapócs
- Buda Family-Centered Mental Health Centre, Department of Psychiatry and Psychiatric Rehabilitation, Teaching Department of Semmelweis University, New Saint John Hospital, Budapest, Hungary
- Institute for Behavioral Sciences, Semmelweis University, Budapest, Hungary
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