1
|
Liu D, Chen D, Xiao J, Wang W, Zhang LJ, Peng H, Han C, Yao H. High-altitude-induced alterations in intestinal microbiota. Front Microbiol 2024; 15:1369627. [PMID: 38784803 PMCID: PMC11111974 DOI: 10.3389/fmicb.2024.1369627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
In high-altitude environments characterized by low pressure and oxygen levels, the intestinal microbiota undergoes significant alterations. Whether individuals are subjected to prolonged exposure or acute altitude changes, these conditions lead to shifts in both the diversity and abundance of intestinal microbiota and changes in their composition. While these alterations represent adaptations to high-altitude conditions, they may also pose health risks through certain mechanisms. Changes in the intestinal microbiota induced by high altitudes can compromise the integrity of the intestinal mucosal barrier, resulting in gastrointestinal dysfunction and an increased susceptibility to acute mountain sickness (AMS). Moreover, alterations in the intestinal microbiota have been implicated in the induction or exacerbation of chronic heart failure. Targeted modulation of the intestinal microbiota holds promise in mitigating high-altitude-related cardiac damage. Dietary interventions, such as adopting a high-carbohydrate, high-fiber, low-protein, and low-fat diet, can help regulate the effects of intestinal microbiota and their metabolic byproducts on intestinal health. Additionally, supplementation with probiotics, either through dietary sources or medications, offers a means of modulating the composition of the intestinal microbiota. These interventions may offer beneficial effects in preventing and alleviating AMS following acute exposure to high altitudes.
Collapse
Affiliation(s)
- Dan Liu
- Department of Endocrinology, General Hospital of the Chinese People’s Liberation Army Western Theater, Chengdu, Sichuan, China
| | - Dan Chen
- Department of Hematology and Hematopoietic Stem Cell Transplantation Center, General Hospital of the Chinese People’s Liberation Army Western Theater, Chengdu, Sichuan, China
| | - Jian Xiao
- Department of Endocrinology, General Hospital of the Chinese People’s Liberation Army Western Theater, Chengdu, Sichuan, China
| | - Wei Wang
- Department of Endocrinology, General Hospital of the Chinese People’s Liberation Army Western Theater, Chengdu, Sichuan, China
| | - Li-Juan Zhang
- Department of Endocrinology, General Hospital of the Chinese People’s Liberation Army Western Theater, Chengdu, Sichuan, China
| | - Hui Peng
- Department of Endocrinology, General Hospital of the Chinese People’s Liberation Army Western Theater, Chengdu, Sichuan, China
| | - Chuan Han
- Department of Endocrinology, General Hospital of the Chinese People’s Liberation Army Western Theater, Chengdu, Sichuan, China
| | - Hao Yao
- Department of Hematology and Hematopoietic Stem Cell Transplantation Center, General Hospital of the Chinese People’s Liberation Army Western Theater, Chengdu, Sichuan, China
| |
Collapse
|
2
|
Gul F, Herrema H, Davids M, Keating C, Nasir A, Ijaz UZ, Javed S. Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathog 2024; 16:5. [PMID: 38254227 PMCID: PMC10801943 DOI: 10.1186/s13099-024-00596-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC). METHODS 16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through [Formula: see text] test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment. RESULTS A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history. CONCLUSIONS This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings.
Collapse
Affiliation(s)
- Farzana Gul
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Mark Davids
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Ciara Keating
- School of Biodiversity, One Health & Veterinary Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Arshan Nasir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
- Moderna, Inc., Cambridge, MA, USA
| | - Umer Zeeshan Ijaz
- Water & Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, G11 6EW, UK.
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, L69 7BE, UK.
- National University of Ireland, Galway, University Road, Galway, H91 TK33, Ireland.
| | - Sundus Javed
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan.
| |
Collapse
|
3
|
Csader S, Chen X, Leung H, Männistö V, Pentikäinen H, Tauriainen MM, Savonen K, El-Nezami H, Schwab U, Panagiotou G. Gut ecological networks reveal associations between bacteria, exercise, and clinical profile in non-alcoholic fatty liver disease patients. mSystems 2023; 8:e0022423. [PMID: 37606372 PMCID: PMC10654067 DOI: 10.1128/msystems.00224-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/15/2023] [Indexed: 08/23/2023] Open
Abstract
IMPORTANCE Our study is applying a community-based approach to examine the influence of exercise on gut microbiota (GM) and discover GM structures linked with NAFLD improvements during exercise. The majority of microbiome research has focused on finding specific species that may contribute to the development of human diseases. However, we believe that complex diseases, such as NAFLD, would be more efficiently treated using consortia of species, given that bacterial functionality is based not only on its own genetic information but also on the interaction with other microorganisms. Our results revealed that exercise significantly changes the GM interaction and that structural alterations can be linked with improvements in intrahepatic lipid content and metabolic functions. We believe that the identification of these characteristics in the GM enhances the development of exercise treatment for NAFLD and will attract general interest in this field.
Collapse
Affiliation(s)
- Susanne Csader
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Xiuqiang Chen
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Howell Leung
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Ville Männistö
- Departments of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Milla-Maria Tauriainen
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Departments of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kai Savonen
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Hani El-Nezami
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- University of Hong Kong School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Ursula Schwab
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Gianni Panagiotou
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
4
|
Song H, Lee J, Yi S, Kim WH, Kim Y, Namgoong B, Choe A, Cho G, Shin J, Park Y, Kim MS, Cho S. Red Ginseng Dietary Fiber Shows Prebiotic Potential by Modulating Gut Microbiota in Dogs. Microbiol Spectr 2023; 11:e0094923. [PMID: 37367492 PMCID: PMC10433987 DOI: 10.1128/spectrum.00949-23] [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: 03/03/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023] Open
Abstract
Red ginseng, widely used in traditional medicine for various conditions, imparts health benefits mainly by modulating the gut microbiota in humans. Given the similarities in gut microbiota between humans and dogs, red ginseng-derived dietary fiber may have prebiotic potential in dogs; however, its effects on the gut microbiota in dogs remain elusive. This double-blinded, longitudinal study investigated the impact of red ginseng dietary fiber on the gut microbiota and host response in dogs. A total of 40 healthy household dogs were randomly assigned to low-dose (n = 12), high-dose (n = 16), or control (n = 12) groups and fed a normal diet supplemented with red ginseng dietary fiber (3 g/5 kg body weight per day, 8 g/5 kg per day, or no supplement, respectively) for 8 weeks. The gut microbiota of the dogs was analyzed at 4 weeks and 8 weeks using 16S rRNA gene sequencing of fecal samples. Alpha diversity was significantly increased at 8 and 4 weeks in the low-dose and high-dose groups, respectively. Moreover, biomarker analysis showed that short-chain fatty acid producers such as Sarcina and Proteiniclasticum were significantly enriched, while potential pathogens such as Helicobacter were significantly decreased, indicating the increased gut health and pathogen resistance by red ginseng dietary fiber. Microbial network analysis showed that the complexity of microbial interactions was increased by both doses, indicating the increased stability of the gut microbiota. These findings suggest that red ginseng-derived dietary fiber could be used as a prebiotic to modulate gut microbiota and improve gut health in dogs. IMPORTANCE The canine gut microbiota is an attractive model for translational studies, as it responds to dietary interventions similarly to those in humans. Investigating the gut microbiota of household dogs that share the environment with humans can produce highly generalizable and reproducible results owing to their representativeness of the general canine population. This double-blind and longitudinal study investigated the impact of dietary fiber derived from red ginseng on the gut microbiota of household dogs. Red ginseng dietary fiber altered the canine gut microbiota by increasing diversity, enriching short-chain fatty acid-producing microbes, decreasing potential pathogens, and increasing the complexity of microbial interactions. These findings indicate that red ginseng-derived dietary fiber may promote canine gut health by modulating gut microbiota, suggesting the possibility of its use as a potential prebiotic.
Collapse
Affiliation(s)
- Hyokeun Song
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Junbum Lee
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Saehah Yi
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Woo-Hyun Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Yuna Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Beomkwan Namgoong
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Ahreum Choe
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Gunhee Cho
- Korea Ginseng Corporation, Daejeon, South Korea
| | - Jangmi Shin
- Korea Ginseng Corporation, Daejeon, South Korea
| | | | - Min Su Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
- Center for Veterinary Integrated Medicine Research, Seoul National University, Seoul, South Korea
| | - Seongbeom Cho
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
- Center for Veterinary Integrated Medicine Research, Seoul National University, Seoul, South Korea
| |
Collapse
|
5
|
Aurich S, Müller L, Kovacs P, Keller M. Implication of DNA methylation during lifestyle mediated weight loss. Front Endocrinol (Lausanne) 2023; 14:1181002. [PMID: 37614712 PMCID: PMC10442821 DOI: 10.3389/fendo.2023.1181002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/18/2023] [Indexed: 08/25/2023] Open
Abstract
Over the past 50 years, the number of overweight/obese people increased significantly, making obesity a global public health challenge. Apart from rare monogenic forms, obesity is a multifactorial disease, most likely resulting from a concerted interaction of genetic, epigenetic and environmental factors. Although recent studies opened new avenues in elucidating the complex genetics behind obesity, the biological mechanisms contributing to individual's risk to become obese are not yet fully understood. Non-genetic factors such as eating behaviour or physical activity are strong contributing factors for the onset of obesity. These factors may interact with genetic predispositions most likely via epigenetic mechanisms. Epigenome-wide association studies or methylome-wide association studies are measuring DNA methylation at single CpGs across thousands of genes and capture associations to obesity phenotypes such as BMI. However, they only represent a snapshot in the complex biological network and cannot distinguish between causes and consequences. Intervention studies are therefore a suitable method to control for confounding factors and to avoid possible sources of bias. In particular, intervention studies documenting changes in obesity-associated epigenetic markers during lifestyle driven weight loss, make an important contribution to a better understanding of epigenetic reprogramming in obesity. To investigate the impact of lifestyle in obesity state specific DNA methylation, especially concerning the development of new strategies for prevention and individual therapy, we reviewed 19 most recent human intervention studies. In summary, this review highlights the huge potential of targeted interventions to alter disease-associated epigenetic patterns. However, there is an urgent need for further robust and larger studies to identify the specific DNA methylation biomarkers which influence obesity.
Collapse
Affiliation(s)
- Samantha Aurich
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Luise Müller
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany
| | - Maria Keller
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| |
Collapse
|
6
|
Pös O, Styk J, Buglyó G, Zeman M, Lukyova L, Bernatova K, Hrckova Turnova E, Rendek T, Csók Á, Repiska V, Nagy B, Szemes T. Cross-Kingdom Interaction of miRNAs and Gut Microbiota with Non-Invasive Diagnostic and Therapeutic Implications in Colorectal Cancer. Int J Mol Sci 2023; 24:10520. [PMID: 37445698 DOI: 10.3390/ijms241310520] [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: 05/17/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Colorectal cancer (CRC) has one of the highest incidences among all types of malignant diseases, affecting millions of people worldwide. It shows slow progression, making it preventable. However, this is not the case due to shortcomings in its diagnostic and management procedure and a lack of effective non-invasive biomarkers for screening. Here, we discuss CRC-associated microRNAs (miRNAs) and gut microbial species with potential as CRC diagnostic and therapy biomarkers. We provide rich evidence of cross-kingdom miRNA-mediated interactions between the host and gut microbiome. miRNAs have emerged with the ability to shape the composition and dynamics of gut microbiota. Intestinal microbes can uptake miRNAs, which in turn influence microbial growth and provide the ability to regulate the abundance of various microbial species. In the context of CRC, targeting miRNAs could aid in manipulating the balance of the microbiota. Our findings suggest the need for correlation analysis between the composition of the gut microbiome and the miRNA expression profile.
Collapse
Affiliation(s)
- Ondrej Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Jakub Styk
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Michal Zeman
- Comenius University Science Park, 841 04 Bratislava, Slovakia
| | - Lydia Lukyova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 05 Bratislava, Slovakia
| | - Kamila Bernatova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 05 Bratislava, Slovakia
| | - Evelina Hrckova Turnova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Slovgen Ltd., 841 04 Bratislava, Slovakia
| | - Tomas Rendek
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Ádám Csók
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
- Medirex Group Academy, n.p.o., 949 05 Nitra, Slovakia
| | - Bálint Nagy
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 05 Bratislava, Slovakia
| |
Collapse
|
7
|
He Y, Chen Y. The potential mechanism of the microbiota-gut-bone axis in osteoporosis: a review. Osteoporos Int 2022; 33:2495-2506. [PMID: 36169678 DOI: 10.1007/s00198-022-06557-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/16/2022] [Indexed: 10/14/2022]
Abstract
Osteoporosis is the prevalent metabolic bone disease characterized by a decrease in bone quantity and/or quality and an increase in skeletal fragility, which increases susceptibility to fractures. Osteoporotic fractures severely affect the patients' quality of life and mortality. A plethora of evidences have suggested that the alterations in gut microbiome are associated with the changes in bone mass and microstructure. We summarized pre-clinical and clinical studies to elucidate the underlying mechanism of gut microbiota in osteoporosis. Probiotics, prebiotics, and traditional Chinese medicine may reverse the gut microbiota dysbiosis and consequently improve bone metabolism. However, the causality of gut microbiota on bone metabolism need to be investigated more in depth. In the present review, we focused on the potential mechanism of the microbiota-gut-bone axis and the positive therapeutic effect of probiotics, prebiotics, and traditional Chinese medicine on osteoporosis. Overall, the current scientific literatures support that the gut microbiota may be a novel therapeutic target in treatment of osteoporosis and fracture prevention.
Collapse
Affiliation(s)
- Yinxi He
- Department of Orthopaedic Trauma, The Third Hospital of Shijiazhuang, Shijiazhuang, Hebei, 050000, People's Republic of China
| | - Yanxia Chen
- Department of Endocrinology, The Second Hospital of Hebei Medical University, 215 Hepingxi Road, Shijiazhuang, Hebei, 050000, People's Republic of China.
| |
Collapse
|
8
|
Hazarika P, Chattopadhyay I, Umpo M, Choudhury Y, Sharma I. Elucidating the gut microbiome alterations of tribal community of Arunachal Pradesh: perspectives on their lifestyle or food habits. Sci Rep 2022; 12:18296. [PMID: 36316382 PMCID: PMC9622709 DOI: 10.1038/s41598-022-23124-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 10/25/2022] [Indexed: 11/07/2022] Open
Abstract
Gut microbiota studies of ethnic populations reveal gut microbial biomarkers for therapeutic options and detection of the disease state. The present study aimed to analyze the gut microbiome signatures in thirty individuals from the Adi, Apatani and Nyshi tribes of Arunachal Pradesh (ten in each cohort) by sequencing the V3 and V4 regions of 16S rRNA on the Illumina MiSeq Platform. The gut microbiome was highly predominated by Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidates in the three studied tribal groups. At the genus level, significant abundance of Bifidobacterium, Collinsella, Bacteroides, Prevotella, Lactobacillus, Streptococcus, Clostridium, Coprococcus, Dorea, Lachnospira, Roseburia, Ruminococcus, Faecalibacterium, Catenibacterium, Eubacterium, Citrobacter and Enterobacter were observed amongst the three tribes. The tribal communities residing in remote areas and following traditional lifestyle had higher gut microbiome diversity with a high prevalence of Prevotella and Collinsella in the Adi and Nyshi tribes, and Bifidobacterium and Catenibacterium in the Apatani tribe. Elucidating the gut microbiome of the tribal community of Arunachal Pradesh will add to the knowledge on relationships between microbial communities, dietary food factors, and the overall state of health of humans worldwide.
Collapse
Affiliation(s)
- Parijat Hazarika
- grid.411460.60000 0004 1767 4538Department of Microbiology, Assam University, Silchar, 788011 India
| | - Indranil Chattopadhyay
- grid.448768.10000 0004 1772 7660Department of Life Sciences, Central University of Tamil Nadu, 610 101, Thiruvarur, India
| | - Mika Umpo
- Department of Microbiology, Tomo Riba Institute of Health and Medical Sciences, Nahrlagun, 791110 India
| | - Yashmin Choudhury
- grid.411460.60000 0004 1767 4538Department of Biotechnology, Assam University, Silchar, 788011 India
| | - Indu Sharma
- grid.411460.60000 0004 1767 4538Department of Microbiology, Assam University, Silchar, 788011 India
| |
Collapse
|
9
|
He C, Liao Q, Fu P, Li J, Zhao X, Zhang Q, Gui Q. Microbiological characteristics of different tongue coatings in adults. BMC Microbiol 2022; 22:214. [PMID: 36085010 PMCID: PMC9461261 DOI: 10.1186/s12866-022-02626-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Tongue coating is an important health indicator in traditional Chinese medicine (TCM). The tongue coating microbiome can distinguish disease patients from healthy controls. To study the relationship between different types of tongue coatings and health, we analyzed the species composition of different types of tongue coatings and the co-occurrence relationships between microorganisms in Chinese adults.
From June 2019 to October 2020, 158 adults from Hangzhou and Shaoxing City, Zhejiang Province, were enrolled. We classified the TCM tongue coatings into four different types: thin white tongue fur (TWF), thin yellow tongue fur (TYF), white greasy tongue fur (WGF), and yellow greasy tongue fur (YGF). Tongue coating specimens were collected and used for 16S rRNA gene sequencing using the Illumina MiSeq system. Wilcoxon rank-sum and permutational multivariate analysis of variance tests were used to analyze the data. The microbial networks in the four types of tongue coatings were inferred independently using sparse inverse covariance estimation for ecological association inference.
Results
The microbial composition was similar among the different tongue coatings; however, the abundance of microorganisms differed. TWF had a higher abundance of Fusobacterium periodonticum and Neisseria mucosa, the highest α-diversity, and a highly connected community (average degree = 3.59, average closeness centrality = 0.33). TYF had the lowest α-diversity, but the most species in the co-occurrence network diagram (number of nodes = 88). The platelet-to-lymphocyte ratio (PLR) was associated with tongue coating (P = 0.035), and the YGF and TYF groups had higher PLR values. In the co-occurrence network, Aggregatibacter segnis was the “driver species” of the TWF and TYF groups and correlated with C-reactive protein (P < 0.05). Streptococcus anginosus was the “driver species” in the YGF and TWF groups and was positively correlated with body mass index and weight (P < 0.05).
Conclusion
Different tongue coatings have similar microbial compositions but different abundances of certain bacteria. The co-occurrence of microorganisms in the different tongue coatings also varies. The significance of different tongue coatings in TCM theory is consistent with the characteristics and roles of the corresponding tongue-coating microbes. This further supports considering tongue coating as a risk factor for disease.
Collapse
|
10
|
Song H, Yi S, Kim WH, Guk JH, Ha M, Kwak I, Han J, Yeon SC, Cho S. Environmental Perturbations during the Rehabilitation of Wild Migratory Birds Induce Gut Microbiome Alteration and Antibiotic Resistance Acquisition. Microbiol Spectr 2022; 10:e0116322. [PMID: 35730950 PMCID: PMC9430529 DOI: 10.1128/spectrum.01163-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/04/2022] [Indexed: 11/21/2022] Open
Abstract
Wild migratory birds are essential for sustaining healthy ecosystems, but the effects of a rehabilitation period on their gut microbiomes are still unclear. Here, we performed longitudinal sampling, 16S rRNA sequencing, and antibiotic resistance monitoring of the gut microbiome of six species of wild migratory birds protected as natural monuments in South Korea that are subject to short- or long-term rehabilitation periods. Overall, gut microbiome diversity was significantly decreased in the early stages of rehabilitation, and it did not recover to a level comparable to that of wild birds. Moreover, while the abundance of short-chain fatty acid-producing bacteria decreased, that of zoonotic pathogens increased, indicating rehabilitation-induced dysbiosis. The metabolic pathways involved in the degradation of aromatic pollutants were significantly downregulated, suggesting the depletion of pollutant-degrading microorganisms. Antibiotic resistance of Escherichia coli significantly increased during rehabilitation, particularly ciprofloxacin and tetracycline resistance, and seven of the rehabilitated wild birds acquired multidrug resistance. The diet and habitat changes experienced by wild migratory birds during rehabilitation may have induced the observed gut microbiome dysbiosis and acquisition of antibiotic resistance. These rehabilitation-induced alterations might affect the adaptability of wild birds to their natural environments and contribute to the spread of antibiotic resistance after their release. IMPORTANCE Wild migratory birds are key for ecosystem health but highly sensitive to anthropogenic activities. Therefore, wild migratory birds often undergo rehabilitation to prevent species extinction or biodiversity monitoring. However, the impact of rehabilitation on the gut microbiome of wild migratory birds, which is closely associated with host fitness, remains unclear. For the migratory bird species considered natural monuments in South Korea evaluated here, such impacts could include rehabilitation-induced gut microbiome dysbiosis and acquisition of antibiotic resistance, with possible repercussions on the adaptability of wild birds and spread of antibiotic resistance in the environment after their release. Therefore, the dynamics of the gut microbiome and antibiotic resistance should be considered for implementing sustainable rehabilitation strategies.
Collapse
Affiliation(s)
- Hyokeun Song
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Saehah Yi
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Woo-Hyun Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Jae-Ho Guk
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Minjong Ha
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
- Seoul Wildlife Center, Seoul, South Korea
| | - Insik Kwak
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
- Seoul Wildlife Center, Seoul, South Korea
| | - Janghee Han
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
- Seoul Wildlife Center, Seoul, South Korea
| | - Seong-Chan Yeon
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
- Seoul Wildlife Center, Seoul, South Korea
| | - Seongbeom Cho
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
- Center for Veterinary Integrated Medicine Research, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| |
Collapse
|
11
|
Shen Y, Laue HE, Shrubsole MJ, Wu H, Bloomquist TR, Larouche A, Zhao K, Gao F, Boivin A, Prada D, Hunting DJ, Gillet V, Takser L, Baccarelli AA. Associations of Childhood and Perinatal Blood Metals with Children's Gut Microbiomes in a Canadian Gestation Cohort. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:17007. [PMID: 35037767 PMCID: PMC8763169 DOI: 10.1289/ehp9674] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND The gut microbiome is important in modulating health in childhood. Metal exposures affect multiple health outcomes, but their ability to modify bacterial communities in children is poorly understood. OBJECTIVES We assessed the associations of childhood and perinatal blood metal levels with childhood gut microbiome diversity, structure, species, gene family-inferred species, and potential pathway alterations. METHODS We assessed the gut microbiome using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing in stools collected from 6- to 7-year-old children participating in the GESTation and Environment (GESTE) cohort study. We assessed blood metal concentrations [cadmium (Cd), manganese (Mn), mercury (Hg), lead (Pb), selenium (Se)] at two time points, namely, perinatal exposures at delivery (N = 70 ) and childhood exposures at the 6- to 7-y follow-up (N = 68 ). We used multiple covariate-adjusted statistical models to determine microbiome associations with continuous blood metal levels, including linear regression (Shannon and Pielou alpha diversity indexes), permutational multivariate analysis of variance (adonis; beta diversity distance matrices), and multivariable association model (MaAsLin2; phylum, family, species, gene family-inferred species, and pathways). RESULTS Children's blood Mn and Se significantly associated with microbiome phylum [e.g., Verrucomicrobiota (coef = - 0.305 , q = 0.031 ; coef = 0.262 , q = 0.084 , respectively)] and children's blood Mn significantly associated with family [e.g., Eggerthellaceae (coef = - 0.228 , q = 0.052 )]-level differences. Higher relative abundance of potential pathogens (e.g., Flavonifractor plautii), beneficial species (e.g., Bifidobacterium longum, Faecalibacterium prausnitzii), and both potentially pathogenic and beneficial species (e.g., Bacteriodes vulgatus, Eubacterium rectale) inferred from gene families were associated with higher childhood or perinatal blood Cd, Hg, and Pb (q < 0.1 ). We found significant negative associations between childhood blood Pb and acetylene degradation pathway abundance (q < 0.1 ). Finally, neither perinatal nor childhood metal concentrations were associated with children's gut microbial inter- and intrasubject diversity. DISCUSSION Our findings suggest both long- and short-term associations between metal exposure and the childhood gut microbiome, with stronger associations observed with more recent exposure. Future epidemiologic analyses may elucidate whether the observed changes in the microbiome relate to children's health. https://doi.org/10.1289/EHP9674.
Collapse
Affiliation(s)
- Yike Shen
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Hannah E. Laue
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Martha J. Shrubsole
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Tessa R. Bloomquist
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Annie Larouche
- Département de Pédiatrie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Feng Gao
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Amélie Boivin
- Département de Pédiatrie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Diddier Prada
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
- Department of Basic Science, Instituto Nacional de Cancerologia, Ciudad de México, México
| | - Darel J. Hunting
- Department of Nuclear Medicine and Radiobiology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Virginie Gillet
- Département de Pédiatrie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Larissa Takser
- Département de Pédiatrie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Departement de Psychiatrie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| |
Collapse
|
12
|
Feng L, Zhou N, Li Z, Fu D, Guo Y, Gao X, Liu X. Co-occurrence of gut microbiota dysbiosis and bile acid metabolism alteration is associated with psychological disorders in Crohn's disease. FASEB J 2021; 36:e22100. [PMID: 34939244 DOI: 10.1096/fj.202101088rrr] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022]
Abstract
This study aims to elucidate the relationships between gut microbiota, bile acid metabolism, and psychological comorbidity in Crohn's disease (CD). We profiled the fecal microbiota composition and quantified the bile acid pool of 39 CD patients and 14 healthy controls using 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry, respectively. Significant reductions in the secondary bile acids, LCA and DCA, were found in both the feces and serum samples of CD patients, while the concentration of 7-DHCA was particularly higher in the serum of CD patients with psychological disorders. The fecal levels of HDCA and 12-DHCA of the CD patients were inversely correlated with their Self-Rated Depression Scale (SDS) scores, whereas the serum level of 7-DHCA was positively correlated with the SDS scores. In addition, the fecal levels of TDCA, TLCA, and TβMCA showed a positive correlation with the Self-Rated Anxiety Scale (SAS) scores. The fecal microbiota biodiversity was particularly declined in CD patients with psychological disorders. An enrichment of Ruminococcus gnavus in CD patients may cause psychological disorders by affecting the microbiota-gut-brain axis via its ability to degrade the gut barrier, regulate the tryptophan-kynurenine metabolism, and modulate bile acid metabolism. In addition, the overabundant Enterobacteriaceae and Lachnospiraceae in CD patients may contribute to psychological comorbidity via dysregulating their bile acids metabolism. Taken together, changes in the gut microbiota composition may cooperate with alterations in the bile acid metabolism that are involved in the development of psychological disorders in CD.
Collapse
Affiliation(s)
- Lijuan Feng
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China.,Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, China
| | - Nan Zhou
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
| | - Zichun Li
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
| | - Dongni Fu
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
| | - Ying Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Xuefeng Gao
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, China.,Central Laboratory, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Xiaowei Liu
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
13
|
Nabwera HM, Espinoza JL, Worwui A, Betts M, Okoi C, Sesay AK, Bancroft R, Agbla SC, Jarju S, Bradbury RS, Colley M, Jallow AT, Liu J, Houpt ER, Prentice AM, Antonio M, Bernstein RM, Dupont CL, Kwambana-Adams BA. Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children. EBioMedicine 2021; 73:103644. [PMID: 34695658 PMCID: PMC8550991 DOI: 10.1016/j.ebiom.2021.103644] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The specific roles that gut microbiota, known pathogens, and host energy-regulating hormones play in the pathogenesis of non-edematous severe acute malnutrition (marasmus SAM) and moderate acute malnutrition (MAM) during outpatient nutritional rehabilitation are yet to be explored. METHODS We applied an ensemble of sample-specific (intra- and inter-modality) association networks to gain deeper insights into the pathogenesis of acute malnutrition and its severity among children under 5 years of age in rural Gambia, where marasmus SAM is most prevalent. FINDINGS Children with marasmus SAM have distinct microbiome characteristics and biologically-relevant multimodal biomarkers not observed among children with moderate acute malnutrition. Marasmus SAM was characterized by lower microbial richness and biomass, significant enrichments in Enterobacteriaceae, altered interactions between specific Enterobacteriaceae and key energy regulating hormones and their receptors. INTERPRETATION Our findings suggest that marasmus SAM is characterized by the collapse of a complex system with nested interactions and key associations between the gut microbiome, enteric pathogens, and energy regulating hormones. Further exploration of these systems will help inform innovative preventive and therapeutic interventions. FUNDING The work was supported by the UK Medical Research Council (MRC; MC-A760-5QX00) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement; Bill and Melinda Gates Foundation (OPP 1066932) and the National Institute of Medical Research (NIMR), UK. This network analysis was supported by NIH U54GH009824 [CLD] and NSF OCE-1558453 [CLD].
Collapse
Affiliation(s)
- Helen M Nabwera
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Josh L Espinoza
- J. Craig Venture Institute, 4120 Capricorn Ln, La Jolla, CA 92037, USA; Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Archibald Worwui
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Modupeh Betts
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Catherine Okoi
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Rowan Bancroft
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Schadrac C Agbla
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | | | - Mariama Colley
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Amadou T Jallow
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Jie Liu
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Robin M Bernstein
- Growth and Development Lab, Department of Anthropology, University of Colorado, Boulder, CO, United States of America
| | | | - Brenda A Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom.
| |
Collapse
|
14
|
Abstract
PURPOSE OF REVIEW Patients with diabetes mellitus (DM) are at increased risk of developing osteopathogenesis and skeletal fragility. The role of the gut microbiota in both DM and osteopathy is not fully explored and may be involved in the pathology of both diseases. RECENT FINDINGS Gut microbiota alterations have been observed in DM and osteopathogenic disorders as compared with healthy controls, such as significantly lower abundance of Prevotella and higher abundance of Lactobacillus, with a diminished bacterial diversity. Other overlapping gastro-intestinal features include the loss of intestinal barrier function with translocation of bacterial metabolites to the blood stream, induction of immunological deficits and changes in hormonal and endocrinal signalling, which may lead to the development of diabetic osteopathy. Signalling pathways involved in both DM and osteopathy are affected by gut bacteria and their metabolites. Future studies should focus on gut microbiota involvement in both diseases.
Collapse
Affiliation(s)
- Julie Kristine Knudsen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjørring, Denmark.
- Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, Aalborg, Denmark.
| | - Peter Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjørring, Denmark
- Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, Aalborg, Denmark
- Steno Diabetes Center North Jutland, Mølleparkvej 4, Aalborg, Denmark
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjørring, Denmark
- Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, Aalborg, Denmark
- Steno Diabetes Center North Jutland, Mølleparkvej 4, Aalborg, Denmark
| |
Collapse
|
15
|
Nichols RG, Davenport ER. The relationship between the gut microbiome and host gene expression: a review. Hum Genet 2021; 140:747-760. [PMID: 33221945 PMCID: PMC7680557 DOI: 10.1007/s00439-020-02237-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022]
Abstract
Despite the growing knowledge surrounding host-microbiome interactions, we are just beginning to understand how the gut microbiome influences-and is influenced by-host gene expression. Here, we review recent literature that intersects these two fields, summarizing themes across studies. Work in model organisms, human biopsies, and cell culture demonstrate that the gut microbiome is an important regulator of several host pathways relevant for disease, including immune development and energy metabolism, and vice versa. The gut microbiome remodels host chromatin, causes differential splicing, alters the epigenetic landscape, and directly interrupts host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to refine our understanding of the relationship between the gut microbiome and host gene expression in the future. By intersecting microbiome and host gene expression, we gain a window into the physiological processes important for fostering the extensive cross-kingdom interactions and ultimately our health.
Collapse
Affiliation(s)
- Robert G. Nichols
- Department of Biology, The Pennsylvania State University, University Park, PA 16802 USA
| | - Emily R. Davenport
- Department of Biology, The Pennsylvania State University, University Park, PA 16802 USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802 USA
| |
Collapse
|
16
|
PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:154-167. [PMID: 33581337 PMCID: PMC8498968 DOI: 10.1016/j.gpb.2020.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/28/2020] [Accepted: 08/09/2020] [Indexed: 11/21/2022]
Abstract
The dysbiosis of gut microbiota is associated with the pathogenesis of human diseases. However, observing shifts in the microbe abundance cannot fully reveal underlying perturbations. Examining the relationship alterations (RAs) in the microbiome between health and disease statuses provides additional hints about the pathogenesis of human diseases, but no methods were designed to detect and quantify the RAs between different conditions directly. Here, we present profile monitoring for microbial relationship alteration (PM2RA), an analysis framework to identify and quantify the microbial RAs. The performance of PM2RA was evaluated with synthetic data, and it showed higher specificity and sensitivity than the co-occurrence-based methods. Analyses of real microbial datasets showed that PM2RA was robust for quantifying microbial RAs across different datasets in several diseases. By applying PM2RA, we identified several novel or previously reported microbes implicated in multiple diseases. PM2RA is now implemented as a web-based application available at http://www.pm2ra-xingyinliulab.cn/.
Collapse
|
17
|
Nagpal S, Singh R, Yadav D, Mande SS. MetagenoNets: comprehensive inference and meta-insights for microbial correlation networks. Nucleic Acids Res 2020; 48:W572-W579. [PMID: 32338757 PMCID: PMC7319469 DOI: 10.1093/nar/gkaa254] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/28/2020] [Accepted: 04/02/2020] [Indexed: 11/15/2022] Open
Abstract
Microbial association networks are frequently used for understanding and comparing community dynamics from microbiome datasets. Inferring microbial correlations for such networks and obtaining meaningful biological insights, however, requires a lengthy data management workflow, choice of appropriate methods, statistical computations, followed by a different pipeline for suitably visualizing, reporting and comparing the associations. The complexity is further increased with the added dimension of multi-group 'meta-data' and 'inter-omic' functional profiles that are often associated with microbiome studies. This not only necessitates the need for categorical networks, but also integrated and bi-partite networks. Multiple options of network inference algorithms further add to the efforts required for performing correlation-based microbiome interaction studies. We present MetagenoNets, a web-based application, which accepts multi-environment microbial abundance as well as functional profiles, intelligently segregates 'continuous and categorical' meta-data and allows inference as well as visualization of categorical, integrated (inter-omic) and bi-partite networks. Modular structure of MetagenoNets ensures logical flow of analysis (inference, integration, exploration and comparison) in an intuitive and interactive personalized dashboard driven framework. Dynamic choice of filtration, normalization, data transformation and correlation algorithms ensures, that end-users get a one-stop solution for microbial network analysis. MetagenoNets is freely available at https://web.rniapps.net/metagenonets.
Collapse
Affiliation(s)
- Sunil Nagpal
- Bio-Sciences R&D Division, TCS Research, Pune, Maharashtra 411013, India
| | - Rashmi Singh
- Bio-Sciences R&D Division, TCS Research, Pune, Maharashtra 411013, India
| | - Deepak Yadav
- Bio-Sciences R&D Division, TCS Research, Pune, Maharashtra 411013, India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Pune, Maharashtra 411013, India
| |
Collapse
|
18
|
Liu RT, Rowan-Nash AD, Sheehan AE, Walsh RFL, Sanzari CM, Korry BJ, Belenky P. Reductions in anti-inflammatory gut bacteria are associated with depression in a sample of young adults. Brain Behav Immun 2020; 88:308-324. [PMID: 32229219 PMCID: PMC7415740 DOI: 10.1016/j.bbi.2020.03.026] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/07/2020] [Accepted: 03/25/2020] [Indexed: 12/15/2022] Open
Abstract
We assessed the gut microbiota of 90 American young adults, comparing 43 participants with major depressive disorder (MDD) and 47 healthy controls, and found that the MDD subjects had significantly different gut microbiota compared to the healthy controls at multiple taxonomic levels. At the phylum level, participants with MDD had lower levels of Firmicutes and higher levels of Bacteroidetes, with similar trends in the at the class (Clostridia and Bacteroidia) and order (Clostridiales and Bacteroidales) levels. At the genus level, the MDD group had lower levels of Faecalibacterium and other related members of the family Ruminococcaceae, which was also reduced relative to healthy controls. Additionally, the class Gammaproteobacteria and genus Flavonifractor were enriched in participants with MDD. Accordingly, predicted functional differences between the two groups include a reduced abundance of short-chain fatty acid production pathways in the MDD group. We also demonstrated that the magnitude of taxonomic changes was associated with the severity of depressive symptoms in many cases, and that most changes were present regardless of whether depressed participants were taking psychotropic medications. Overall, our results support a link between MDD and lower levels of anti-inflammatory, butyrate-producing bacteria, and may support a connection between the gut microbiota and the chronic, low-grade inflammation often observed in MDD patients.
Collapse
Affiliation(s)
- Richard T Liu
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA.
| | - Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Ana E Sheehan
- Department of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - Rachel F L Walsh
- Department of Psychology, Temple University, Philadelphia, PA, USA
| | - Christina M Sanzari
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| |
Collapse
|
19
|
Abstract
Circadian rhythm misalignment due to social jet lag, shift work, early morning starts, and delayed bedtimes is becoming common in our modern society. Disturbances of sleep and the underlying circadian rhythms are related to multiple human diseases, such as obesity, diabetes, cardiovascular disorders, and cognitive impairments. Given the crucial role of microbiota in the same pathologies as are caused by sleep disturbance, how the gut microbiota is affected by sleep is of increasing interest. The results of this study indicate that the acute circadian rhythm disturbance caused by sleep-wake shifts affect the human gut microbiota, especially the functional profiles of gut microbes and interactions among them. Further experiments with a longer-time-scale intervention and larger sample size are needed to assess the effects of chronic circadian rhythm disruption on the gut microbiome and to guide possible microbial therapies for clinical intervention in the related diseases. Disturbances of sleep and the underlying circadian rhythm are related to many human diseases, such as obesity, diabetes, cardiovascular disorders, and cognitive impairments. Dysbiosis of the gut microbiome has also been reported to be associated with the pathologies of these diseases. Therefore, we proposed that disturbed sleep may regulate gut microbiota homeostasis. In this study, we mimicked the sleep-wake cycle shift, one typical type of circadian rhythm disturbances in young people, in recruited subjects. We used 16S rRNA gene amplicon sequencing to define microbial taxa from their fecal samples. Although the relative abundances of the microbes were not significantly altered, the functional-profile analysis of gut microbiota revealed functions enriched during the sleep-wake cycle shift. In addition, the microbial networks were quite distinct among baseline, shift, and recovery stages. These results suggest that an acute sleep-wake cycle shift may exert a limited influence on the gut microbiome, mainly including the functional profiles of the microbes and the microbial relationships within the microbial community. IMPORTANCE Circadian rhythm misalignment due to social jet lag, shift work, early morning starts, and delayed bedtimes is becoming common in our modern society. Disturbances of sleep and the underlying circadian rhythms are related to multiple human diseases, such as obesity, diabetes, cardiovascular disorders, and cognitive impairments. Given the crucial role of microbiota in the same pathologies as are caused by sleep disturbance, how the gut microbiota is affected by sleep is of increasing interest. The results of this study indicate that the acute circadian rhythm disturbance caused by sleep-wake shifts affect the human gut microbiota, especially the functional profiles of gut microbes and interactions among them. Further experiments with a longer-time-scale intervention and larger sample size are needed to assess the effects of chronic circadian rhythm disruption on the gut microbiome and to guide possible microbial therapies for clinical intervention in the related diseases.
Collapse
|
20
|
Singh R, Haque MM, Mande SS. Lifestyle-Induced Microbial Gradients: An Indian Perspective. Front Microbiol 2019; 10:2874. [PMID: 31921052 PMCID: PMC6928055 DOI: 10.3389/fmicb.2019.02874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/28/2019] [Indexed: 02/06/2023] Open
Abstract
Introduction: Urbanization is a globally pervasive trend. Although urban settings provide better access to infrastructure and opportunities, urban lifestyles have certain negative consequences on human health. A number of recent studies have found interesting associations between the structure of human gut microbiota and the prevalence of metabolic conditions characterizing urban populations. The present study attempts to expand the footprint of these investigations to an Indian context. The objectives include elucidating specific patterns and gradients based on resident habitat and lifestyles (i.e., tribal and urban) that characterize gut microbial communities. Methods: Available 16S rRNA sequence datasets corresponding to the gut microbiota of urban and tribal populations from multiple regions of India have been rigorously compared. This analysis was carried out to understand the overall community structure, resident taxa, and their (inferred) functional components as well as their correlations with available meta-information. Results: The gut microbiota of urban and tribal communities are observed to have characteristically different signatures with respect to diversity as well as taxonomic and functional composition. Primarily, the gut microbiota in tribal communities is found to harbor significantly higher species diversity and richness as compared to that in urban populations. In spite of geographical segregation and diet-related differences, gut microbial diversity was not found to differ significantly between tribal groups. Furthermore, while the taxonomic profiles of different tribal communities cluster together irrespective of their geographic location, enterotype analysis indicates that samples from urban communities form two distinct clusters. Taxonomic analysis of samples in one of these clusters reveals the presence of microbes that are common to both urban and tribal cohorts, indicating a probable transient evolutionary state. Prevotella, previously reported to be the dominant genus resident in Indian gut microbiota, is found to have distinct OTUs and strain-specific oligotypes characterizing resident habitats and diet patterns. Certain interesting associations between microbial abundances and specific metadata have also been observed. Overall, urban lifestyle and diet appear to impact the structure and function of gut microbial communities, and the results of this study provide further evidence of this likely detrimental association. Conclusion: This study attempts to analyze, in an Indian context, the impact of urbanization on the human gut microbiota. Overall, the analysis elucidates interesting taxonomic and functional signatures characterizing the evolutionary transition in gut microbiota from tribal to urban.
Collapse
Affiliation(s)
- Rashmi Singh
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
| | | | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
| |
Collapse
|
21
|
Senapati T, Kothidar A, Banerjee SK, DAS B. Insights into the gastrointestinal tract microbiomes of Indian population. J Biosci 2019; 44:113. [PMID: 31719222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trillions of microbes living in the gastrointestinal tract (GIT) of the human body finely tune homeostatic equilibrium in the GIT ecosystem and encode key functionalities that play crucial role in host metabolic functions, synthesis of macro- and micronutrients, xenobiotics metabolisms, development of innate and adaptive immune systems, tissue and organ developments and resistance against invasion of enteric pathogens. The microbial diversity and richness of GIT ecosystem varies greatly between individuals and over time. Extent of taxonomic and functional variations in GIT ecosystem is linked with dietary habit, pharmaceuticals usages, age, sex, body mass index, ethnicity, geography, altitude and civilization. Understanding a holistic picture of GIT microbiome of healthy people living across geography and identifying population specific 'keystone' taxa is of immense importance for identifying microbial species that may provide protection against chronic and metabolic diseases. Knowledge on geographic or ethnicity specific microbial signatures may also help us to understand the varied efficacy of different drugs and vaccines in different population. India is the home of more than 1.36 billion people belonging to 2000 human communities residing in well distinct geography. In the present review, we discuss the microbial signatures in health and diseases of the rural and urban Indians living in sea level and high altitude areas.
Collapse
Affiliation(s)
- Tarosi Senapati
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121 001, India
| | | | | | | |
Collapse
|
22
|
Senapati T, Kothidar A, Banerjee SK, Das B. Insights into the gastrointestinal tract microbiomes of Indian population. J Biosci 2019. [DOI: 10.1007/s12038-019-9927-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
23
|
Dubey AK, Uppadhyaya N, Nilawe P, Chauhan N, Kumar S, Gupta UA, Bhaduri A. LogMPIE, pan-India profiling of the human gut microbiome using 16S rRNA sequencing. Sci Data 2018; 5:180232. [PMID: 30375992 PMCID: PMC6207063 DOI: 10.1038/sdata.2018.232] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/17/2018] [Indexed: 02/06/2023] Open
Abstract
The "Landscape Of Gut Microbiome - Pan-India Exploration", or LogMPIE study, is the first large-scale, nationwide record of the Indian gut microbiome. The primary objective of the study was to identify and map the Indian gut microbiome baseline. This observational study was conducted across 14 geographical locations in India. Enrolled subjects were uniformly distributed across geographies (north, east, west and south) and body mass index (obese and non-obese). Furthermore, factors influencing the microbiome, such as age and physical activity, were also considered in the study design. The LogMPIE study recorded data from 1004 eligible subjects and reported 993 unique microorganisms across the Indian microbiome diaspora. The data not only map the Indian gut microbiome baseline but also function as a useful resource to study, analyse and identify signatures characterizing the physiological dispositions of the subjects. Furthermore, they provide insight into the unique features describing the Indian microbiome. The data are open and may be accessed from the European Nucleotide Archive (ENA) portal of the European Bioinformatics Institute (https://www.ebi.ac.uk/ena/data/view/PRJEB25642).
Collapse
Affiliation(s)
- Ashok Kumar Dubey
- Innovation Center, Tata Chemicals Ltd, Ambedveth, Pune, Maharashtra, 412111, India
| | - Niyati Uppadhyaya
- Innovation Center, Tata Chemicals Ltd, Ambedveth, Pune, Maharashtra, 412111, India
| | - Pravin Nilawe
- Thermo Fisher Scientific, Invitrogen BioServices India Pvt Ltd, Mumbai, Maharashtra, 400076, India
| | - Neeraj Chauhan
- Thermo Fisher Scientific, Life Science Solutions, Gurgaon, Haryana, 122016, India
| | - Santosh Kumar
- JSS Medical Research India Pvt. Ltd, Faridabad, Haryana, 121003, India
| | | | - Anirban Bhaduri
- Innovation Center, Tata Chemicals Ltd, Ambedveth, Pune, Maharashtra, 412111, India
| |
Collapse
|
24
|
Kuntal BK, Chandrakar P, Sadhu S, Mande SS. 'NetShift': a methodology for understanding 'driver microbes' from healthy and disease microbiome datasets. ISME JOURNAL 2018; 13:442-454. [PMID: 30287886 DOI: 10.1038/s41396-018-0291-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 09/05/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022]
Abstract
The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called 'NetShift' to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as 'drivers' from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The 'NetShift' methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift.
Collapse
Affiliation(s)
- Bhusan K Kuntal
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Pune, 411 008, India
| | - Pranjal Chandrakar
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.,Decision Sciences, Indian Institute of Management Bangalore, Bannerghatta Road, Bengaluru, Karnataka, 560076, India
| | - Sudipta Sadhu
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.
| |
Collapse
|
25
|
Ogilvie LA, Nzakizwanayo J, Guppy FM, Dedi C, Diston D, Taylor H, Ebdon J, Jones BV. Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking. ISME JOURNAL 2017; 12:942-958. [PMID: 29259289 PMCID: PMC5864186 DOI: 10.1038/s41396-017-0015-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/06/2017] [Accepted: 11/11/2017] [Indexed: 12/28/2022]
Abstract
Just as the expansion in genome sequencing has revealed and permitted the exploitation of phylogenetic signals embedded in bacterial genomes, the application of metagenomics has begun to provide similar insights at the ecosystem level for microbial communities. However, little is known regarding this aspect of bacteriophage associated with microbial ecosystems, and if phage encode discernible habitat-associated signals diagnostic of underlying microbiomes. Here we demonstrate that individual phage can encode clear habitat-related 'ecogenomic signatures', based on relative representation of phage-encoded gene homologues in metagenomic data sets. Furthermore, we show the ecogenomic signature encoded by the gut-associated ɸB124-14 can be used to segregate metagenomes according to environmental origin, and distinguish 'contaminated' environmental metagenomes (subject to simulated in silico human faecal pollution) from uncontaminated data sets. This indicates phage-encoded ecological signals likely possess sufficient discriminatory power for use in biotechnological applications, such as development of microbial source tracking tools for monitoring water quality.
Collapse
Affiliation(s)
- Lesley A Ogilvie
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK.
| | | | - Fergus M Guppy
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
| | - Cinzia Dedi
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
| | - David Diston
- Mikrobiologische & Biotechnologische Risiken Bundesamt für Gesundheit BAG, 3003, Bern, Switzerland
| | - Huw Taylor
- School of Environment and Technology, University of Brighton, Brighton, UK
| | - James Ebdon
- School of Environment and Technology, University of Brighton, Brighton, UK
| | - Brian V Jones
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK.
| |
Collapse
|
26
|
Koleva PT, Tun HM, Konya T, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA, Kozyrskyj AL. Sex-specific impact of asthma during pregnancy on infant gut microbiota. Eur Respir J 2017; 50:50/5/1700280. [PMID: 29167295 PMCID: PMC5898939 DOI: 10.1183/13993003.00280-2017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 08/16/2017] [Indexed: 12/27/2022]
Abstract
Asthma during pregnancy is associated with retardation of fetal growth in a sex-specific manner. Lactobacilli microbes influence infant growth. This study aimed to determine whether lactobacilli and other microbes are reduced in the gut of infants born to an asthmatic mother, and whether this differs by the sex of the infant. Mother-infant pairs (N=1021) from the Canadian Healthy Infant Longitudinal Development full-term cohort were studied. The abundance of infant faecal microbiota at 3–4 months, profiled by gene sequencing, was compared between both women with and without asthma treatment during pregnancy. Infant sex, maternal ethnicity, pre-pregnancy overweight and atopy status, birth mode, breastfeeding status and intrapartum antibiotic treatment were tested as covariates. Independent of birth mode and other covariates, male, Caucasian infants born to women with prenatal asthma harboured fewer lactobacilli in the gut at 3–4 months of age. If asthmatic mothers had pre-pregnancy overweight, the abundance of Lactobacillus in males was further reduced in the infant gut, whereas the microbiota of female infants was enriched with Bacteroidaceae. Similar differences in infant gut microbial composition according to maternal prenatal asthma status were also more evident among women with food or environmental allergies. Gut lactobacilli were less abundant in male infants, but Bacteroidaceae were more abundant in female infants at 3–4 months of age, following maternal asthma during pregnancy. Gut lactobacilli are less abundant at 3–4 months in male but not female infants following maternal prenatal asthmahttp://ow.ly/jXnl30fU9xH
Collapse
Affiliation(s)
- Petya T Koleva
- Dept of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Hein M Tun
- Dept of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Theodore Konya
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - David S Guttman
- Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Allan B Becker
- Dept of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | | | - Stuart E Turvey
- Dept of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Padmaja Subbarao
- Dept of Pediatric Respiratory Medicine, University of Toronto, Toronto, ON, Canada
| | | | - James A Scott
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | | | | |
Collapse
|
27
|
Zabell A, Tang WHW. Targeting the Microbiome in Heart Failure. CURRENT TREATMENT OPTIONS IN CARDIOVASCULAR MEDICINE 2017; 19:27. [DOI: 10.1007/s11936-017-0528-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
28
|
Colorectal Carcinoma: A General Overview and Future Perspectives in Colorectal Cancer. Int J Mol Sci 2017; 18:ijms18010197. [PMID: 28106826 PMCID: PMC5297828 DOI: 10.3390/ijms18010197] [Citation(s) in RCA: 708] [Impact Index Per Article: 101.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/06/2017] [Accepted: 01/11/2017] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the fourth most common cause of cancer-related death. Most cases of CRC are detected in Western countries, with its incidence increasing year by year. The probability of suffering from colorectal cancer is about 4%–5% and the risk for developing CRC is associated with personal features or habits such as age, chronic disease history and lifestyle. In this context, the gut microbiota has a relevant role, and dysbiosis situations can induce colonic carcinogenesis through a chronic inflammation mechanism. Some of the bacteria responsible for this multiphase process include Fusobacterium spp, Bacteroides fragilis and enteropathogenic Escherichia coli. CRC is caused by mutations that target oncogenes, tumour suppressor genes and genes related to DNA repair mechanisms. Depending on the origin of the mutation, colorectal carcinomas can be classified as sporadic (70%); inherited (5%) and familial (25%). The pathogenic mechanisms leading to this situation can be included in three types, namely chromosomal instability (CIN), microsatellite instability (MSI) and CpG island methylator phenotype (CIMP). Within these types of CRC, common mutations, chromosomal changes and translocations have been reported to affect important pathways (WNT, MAPK/PI3K, TGF-β, TP53), and mutations; in particular, genes such as c-MYC, KRAS, BRAF, PIK3CA, PTEN, SMAD2 and SMAD4 can be used as predictive markers for patient outcome. In addition to gene mutations, alterations in ncRNAs, such as lncRNA or miRNA, can also contribute to different steps of the carcinogenesis process and have a predictive value when used as biomarkers. In consequence, different panels of genes and mRNA are being developed to improve prognosis and treatment selection. The choice of first-line treatment in CRC follows a multimodal approach based on tumour-related characteristics and usually comprises surgical resection followed by chemotherapy combined with monoclonal antibodies or proteins against vascular endothelial growth factor (VEGF) and epidermal growth receptor (EGFR). Besides traditional chemotherapy, alternative therapies (such as agarose tumour macrobeads, anti-inflammatory drugs, probiotics, and gold-based drugs) are currently being studied to increase treatment effectiveness and reduce side effects.
Collapse
|