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Aktas B, Aslim B, Ozdemir DA. A neurotherapeutic approach with Lacticaseibacillus rhamnosus E9 on gut microbiota and intestinal barrier in MPTP-induced mouse model of Parkinson's disease. Sci Rep 2024; 14:15460. [PMID: 38965287 PMCID: PMC11224381 DOI: 10.1038/s41598-024-65061-w] [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: 02/01/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024] Open
Abstract
The gut microbiota plays a crucial role in neural development and progression of neural disorders like Parkinson's disease (PD). Probiotics have been suggested to impact neurodegenerative diseases via gut-brain axis. This study aims to investigate the therapeutic potential of Lacticaseibacillus rhamnosus E9, a high exopolysaccharide producer, on 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine(MPTP)-induced mouse model of PD. C57BL/6 mice subjected to MPTP were fed L. rhamnosus E9 for fifteen days and sacrificed after the last administration. Motor functions were determined by open-field, catalepsy, and wire-hanging tests. The ileum and the brain tissues were collected for ELISA, qPCR, and immunohistochemistry analyses. The cecum content was obtained for microbiota analysis. E9 supplementation alleviated MPTP-induced motor dysfunctions accompanied by decreased levels of striatal TH and dopamine. E9 also reduced the level of ROS in the striatum and decreased the DAT expression while increasing the DR1. Furthermore, E9 improved intestinal integrity by enhancing ZO-1 and Occludin levels and reversed the dysbiosis of the gut microbiota induced by MPTP. In conclusion, E9 supplementation improved the MPTP-induced motor deficits and neural damage as well as intestinal barrier by modulating the gut microbiota in PD mice. These findings suggest that E9 supplementation holds therapeutic potential in managing PD through the gut-brain axis.
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Affiliation(s)
- Busra Aktas
- Department of Molecular Biology and Genetics, Burdur Mehmet Akif Ersoy University, Burdur, 15200, Turkey.
| | - Belma Aslim
- Department of Biology, Faculty of Science, Gazi University, Ankara, 06500, Turkey
| | - Deniz Ates Ozdemir
- Department of Pathology, Faculty of Medicine, Hacettepe University, Ankara, 06230, Turkey
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2
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Wang KY, Zhong XQ. Overview of relationship between intestinal flora imbalance and diseases. WORLD CHINESE JOURNAL OF DIGESTOLOGY 2024; 32:280-284. [DOI: 10.11569/wcjd.v32.i4.280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
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3
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Guo L, Liu Q, Yin X. Clostridiales in the Gut Against Listeria monocytogenes Infection Through Growth Inhibition. Foodborne Pathog Dis 2024; 21:248-256. [PMID: 38150235 DOI: 10.1089/fpd.2023.0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Listeria monocytogenes (Lm) mainly infect pregnant women, children, the elderly, and other populations with low immunity causing septicemia and meningitis. Healthy people can tolerate higher doses of Lm and only cause gastrointestinal symptoms such as abdominal pain and diarrhea after infection. Compared to the above population, healthy people have a richer and more diverse gut microbiota. In this study, we show that the microbiota in the large intestine and the feces of mice can significantly inhibit the growth of Lm compared to the microbiota in the small intestine. Bacteria larger than 1 μm in the gut microbiota play an important role in inhibiting Lm growth. 16s rRNA sequencing results show that these bacteria are mainly composed of Clostridiales under the phylum Firmicutes, including Ruminiclostridium, Butyricicoccus, Lachnoclostridium, Roseburia, Coprooccus, and Blautia. Thus, we demonstrate that there are some potential functional bacteria in the gut microbiota that can increase resistance against Lm.
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Affiliation(s)
- Liang Guo
- Zaozhuang University, Shandong, China
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qing Liu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
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4
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Abstract
Biogeography is the study of species distribution and diversity within an ecosystem and is at the core of how we understand ecosystem dynamics and interactions at the macroscale. In gut microbial communities, a historical reliance on bulk sequencing to probe community composition and dynamics has overlooked critical processes whereby microscale interactions affect systems-level microbiota function and the relationship with the host. In recent years, higher-resolution sequencing and novel single-cell level data have uncovered an incredible heterogeneity in microbial composition and have enabled a more nuanced spatial understanding of the gut microbiota. In an era when spatial transcriptomics and single-cell imaging and analysis have become key tools in mammalian cell and tissue biology, many of these techniques are now being applied to the microbiota. This fresh approach to intestinal biogeography has given important insights that span temporal and spatial scales, from the discovery of mucus encapsulation of the microbiota to the quantification of bacterial species throughout the gut. In this Review, we highlight emerging knowledge surrounding gut biogeography enabled by the observation and quantification of heterogeneity across multiple scales.
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Affiliation(s)
- Giselle McCallum
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carolina Tropini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
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5
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Martín R, Rios-Covian D, Huillet E, Auger S, Khazaal S, Bermúdez-Humarán LG, Sokol H, Chatel JM, Langella P. Faecalibacterium: a bacterial genus with promising human health applications. FEMS Microbiol Rev 2023; 47:fuad039. [PMID: 37451743 PMCID: PMC10410495 DOI: 10.1093/femsre/fuad039] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/08/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
In humans, many diseases are associated with alterations in gut microbiota, namely increases or decreases in the abundance of specific bacterial groups. One example is the genus Faecalibacterium. Numerous studies have underscored that low levels of Faecalibacterium are correlated with inflammatory conditions, with inflammatory bowel disease (IBD) in the forefront. Its representation is also diminished in the case of several diseases, including colorectal cancer (CRC), dermatitis, and depression. Additionally, the relative presence of this genus is considered to reflect, at least in part, intestinal health status because Faecalibacterium is frequently present at reduced levels in individuals with gastrointestinal diseases or disorders. In this review, we first thoroughly describe updates to the taxonomy of Faecalibacterium, which has transformed a single-species taxon to a multispecies taxon over the last decade. We then explore the links discovered between Faecalibacterium abundance and various diseases since the first IBD-focused studies were published. Next, we examine current available strategies for modulating Faecalibacterium levels in the gut. Finally, we summarize the mechanisms underlying the beneficial effects that have been attributed to this genus. Together, epidemiological and experimental data strongly support the use of Faecalibacterium as a next-generation probiotic (NGP) or live biotherapeutic product (LBP).
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Affiliation(s)
- Rebeca Martín
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - David Rios-Covian
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Eugénie Huillet
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sandrine Auger
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sarah Khazaal
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Luis G Bermúdez-Humarán
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Harry Sokol
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, F-75012 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, F-75012, Paris, France
| | - Jean-Marc Chatel
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Philippe Langella
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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6
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Luu HN, Tran CTD, Wang R, Nguyen MVT, Tran MT, Tuong TTV, Tran QH, Le LC, Pham HTT, Vu HH, Bui NC, Ha HTT, Trinh DT, Thomas CE, Adams-Haduch J, Velikokhatnaya L, Schoen RE, Xie G, Jia W, Boffetta P, Clemente JC, Yuan JM. Associations between Ileal Juice Bile Acids and Colorectal Advanced Adenoma. Nutrients 2023; 15:2930. [PMID: 37447256 DOI: 10.3390/nu15132930] [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: 05/17/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND There is an urgent need to identify biomarkers for advanced adenoma, an important precursor of colorectal cancer (CRC). We aimed to determine alterations in ileal juice bile acids associated with colorectal advanced adenoma. METHODS We quantified a comprehensive panel of primary and secondary bile acids and their conjugates using an ultraperformance liquid chromatography triple-quadrupole mass spectrometric assay in ileal juice collected at colonoscopy from 46 study subjects (i.e., 14 biopsy-confirmed advanced adenomas and 32 controls free of adenoma or cancer). Using analysis of covariance (ANCOVA), we examined the differences in bile acid concentrations by disease status, adjusting for age, sex, body mass index, smoking status and type 2 diabetes. RESULTS The concentrations of hyodeoxycholic acid (HCA) species in ileal juice of the advanced adenoma patients (geometric mean = 4501.9 nM) were significantly higher than those of controls (geometric mean = 1292.3 nM, p = 0.001). The relative abundance of ursodeoxycholic acid (UDCA) in total bile acids was significantly reduced in cases than controls (0.73% in cases vs. 1.33% in controls; p = 0.046). No significant difference between cases and controls was observed for concentrations of total or specific primary bile acids (i.e., cholic acid (CA), chenodeoxycholic acid (CDCA) and their glycine- and taurine-conjugates) and total and specific major secondary bile acids (i.e., deoxycholic acid and lithocholic acid). CONCLUSIONS Colorectal advanced adenoma was associated with altered bile acids in ileal juice. The HCA species may promote the development of colorectal advanced adenoma, whereas gut microbiota responsible for the conversion of CDCA to UDCA may protect against it. Our findings have important implications for the use of bile acids as biomarkers in early detection of colorectal cancer.
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Affiliation(s)
- Hung N Luu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Chi Thi-Du Tran
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
- College of Health Sciences, VinUniversity (VinUni), Hanoi 10000, Vietnam
- Center of Applied Sciences, Regenerative Medicine and Advanced Technologies, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Renwei Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Mai Vu-Tuyet Nguyen
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Mo Thi Tran
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Thuy Thi-Van Tuong
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Quang Hong Tran
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Linh Cu Le
- College of Health Sciences, VinUniversity (VinUni), Hanoi 10000, Vietnam
| | - Huong Thi-Thu Pham
- Department of Gastroenterology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Hien Huy Vu
- Department of Gastroenterology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Nam Chi Bui
- Department of Gastroenterology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Hien Thi-Thu Ha
- Department of Cytopathology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Dung Tuan Trinh
- Department of Cytopathology, Vinmec Healthcare System, Hanoi 10000, Vietnam
- Department of Cytopathology, Tam Anh General Hospital, Hanoi 10000, Vietnam
| | - Claire E Thomas
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | | | | | - Robert E Schoen
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Guoxiang Xie
- University of Hawai'i Cancer Center, University of Hawaii, Honolulu, HI 96813, USA
| | - Wei Jia
- University of Hawai'i Cancer Center, University of Hawaii, Honolulu, HI 96813, USA
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Jose C Clemente
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian-Min Yuan
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
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7
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MIRMOHAMMADALI SN, ROSENKRANZ SK. Dietary phytochemicals, gut microbiota composition, and health outcomes in human and animal models. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 42:152-171. [PMID: 37404568 PMCID: PMC10315191 DOI: 10.12938/bmfh.2022-078] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/17/2023] [Indexed: 07/06/2023]
Abstract
The role of the composition of the gut microbiota on human health is not well understood. However, during the past decade, an increased emphasis has been placed on the influence of the impact of nutrition on the composition of gut microbiota and how the gut microbiota affects human health. The current review focuses on the role of some of the most studied phytochemicals on the composition of the gut microbiota. First, the review highlights the state of the research evidence regarding dietary phytochemical consumption and gut microbiota composition, including the influence of phytochemicals such as polyphenols, glucosinolates, flavonoids, and sterols that are present in vegetables, nuts, beans, and other foods. Second, the review identifies changes in health outcomes with altered gut microbiota composition, in both animal and human model studies. Third, the review highlights research that includes both associations between dietary phytochemical consumption and gut microbiota composition, and associations between the gut microbiota composition and health outcomes, in order to elucidate the role of the gut microbiota in the relationship between dietary phytochemical consumption and health outcomes in humans and animals. The current review indicated that phytochemicals can beneficially alter gut microbiota composition and decrease the risk for some diseases, such as cancers, and improve some cardiovascular and metabolic risk biomarkers. There is an urgent demand for high-quality studies that determine the relationships between the consumption of phytochemicals and health outcomes, examining gut microbiota as a moderator or mediator.
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Affiliation(s)
- Seyedeh Nooshan MIRMOHAMMADALI
- Department of Food, Nutrition, Dietetics and Health, Kansas
State University, 110 Anderson Hall, 919 Mid-Campus Drive North, Manhattan, KS 66506-0110,
USA
| | - Sara K. ROSENKRANZ
- Department of Kinesiology and Nutrition Sciences, University
of Nevada Las Vegas, 4505 S. Maryland Pkwy, Las Vegas, NV 89154, USA
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8
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Levitan O, Ma L, Giovannelli D, Burleson DB, McCaffrey P, Vala A, Johnson DA. The gut microbiome–Does stool represent right? Heliyon 2023; 9:e13602. [PMID: 37101508 PMCID: PMC10123208 DOI: 10.1016/j.heliyon.2023.e13602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Many stool-based gut microbiome studies have highlighted the importance of the microbiome. However, we hypothesized that stool is a poor proxy for the inner-colonic microbiome and that studying stool samples may be inadequate to capture the true inner-colonic microbiome. To test this hypothesis, we conducted prospective clinical studies with up to 20 patients undergoing an FDA-cleared gravity-fed colonic lavage without oral purgative pre-consumption. The objective of this study was to present the analysis of inner-colonic microbiota obtained non-invasively during the lavage and how these results differ from stool samples. The inner-colonic samples represented the descending, transverse, and ascending colon. All samples were analyzed for 16S rRNA and shotgun metagenomic sequences. The taxonomic, phylogenetic, and biosynthetic gene cluster analyses showed a distinctive biogeographic gradient and revealed differences between the sample types, especially in the proximal colon. The high percentage of unique information found only in the inner-colonic effluent highlights the importance of these samples and likewise the importance of collecting them using a method that can preserve these distinctive signatures. We proposed that these samples are imperative for developing future biomarkers, targeted therapeutics, and personalized medicine.
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9
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Aktas B. Gut Microbial Alteration in MPTP Mouse Model of Parkinson Disease is Administration Regimen Dependent. Cell Mol Neurobiol 2023:10.1007/s10571-023-01319-7. [PMID: 36708421 PMCID: PMC9883829 DOI: 10.1007/s10571-023-01319-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/18/2023] [Indexed: 01/29/2023]
Abstract
Parkinson Disease (PD) is one of the most common neurodegenerative disorders characterized by loss of dopaminergic neurons involved in motor functions. Growing evidence indicates that gut microbiota communicates with the brain known as the gut-brain axis (GBA). Mitochondrial toxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is commonly used in animal studies to investigate the GBA in PD. Various MPTP administration regimens are performed in PD mouse models involving one to multiple injections in 1 day or one injection per day for several days. The aim of this study is to investigate if the impact of MPTP on gut microbiota differs depending on the administration regimen. C57BL/6 mice were treated with acute or subchronic regimens of MPTP. Motor functions were assessed by open-field, catalepsy, and wire hanging tests. The cecum and the brain samples were obtained for microbiota and gene expression analyses, respectively. MPTP administration regimens differed in their ability to alter the gut microbiota. Firmicutes and Bacteroidota were both increased in subchronic mice while did not change and decreased, respectively, in acute mice. Verrucomicrobiota was elevated in acute MPTP mice but dropped in subchronic MPTP mice. Muribaculaceae was the predominant genus in all groups but acute mice. In acute mice, Akkermansia was increased and Colidextribacter was decreased; however, they showed an opposite trend in subchronic mice. These data suggest that MPTP mouse model cause a gut microbiota dysbiosis in an administration regimen dependent manner, and it is important to take consideration of mouse model to investigate the GBA in neurodegenerative diseases including PD.
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Affiliation(s)
- Busra Aktas
- Department of Molecular Biology and Genetics, Burdur Mehmet Akif Ersoy University Burdur, 15030 Burdur, Turkey
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10
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Johnson KVA, Watson KK, Dunbar RIM, Burnet PWJ. Sociability in a non-captive macaque population is associated with beneficial gut bacteria. Front Microbiol 2022; 13:1032495. [PMID: 36439813 PMCID: PMC9691693 DOI: 10.3389/fmicb.2022.1032495] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 11/12/2022] Open
Abstract
The relationship between social behaviour and the microbiome is known to be reciprocal. Research in wild animal populations, particularly in primate social groups, has revealed the role that social interactions play in microbial transmission, whilst studies in laboratory animals have demonstrated that the gut microbiome can affect multiple aspects of behaviour, including social behaviour. Here we explore behavioural variation in a non-captive animal population with respect to the abundance of specific bacterial genera. Social behaviour based on grooming interactions is assessed in a population of rhesus macaques (Macaca mulatta), and combined with gut microbiome data. We focus our analyses on microbiome genera previously linked to sociability and autistic behaviours in rodents and humans. We show in this macaque population that some of these genera are also related to an individual's propensity to engage in social interactions. Interestingly, we find that several of the genera positively related to sociability, such as Faecalibacterium, are well known for their beneficial effects on health and their anti-inflammatory properties. In contrast, the genus Streptococcus, which includes pathogenic species, is more abundant in less sociable macaques. Our results indicate that microorganisms whose abundance varies with individual social behaviour also have functional links to host immune status. Overall, these findings highlight the connections between social behaviour, microbiome composition, and health in an animal population.
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Affiliation(s)
- Katerina V.-A. Johnson
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom,Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom,*Correspondence: Katerina V.-A. Johnson,
| | - Karli K. Watson
- Institute of Cognitive Science, University of Colorado Boulder, Boulder, CO, United States
| | - Robin I. M. Dunbar
- Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom
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11
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Pan X, Cai Y, Kong L, Xiao C, Zhu Q, Song Z. Probiotic Effects of Bacillus licheniformis DSM5749 on Growth Performance and Intestinal Microecological Balance of Laying Hens. Front Nutr 2022; 9:868093. [PMID: 35571886 PMCID: PMC9093703 DOI: 10.3389/fnut.2022.868093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/18/2022] [Indexed: 12/17/2022] Open
Abstract
This study was conducted to investigate the effects of Bacillus licheniformis DSM5749 on the production performance and intestinal health in laying hens. A total of 32-week-old laying hens (Hyline Brown) were randomly assigned to two dietary groups (10 replicates of 27 laying hens), namely, basal diet and basal diet complemented with 200 g/t B. licheniformis (3.2 × 109 CFU/kg). The trial lasted for 8 weeks, and samples were collected at the last week. Results revealed that B. licheniformis DSM5749 significantly improved laying performance, including an increase in egg production rate and average daily egg yield, and a decrease in the feed-to-egg ratio during the entire 8-week experimental period (P < 0.05). B. licheniformis DSM5749 increased the levels of superoxide dismutase and glutathione peroxidase in the liver and decreased the IL-1 level in the serum (P < 0.05). In addition, the integrity of intestinal morphology (villus height, crypt depth, and villus height/crypt depth), tight junctions (ZO-1, Claudin-1, and Occludin), and lipase vitality in the intestine were potentiated by B. licheniformis DSM5749 in laying hens (P < 0.05). B. licheniformis DSM5749 decreased the Firmicutes/Bacteroidetes ratio (P < 0.05) in the cecum. Furthermore, B. licheniformis DSM5749 modulated the microbiota in the cecum of the laying hens, increased the relative abundance of beneficial bacteria (e.g., Prevotella) at the genus level and decreased the relative abundance of potential pathogens (e.g., Desulfovibrio). In conclusion, B. licheniformis DSM5749 can improve laying performance, promote intestinal health, affect the composition of cecal microorganisms, and regulate the intestinal micro-ecological balance, making B. licheniformis a good probiotic candidate for application in the laying hens industry.
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Affiliation(s)
- Xue Pan
- Department of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Yuanli Cai
- College of Life Science, Qilu Normal University, Jinan, China
| | - Linglian Kong
- Department of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Chuanpi Xiao
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Qidong Zhu
- Department of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Zhigang Song
- Department of Animal Science and Technology, Shandong Agricultural University, Taian, China
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12
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Maioli TU, Borras-Nogues E, Torres L, Barbosa SC, Martins VD, Langella P, Azevedo VA, Chatel JM. Possible Benefits of Faecalibacterium prausnitzii for Obesity-Associated Gut Disorders. Front Pharmacol 2021; 12:740636. [PMID: 34925006 PMCID: PMC8677946 DOI: 10.3389/fphar.2021.740636] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
Metabolic disorders are an increasing concern in the industrialized world. Current research has shown a direct link between the composition of the gut microbiota and the pathogenesis of obesity and diabetes. In only a few weeks, an obesity-inducing diet can lead to increased gut permeability and microbial dysbiosis, which contributes to chronic inflammation in the gut and adipose tissues, and to the development of insulin resistance. In this review, we examine the interplay between gut inflammation, insulin resistance, and the gut microbiota, and discuss how some probiotic species can be used to modulate gut homeostasis. We focus primarily on Faecalibacterium prausnitzii, a highly abundant butyrate-producing bacterium that has been proposed both as a biomarker for the development of different gut pathologies and as a potential treatment due to its production of anti-inflammatory metabolites.
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Affiliation(s)
- Tatiani Uceli Maioli
- Departamento de Nutrição, Escola de Enfermagem, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Université Paris Saclay, INRAE, AgroParisTech, Micalis, Jouy-en-Josas, France
| | | | - Licia Torres
- Programa de Pós-Graduação em Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sara Candida Barbosa
- Programa de Pós-Graduação em Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vinicius Dantas Martins
- Programa de Pós-Graduação em Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Philippe Langella
- Université Paris Saclay, INRAE, AgroParisTech, Micalis, Jouy-en-Josas, France
| | - Vasco Ariston Azevedo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jean-Marc Chatel
- Université Paris Saclay, INRAE, AgroParisTech, Micalis, Jouy-en-Josas, France
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13
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Kim D, Jung JY, Oh HS, Jee SR, Park SJ, Lee SH, Yoon JS, Yu SJ, Yoon IC, Lee HS. Comparison of sampling methods in assessing the microbiome from patients with ulcerative colitis. BMC Gastroenterol 2021; 21:396. [PMID: 34686128 PMCID: PMC8614001 DOI: 10.1186/s12876-021-01975-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background Dysbiosis of ulcerative colitis (UC) has been frequently investigated using readily accessible stool samples. However, stool samples might insufficiently represent the mucosa-associated microbiome status. We hypothesized that luminal contents including loosely adherent luminal bacteria after bowel preparation may be suitable for diagnosing the dysbiosis of UC. Methods This study included 16 patients with UC (9 men and 7 women, mean age: 52.13 ± 14.09 years) and 15 sex- and age-matched healthy individuals (8 men and 7 women, mean age: 50.93 ± 14.11 years). They donated stool samples before colonoscopy and underwent luminal content aspiration and endoscopic biopsy during the colonoscopy. Then, the composition of each microbiome sample was analyzed by 16S rRNA-based next-generation sequencing. Results The microbiome between stool, luminal contents, and biopsy was significantly different in alpha and beta diversities. However, a correlation existed between stool and luminal contents in the Procrustes test (p = 0.001) and Mantel test (p = 0.0001). The stool microbiome was different between patients with UC and the healthy controls. Conversely, no difference was found in the microbiome of luminal content and biopsy samples between the two subject groups. The microbiome of stool and lavage predicted UC, with AUC values of 0.85 and 0.81, respectively. Conclusion The microbiome of stool, luminal contents, and biopsy was significantly different. However, the microbiome of luminal contents during colonoscopy can predict UC, with AUC values of 0.81. Colonoscopic luminal content aspiration analysis could determine microbiome differences between patients with UC and the healthy control, thereby beneficial in screening dysbiosis via endoscopy. Trial registration: This trial was registered at http://cris.nih.go.kr. Registration No.: KCT0003352), Date: 2018–11-13.
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Affiliation(s)
- Dan Kim
- Department of Internal Medicine, Inje University College of Medicine, Busan Paik Hospital, 75 Bokji-ro, Busanjin-gu, Busan, 47392, Korea
| | - Jun-Young Jung
- Department of Internal Medicine, Inje University College of Medicine, Busan Paik Hospital, 75 Bokji-ro, Busanjin-gu, Busan, 47392, Korea
| | - Hyun-Seok Oh
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea.,ChunLab Inc, Seoul, 06725, Korea
| | - Sam-Ryong Jee
- Department of Internal Medicine, Inje University College of Medicine, Busan Paik Hospital, 75 Bokji-ro, Busanjin-gu, Busan, 47392, Korea
| | - Sung Jae Park
- Department of Internal Medicine, Inje University College of Medicine, Busan Paik Hospital, 75 Bokji-ro, Busanjin-gu, Busan, 47392, Korea
| | - Sang-Heon Lee
- Department of Internal Medicine, Inje University College of Medicine, Busan Paik Hospital, 75 Bokji-ro, Busanjin-gu, Busan, 47392, Korea
| | - Jun-Sik Yoon
- Department of Internal Medicine, Inje University College of Medicine, Busan Paik Hospital, 75 Bokji-ro, Busanjin-gu, Busan, 47392, Korea
| | - Seung Jung Yu
- Department of Internal Medicine, Inje University College of Medicine, Busan Paik Hospital, 75 Bokji-ro, Busanjin-gu, Busan, 47392, Korea
| | - In-Cheol Yoon
- Department of Gastroenterology, Myongji Hospital, Hanyang University College of Medicine, Goyang, Korea
| | - Hong Sub Lee
- Department of Internal Medicine, Inje University College of Medicine, Busan Paik Hospital, 75 Bokji-ro, Busanjin-gu, Busan, 47392, Korea.
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14
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Propensity score-matched comparison between totally laparoscopic right hemicolectomy with transcolonic natural orifice specimen extraction and conventional laparoscopic surgery with mini-laparotomy in the treatment of ascending colon cancer (with video). Gastrointest Endosc 2021; 94:642-650. [PMID: 33798538 DOI: 10.1016/j.gie.2021.03.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/21/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Now that the debate about the safety and effectiveness of laparoscopic versus open surgery is over, attention has turned to innovations that can verify whether minimizing the impact of laparoscopy on the abdominal wall can further reduce pain, improve patient comfort, lead to superior cosmesis, and reduce morbidity. The aim of this study was to further explore the application value of totally laparoscopic right hemicolectomy with transcolonic natural orifice specimen extraction (NOSE) and to evaluate the short-term efficacy of transcolonic NOSE surgery for resecting specimens of ascending colon cancer. METHODS From January 2016 to May 2017, a retrospective study was conducted in Guangxi. Propensity score matching was used to minimize the bias from nonrandomized treatment assignment. Patients were followed up through May 2020. RESULTS Forty-nine patients underwent totally laparoscopic right hemicolectomy with transcolonic NOSE and 116 patients laparoscopic right hemicolectomy with mini-laparotomy (ML) procedures at our institution. After propensity score matching, each group included 45 patients, and all covariate imbalances were alleviated. The transcolonic NOSE group and the ML group did not differ significantly in terms of baseline clinical characteristics. The transcolonic NOSE group was associated with a shorter time to first flatus (NOSE vs ML: 1.8 ± .5 vs 3.2 ± .8, P = .032), a shorter length of hospital stay (11.3 ± 2.5 days vs 13.0 ± 3.1 days, P = .034), a shorter time to first liquid intake (2.6 ± .8 vs 3.8 ± .9, P = .068), less pain (1.8 ± .8 vs 4.2 ± .7, P = .013), less analgesia requirement (6 [13.3%] vs 21 [46.7%], P = .001), and lower C-reactive protein levels on postoperative day 1 (3.6 ± 1.7 vs 8.2 ± 2.2, P = .001) and postoperative day 3 (NOSE 2.4 ± 1.4 vs M: 4.6 ± 1.7 [P = .013]) than the ML group. The median follow-up was 28.4 months (interquartile range, 18.0-36.0). The 3-year overall survival rates were similar between the transcolonic NOSE group and the ML group. CONCLUSIONS In total, laparoscopic right hemicolectomy with transcolonic specimen extraction appears to be safe for selected patients with ascending colon cancer as a minimally invasive surgery.
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15
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Greathouse KL, Padgett RN, Petrosino J, Hastings-Tolsma M, Faucher MA. Exploration of Diet Quality by Obesity Severity in Association with Gestational Weight Gain and Distal Gut Microbiota in Pregnant African American Women: Opportunities for Intervention. Matern Child Health J 2021; 26:882-894. [PMID: 34462812 DOI: 10.1007/s10995-021-03198-0] [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] [Accepted: 06/13/2021] [Indexed: 01/29/2023]
Abstract
OBJECTIVE To conduct an exploratory examination of dietary patterns and quality during pregnancy in African-American women who were class I, II, or III obese, and those women with normal pre-pregnancy body mass index (pBMI), as well to identify dietary factors associated with GWG, and changes in the distal gut microbiome. African American women represent the largest group affected by pre-pregnancy obesity, a risk factor for several adverse birth outcomes. METHODS This prospective study investigated the association between diet, distal gut microbiome, and GWG among African-American women (n = 21) with obesity (n = 15) compared to women with a normal pre-pregnancy body mass index (pBMI) (n = 6) at two time points, 27-29 and 37-39 weeks gestation. Dietary patterns associated with obesity severity and GWG gain were assessed using Welch's T-test and Mann-Whitney U. The association between the gut microbiome and dietary patterns was assessed using a regression-based kernel association test and the adaptive microbiome-based sum of powered score test. RESULTS In early pregnancy, dietary intake of Total Fruits and Greens and Beans was significantly different between pBMI and GWG groups; significance was 0.022 and 0.028 respectively. Women with Class II/III obesity and those with GWG above guidelines had Healthy Eating Index (HEI) scores below 50, meeting less than 75% of dietary guidelines, and did not meet recommendations for fruit and vegetable or fiber intake. We found no significant associations between the microbiome composition and diet (HEI Scores). CONCLUSIONS FOR PRACTICE Overall, the results indicate that women with pBMI obesity are not meeting minimum dietary guidelines for nutrient intakes during pregnancy, specifically fruits, vegetables, and fiber, regardless of GWG. Interventions for African-American women with pre-pregnancy obesity, with a focus on increasing consumption of fruits and vegetables, would be beneficial to control GWG and improve birth outcomes.
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Affiliation(s)
- K Leigh Greathouse
- Nutrition Science, Baylor University, One Bear Place 97346, Waco, TX, 76798-7346, USA. .,Department of Biology, Baylor University, One Bear Place 97346, Waco, TX, 76798-7346, USA.
| | - R Noah Padgett
- Educational Psychology, Baylor University, One Bear Place 97346, Waco, TX, 76798-7346, USA
| | - Joseph Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - M Hastings-Tolsma
- Louise Herrington School of Nursing, Dallas, TX; Midwifery Specialty, Baylor University, 333 N. Washington Ave., Dallas, TX, USA
| | - M A Faucher
- Advanced Practice Nursing Women's Centers, Parkland Health and Hospital System, 5200 Harry Hines Boulevard, Dallas, TX, 75235, USA
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16
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Wang Z, Lai Z, Zhang X, Huang P, Xie J, Jiang Q, Zhang Q, Chung KF. Altered gut microbiome compositions are associated with the severity of asthma. J Thorac Dis 2021; 13:4322-4338. [PMID: 34422359 PMCID: PMC8339736 DOI: 10.21037/jtd-20-2189] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/31/2021] [Indexed: 12/31/2022]
Abstract
Background Despite substantial evidence on the contribution of the diversity of the gut microbiome to the pathogenesis of asthma and allergic diseases, little is known about their relationship with asthma severity and/or clinical phenotypes. We analyzed the difference in composition of the gut microbiome between subjects with asthma and healthy subjects and explored its role in the development of asthma. Methods Fecal samples from 15 subjects with severe asthma (SA), 14 with non-severe asthma (NSA), and 15 healthy subjects were assessed by 16S ribosomal RNA gene sequencing methods to identify the gut bacterial composition. Results Compared with those in the NSA group, patients in the SA group had a higher dose of inhaled corticosteroids, and there were more atopic subjects (60% vs. 35.7%, respectively). No significant differences were found at the phylum level either in operational taxonomic unit numbers or in diversity scores among the SA, NSA, and healthy groups. However, at the family level, the relative abundance of Acidaminococcaceae in the SA group was remarkedly lower than that in the group with healthy subjects (P<0.05). Furthermore, Veillonellaceae and Prevotellaceae were significantly more common in samples from the SA group than in those from the NSA group (P<0.05). In the SA group, positive correlations were observed between the relative abundance of Veillonellaceae and mid-expiratory flow 25% (MEF25%) predicted (r=0.538, P=0.047), as well as between the relative abundance of Acidaminococcaceae and body mass index (r=0642, P=0.010). Principal component analysis suggested that the relative abundances of Acidaminococcaceae and Prevotellaceae were associated with severe asthma. Moreover, we found that class Betaproteobacteria, order Burkholderiales, and family Alcaligenaceae were significantly different among the groups defined by serum immunoglobulin E (IgE) levels. Conclusions Our findings suggest that altered gut microbiome compositions are involved in the severity of asthma and that there are specific bacteria related to different asthma phenotypes in terms of serum IgE levels.
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Affiliation(s)
- Zhiqiang Wang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Hexian Memorial Hospital of PanYu District, Guangzhou, China
| | - Zhengdao Lai
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Dongguan Institute of Respiratory and Critical Care Medicine, Afliated Dongguan People's Hospital, Southern Medicial University, Dongguan, China
| | - Xiaoxian Zhang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Peikai Huang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Respiration Medicine, Huizhou Municipal Central Hospital, Huizhou, China
| | - Jiaxing Xie
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qian Jiang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qingling Zhang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kian Fan Chung
- National Heart & Lung Institute, Imperial College London & Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, UK
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17
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Yoon K, Kim N. Roles of Sex Hormones and Gender in the Gut Microbiota. J Neurogastroenterol Motil 2021; 27:314-325. [PMID: 33762473 PMCID: PMC8266488 DOI: 10.5056/jnm20208] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/16/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
The distribution of gut microbiota varies according to age (childhood, puberty, pregnancy, menopause, and old age) and sex. Gut microbiota are known to contribute to gastrointestinal (GI) diseases such as irritable bowel syndrome, inflammatory bowel disease, and colon cancer; however, the exact etiology remains elusive. Recently, sex and gender differences in GI diseases and their relation to gut microbiota has been suggested. Furthermore, the metabolism of estrogen and androgen was reported to be related to the gut microbiome. As gut microbiome is involved in the excretion and circulation process of sex hormones, the concept of “microgenderome” indicating the role of sex hormone on the gut microbiota has been suggested. However, further research is needed for this concept to be universally accepted. In this review, we summarize sex- and gender-differences in gut microbiota and the interplay of microbiota and GI diseases, focusing on sex hormones. We also describe the metabolic role of the microbiota in this regard. Finally, current subjects, such as medication including probiotics, are briefly discussed.
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Affiliation(s)
- Kichul Yoon
- Department of Internal Medicine, Wonkwang University Sanbon Medical Center, Gunpo, Gyeonggi-do, Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, Korea.,Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
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18
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Cataldo MA, Granata G, D'Arezzo S, Tonziello G, Vulcano A, De Giuli C, Meledandri M, Di Caro A, Petrosillo N. Hospitalized patients with diarrhea: Rate of Clostridioides difficile infection underdiagnosis and drivers of clinical suspicion. Anaerobe 2021; 70:102380. [PMID: 33971317 DOI: 10.1016/j.anaerobe.2021.102380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Clostridioides difficile infection (CDI) represents a challenging issue, with an evolving epidemiology. Main objectives of our study were: to assess the frequency of diarrhea of overall etiology, including CDI, as a cause of hospital admission or occurring during hospital stay;- to determine the rate of underdiagnosis of community-acquired (CA-), health care associated (HCA)- and hospital onset (HO-) CDI, and explore factors associated with its clinical suspicion by physicians. METHODS A prospective cohort study included all hospitalized patients with diarrhea at two acute-care hospitals. C. difficile (CD) tests were performed on every stool samples, irrespective of the treating physician request. Factors associated with the likelihood of CD test request by physicians were assessed. RESULTS We enrolled 871 (6%) patients with diarrhea. CD test performed on all diarrheic stool samples was positive in 228 cases (26%); 37, 106, 85 cases of CA- (14%), HCA- (42%) and HO- diarrhea (24%), respectively. Treating physicians did not request CD test in 207 (24%) diarrhea cases. The rate of CDI underdiagnosis was 11% (24/228); it was higher in CA-CDI (27%, 10/37). Logistic regression analysis identified age >65 years (RR 1.1; 95 CI 1.06-1.2) and hospitalizations in the previous 3 months (RR 1.2; 95% CI 1.1-1.3) as independent factors associated with the likelihood of requesting the CD test by the physician. These risk factors differed by epidemiological classification of diarrhea and by hospital. CONCLUSIONS Our study confirmed the relevance of CDI underdiagnosis and provided new insights in the factors underlying the lack of CDI clinical suspicion.
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Affiliation(s)
- Maria Adriana Cataldo
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Via Portuense, 292-00149, Rome, Italy.
| | - Guido Granata
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Via Portuense, 292-00149, Rome, Italy
| | - Silvia D'Arezzo
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Via Portuense, 292-00149, Rome, Italy
| | - Gilda Tonziello
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Via Portuense, 292-00149, Rome, Italy
| | - Antonella Vulcano
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Via Portuense, 292-00149, Rome, Italy
| | - Chiara De Giuli
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Via Portuense, 292-00149, Rome, Italy
| | | | - Antonino Di Caro
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Via Portuense, 292-00149, Rome, Italy
| | - Nicola Petrosillo
- National Institute for Infectious Diseases "Lazzaro Spallanzani", Via Portuense, 292-00149, Rome, Italy
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19
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Strobbe F, Bénard MV, Rossen NG, de Vos WM, Kumar N, Lawley TD, Zoetendal EG, Hugenholtz F, Ponsioen CY. A novel technique capable of taking 'protected' biopsies for reliable assessment of the distribution of microbiota along the colonic mucosa. J Microbiol Methods 2021; 185:106204. [PMID: 33872639 DOI: 10.1016/j.mimet.2021.106204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 02/24/2021] [Accepted: 03/13/2021] [Indexed: 11/18/2022]
Abstract
We evaluated a novel 'protected' biopsy method to reliably ascertain the spatial distribution of the mucosa-adherent colonic microbiota. Apart from minor differences at genus level, overall similarities along the colon were high between the various areas, irrespective of protected or unprotected sampling.
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Affiliation(s)
- Floortje Strobbe
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Medical Center, Amsterdam, the Netherlands
| | - Mèlanie V Bénard
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Medical Center, Amsterdam, the Netherlands
| | - Noortje G Rossen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Medical Center, Amsterdam, the Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands; Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Finland
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger institute, Hinxton, United Kingdom
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger institute, Hinxton, United Kingdom
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Floor Hugenholtz
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Amsterdam Medical Center, Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Medical Center, Amsterdam, the Netherlands.
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20
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Parras-Moltó M, Aguirre de Cárcer D. A comprehensive human minimal gut metagenome extends the host's metabolic potential. Microb Genom 2020; 6. [PMID: 33141656 PMCID: PMC7725322 DOI: 10.1099/mgen.0.000466] [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] [Indexed: 02/01/2023] Open
Abstract
Accumulating evidence suggests that humans could be considered as holobionts in which the gut microbiota play essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis and present in all healthy individuals. This study analyses the minimal gut metagenome of the most comprehensive dataset available, including individuals from agriculturalist and industrialist societies, also embodying highly diverse ethnic and geographical backgrounds. The outcome, based on metagenomic predictions for community composition data, resulted in a minimal metagenome comprising 3412 genes, mapping to 1856 reactions and 128 metabolic pathways predicted to occur across all individuals. These results were substantiated by the analysis of two additional datasets describing the microbial community compositions of larger Western cohorts, as well as a substantial shotgun metagenomics dataset. Subsequent analyses showed the plausible metabolic complementarity provided by the minimal gut metagenome to the human genome.
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Affiliation(s)
- Marcos Parras-Moltó
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid 28049, Spain
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21
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Dysbiosis of the Duodenal Mucosal Microbiota Is Associated With Increased Small Intestinal Permeability in Chronic Liver Disease. Clin Transl Gastroenterol 2020; 10:e00068. [PMID: 31373933 PMCID: PMC6736223 DOI: 10.14309/ctg.0000000000000068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chronic liver disease (CLD) is associated with both alterations of the stool microbiota and increased small intestinal permeability. However, little is known about the role of the small intestinal mucosa-associated microbiota (MAM) in CLD. The aim of this study was to evaluate the relationship between the duodenal MAM and both small intestinal permeability and liver disease severity in CLD.
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22
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Abstract
The gut microbiome is an exciting new area of research in chronic liver disease. It has shown promise in expanding our understanding of these complicated disease processes and has opened up new treatment modalities. The aim of this review is to increase understanding of the microbiome and explain the collection and analysis process in the context of liver disease. It also looks at our current understanding of the role of the microbiome in the wide spectrum of chronic liver diseases and how it is being used in current therapies and treatments.
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Affiliation(s)
- Bradley Reuter
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University, McGuire VA Medical Center, 1201 Broad Rock Boulevard, Richmond, VA 23249, USA
| | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University, McGuire VA Medical Center, 1201 Broad Rock Boulevard, Richmond, VA 23249, USA.
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23
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Shah A, Talley NJ, Koloski N, Macdonald GA, Kendall BJ, Shanahan ER, Walker MM, Keely S, Jones MP, Morrison M, Holtmann GJ. Duodenal bacterial load as determined by quantitative polymerase chain reaction in asymptomatic controls, functional gastrointestinal disorders and inflammatory bowel disease. Aliment Pharmacol Ther 2020; 52:155-167. [PMID: 32412673 DOI: 10.1111/apt.15786] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/12/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Small intestinal bacterial overgrowth may play a role in gastrointestinal and non-gastrointestinal diseases. AIMS To use quantitative polymerase chain reaction (qPCR) to determine and compare bacterial loads of duodenal biopsies in asymptomatic controls, and patients with functional gastrointestinal disorders (FGIDs) and inflammatory bowel disease (IBD) including ulcerative colitis (UC) and Crohn's disease (CD). To define effects of gastric acid inhibition on bacterial load, explore links of bacterial load and gastrointestinal symptoms in response to a standardised nutrient challenge and compare bacterial load with glucose breath test results. METHODS In 237 patients (63 controls, 84 FGID and 90 IBD), we collected mucosal samples under aseptic conditions during endoscopy extracted and total DNA. Bacterial load metric was calculated utilising qPCR measurements of the bacterial 16S rRNA gene, normalised to human beta-actin expression. Standard glucose breath test and nutrient challenge test were performed. RESULTS The duodenal microbial load was higher in patients with FGID (0.22 ± 0.03) than controls (0.07 ± 0.05; P = 0.007) and patients with UC (0.01 ± 0.05) or CD (0.02 ± 0.09), (P = 0.0001). While patients treated with proton pump inhibitors (PPI) had significantly higher bacterial loads than non-users (P < 0.05), this did not explain differences between patient groups and controls. Bacterial load was significantly (r = 0.21, P < 0.016) associated with the symptom response to standardised nutrient challenge test. Methane, but not hydrogen values on glucose breath test were associated with bacterial load measured utilising qPCR. CONCLUSIONS Utilising qPCR, a diagnosis of FGID and treatment with PPI were independently associated with increased bacterial loads. Increased bacterial loads are associated with an augmented symptom response to a standardised nutrient challenge.
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Affiliation(s)
- Ayesha Shah
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Nicholas J Talley
- Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
| | - Natasha Koloski
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Graeme A Macdonald
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Bradley J Kendall
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Erin R Shanahan
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Marjorie M Walker
- Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
| | - Simon Keely
- Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
| | - Michael P Jones
- Psychology Department, Macquarie University, Ryde, NSW, Australia
| | - Mark Morrison
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Diamantina Institute, University of Queensland, Brisbane, Qld, Australia
| | - Gerald J Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Qld, Australia.,Faculty of Medicine and Faulty of Health and Behavioural Sciences, University of Queensland, Brisbane, Qld, Australia
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24
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Jun X, Ning C, Yang S, Zhe W, Na W, Yifan Z, Xinhua R, Yulan L. Alteration of Fungal Microbiota After 5-ASA Treatment in UC Patients. Inflamm Bowel Dis 2020; 26:380-390. [PMID: 31750918 DOI: 10.1093/ibd/izz207] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Indexed: 12/13/2022]
Abstract
The effect of treatment regimens on fungal microbiota is unclear in ulcerative colitis (UC) patients. Here, we aimed to clarify the effect of 5-aminosalicylic acid (5-ASA) treatment on gut fungal microbiota in UC patients. Fifty-seven UC patients, including 20 treatment-naïve and 37 5-ASA-treated, were recruited into an exploration study. We compared the gut fungal profiles of these 2 groups of patients using ITS1-2 rDNA sequencing. Ten out of 20 treatment-naïve UC patients were followed up and enrolled for a validation study and underwent a 5-ASA treatment. We assessed the longitudinal differences of fungal microbiota in these patients before and after 5-ASA treatment. Results acquired from the validation study were accordant to those from the exploration study. Ascomycota was the dominant phylum in both noninflamed and inflamed mucosae. At the phylum level, Ascomycota decreased in inflamed mucosae before 5-ASA treatment. At the genus level, pathogens such as Scytalidium, Morchella, and Paecilomyces increased, and Humicola and Wickerhamomyces decreased in inflamed mucosae. After 5-ASA treatment, Ascomycota and Wickerhamomyces increased and Scytalidium, Fusarium, Morchella, and Paecilomyces decreased in both noninflamed and inflamed mucosae. Additionally, the balanced bacteria-fungi correlation was interrupted in inflamed mucosae, and 5-ASA treatment altered group-specific fungal microbiota and restored bacteria-fungi correlation in UC patients. Our results demonstrated that fungal diversity and composition were altered and the bacteria-fungi correlation was restored in inflamed mucosae after 5-ASA treatment.
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Affiliation(s)
- Xu Jun
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China.,Institute of Clinical Molecular Biology & Central Laboratory, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Chen Ning
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Song Yang
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Wu Zhe
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Wu Na
- Institute of Clinical Molecular Biology & Central Laboratory, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Zhang Yifan
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Ren Xinhua
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Liu Yulan
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
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25
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Rabe A, Gesell Salazar M, Michalik S, Fuchs S, Welk A, Kocher T, Völker U. Metaproteomics analysis of microbial diversity of human saliva and tongue dorsum in young healthy individuals. J Oral Microbiol 2019; 11:1654786. [PMID: 31497257 PMCID: PMC6720020 DOI: 10.1080/20002297.2019.1654786] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 12/29/2022] Open
Abstract
Background: The human oral microbiome influences initiation or progression of diseases like caries or periodontitis. Metaproteomics approaches enable the simultaneous investigation of microbial and host proteins and their interactions to improve understanding of oral diseases. Objective: In this study, we provide a detailed metaproteomics perspective of the composition of salivary and tongue microbial communities of young healthy subjects. Design: Stimulated saliva and tongue samples were collected from 24 healthy volunteers, subjected to shotgun nLC-MS/MS and analyzed by the Trans-Proteomic Pipeline and the Prophane tool. Results: 3,969 bacterial and 1,857 human proteins could be identified from saliva and tongue, respectively. In total, 1,971 bacterial metaproteins and 1,154 human proteins were shared in both sample types. Twice the amount of bacterial metaproteins were uniquely identified for the tongue dorsum compared to saliva. Overall, 107 bacterial genera of seven phyla formed the microbiome. Comparative analysis identified significant functional differences between the microbial biofilm on the tongue and the microbiome of saliva. Conclusion: Even if the microbial communities of saliva and tongue dorsum showed a strong similarity based on identified protein functions and deduced bacterial composition, certain specific characteristics were observed. Both microbiomes exhibit a great diversity with seven genera being most abundant.
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Affiliation(s)
- Alexander Rabe
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Fuchs
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch-Institute, Wernigerode, Germany
| | - Alexander Welk
- Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Kocher
- Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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26
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Rossi G, Pezzuto A, Sini C, Tuzi A, Citarella F, McCusker MG, Nigro O, Tanda E, Russo A. Concomitant medications during immune checkpoint blockage in cancer patients: Novel insights in this emerging clinical scenario. Crit Rev Oncol Hematol 2019; 142:26-34. [PMID: 31352168 DOI: 10.1016/j.critrevonc.2019.07.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 12/17/2022] Open
Abstract
The use of immune checkpoint inhibitors (ICIs) in cancer patients is rapidly growing. However, the potential impact of some widely used concomitant medications is still largely unclear. Emerging data suggest that gut microbiota may affect the efficacy of ICIs, leading to the hypothesis that concurrent antibiotics and proton pump inhibitors use could have a detrimental effect. In addition, steroid use might potentially impair the activity of immunotherapy, due its known immunosuppressive effects, and some safety concerns have been raised in patients receiving commonly used vaccination during ICIs. However, all randomized trials evaluating ICIs consistently excluded patients receiving high corticosteroid doses and data regarding other concomitant medications are lacking. Recently, several retrospective studies have tried to address this unmet medical need. Herein we discuss the latest evidence on the influence of these medications, critically analyzing the data reported so far and the possible implications in our clinical practice.
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Affiliation(s)
- Giovanni Rossi
- Lung Cancer Unit-Ospedale Policlinico San Martino-Genova, Italy
| | - Aldo Pezzuto
- Cardiovascular and Respiratory Science, S. Andrea Hospital- Sapienza University Rome, Italy
| | - Claudio Sini
- Oncologia Medica e CPDO ASSL di Olbia-ATS Sardegna, Italy
| | | | | | - Michael G McCusker
- University of Maryland Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD 21201, United States
| | - Olga Nigro
- ASST Sette Laghi, UO Oncologia, Varese, Italy
| | - Enrica Tanda
- Skin Cancer Unit-Ospedale Policlinico San Martino-Genova, Italy
| | - Alessandro Russo
- University of Maryland Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD 21201, United States; Medical Oncology Unit A.O. Papardo & Department of Human Pathology, University of Messina, Italy.
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27
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Wahlgren M, Axenstrand M, Håkansson Å, Marefati A, Lomstein Pedersen B. In Vitro Methods to Study Colon Release: State of the Art and An Outlook on New Strategies for Better In-Vitro Biorelevant Release Media. Pharmaceutics 2019; 11:E95. [PMID: 30813323 PMCID: PMC6410320 DOI: 10.3390/pharmaceutics11020095] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/18/2019] [Accepted: 02/21/2019] [Indexed: 12/19/2022] Open
Abstract
The primary focus of this review is a discussion regarding in vitro media for colon release, but we also give a brief overview of colon delivery and the colon microbiota as a baseline for this discussion. The large intestine is colonized by a vast number of bacteria, approximately 1012 per gram of intestinal content. The microbial community in the colon is complex and there is still much that is unknown about its composition and the activity of the microbiome. However, it is evident that this complex microbiota will affect the release from oral formulations targeting the colon. This includes the release of active drug substances, food supplements, and live microorganisms, such as probiotic bacteria and bacteria used for microbiota transplantations. Currently, there are no standardized colon release media, but researchers employ in vitro models representing the colon ranging from reasonable simple systems with adjusted pH with or without key enzymes to the use of fecal samples. In this review, we present the pros and cons for different existing in vitro models. Furthermore, we summarize the current knowledge of the colonic microbiota composition which is of importance to the fermentation capacity of carbohydrates and suggest a strategy to choose bacteria for a new more standardized in vitro dissolution medium for the colon.
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Affiliation(s)
- Marie Wahlgren
- Department of Food technology engineering and nutrition, Lund University, P.O. Box 124, 221 00 Lund, Sweden.
| | - Magdalena Axenstrand
- Department of Food technology engineering and nutrition, Lund University, P.O. Box 124, 221 00 Lund, Sweden.
| | - Åsa Håkansson
- Department of Food technology engineering and nutrition, Lund University, P.O. Box 124, 221 00 Lund, Sweden.
| | - Ali Marefati
- Department of Food technology engineering and nutrition, Lund University, P.O. Box 124, 221 00 Lund, Sweden.
| | - Betty Lomstein Pedersen
- Ferring International PharmaScience Center (IPC), Kay Fiskers Plads 11, 2300 Copenhagen, Denmark.
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28
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Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, Knight R. Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol 2019; 17:218-230. [PMID: 30240894 PMCID: PMC6391518 DOI: 10.1016/j.cgh.2018.09.017] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 02/07/2023]
Abstract
Advances in technical capabilities for reading complex human microbiomes are leading to an explosion of microbiome research, leading in turn to intense interest among clinicians in applying these techniques to their patients. In this review, we discuss the content of the human microbiome, including intersubject and intrasubject variability, considerations of study design including important confounding factors, and different methods in the laboratory and on the computer to read the microbiome and its resulting gene products and metabolites. We highlight several common pitfalls for clinicians, including the expectation that an individual's microbiome will be stable, that diet can induce rapid changes that are large compared with the differences among subjects, that everyone has essentially the same core stool microbiome, and that different laboratory and computational methods will yield essentially the same results. We also highlight the current limitations and future promise of these techniques, with the expectation that an understanding of these considerations will help accelerate the path toward routine clinical application of these techniques developed in research settings.
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Affiliation(s)
- Celeste Allaband
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | | | - Jeremiah J. Minich
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California
| | - Anupriya Tripathi
- Division of Biological Sciences, University of California San Diego, La Jolla, California
| | - David A. Brenner
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Rohit Loomba
- Department of Medicine, University of California San Diego, La Jolla, California, Center for Microbiome Innovation, University of California San Diego, La Jolla, California
| | - Larry Smarr
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, California Institute of Telecommunications and Information Technology, University of California San Diego, La Jolla, California
| | - William J. Sandborn
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, Division of Gastroenterology, Veterans Administration San Diego Health System, La Jolla, California
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, California, Center for Microbiome Innovation, University of California San Diego, La Jolla, California, Division of Gastroenterology, Veterans Administration San Diego Health System, La Jolla, California
| | - Pieter Dorrestein
- Department of Pediatrics, University of California San Diego, La Jolla, California, Center for Microbiome Innovation, University of California San Diego, La Jolla, California, Skaggs School of Pharmacy, University of California San Diego, La Jolla, California
| | - Amir Zarrinpar
- Department of Medicine, University of California San Diego, La Jolla, California, Center for Microbiome Innovation, University of California San Diego, La Jolla, California, Division of Gastroenterology, Veterans Administration San Diego Health System, La Jolla, California
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California; Center for Microbiome Innovation, University of California San Diego, La Jolla, California; Department of Computer Science and Engineering, University of California San Diego, La Jolla, California; Department of Bioengineering, University of California San Diego, La Jolla, California.
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29
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Koo SH, Deng J, Ang DSW, Hsiang JC, Lee LS, Aazmi S, Mohamed EHM, Yang H, Yap SY, Teh LK, Salleh MZ, Lee EJD, Ang TL. Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore. Singapore Med J 2018; 60:512-521. [PMID: 30488079 DOI: 10.11622/smedj.2018152] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The objectives of this study were to examine the effects of ethnicity, gender and a proton pump inhibitor (PPI), omeprazole, on the human gut microbiome. PPIs are commonly used for the treatment of acid-related disorders. We hypothesised that PPI therapy might perturb microbial communities and alter the gut microbiome. METHODS Healthy subjects of Chinese (n = 12), Malay (n = 12) and Indian (n = 10) ancestry, aged 21-37 years, were enrolled. They provided a baseline stool sample (Day 1) and were then given a course of omeprazole at therapeutic dose (20 mg daily) for seven days. Stool samples were collected again on Day 7 and 14 (one week after stopping omeprazole). Microbial DNA was extracted from the stool samples, followed by polymerase chain reaction, library construction, 16S rRNA sequencing using Illumina MiSeq, and statistical and bioinformatics analyses. RESULTS The findings showed an increase in species richness (p = 0.018) after omeprazole consumption on Day 7, which reverted to baseline on Day 14. There were significant increases in the relative abundance of Streptococcus vestibularis (p = 0.0001) and Veillonella dispar (p = 0.0001) on Day 7, which diminished on Day 14. Faecalibacterium prausnitzii, Sutterella stercoricanis and Bacteroides denticanum were characteristic of Chinese, Malays and Indians, respectively. Lactobacillaceae and Bacteroides xylanisolvens were the signature taxa of male and female subjects, respectively. CONCLUSION The study demonstrated alterations in the gut microbiome following omeprazole treatment. This may explain the underlying pathology of increased risk of Clostridium difficile infections associated with omeprazole therapy.
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Affiliation(s)
- Seok Hwee Koo
- Clinical Trials and Research Unit, Changi General Hospital, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jing Deng
- Clinical Trials and Research Unit, Changi General Hospital, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Daphne Shih Wen Ang
- Department of Gastroenterology and Hepatology, Changi General Hospital, Singapore
| | - John Chen Hsiang
- Department of Gastroenterology and Hepatology, Changi General Hospital, Singapore
| | - Lian Shien Lee
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor Campus, Selangor, Malaysia
| | - Shafiq Aazmi
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor Campus, Selangor, Malaysia
| | - Elsa Haniffah Mejia Mohamed
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hong Yang
- School of Applied Science, Temasek Polytechnic, Singapore
| | - Siew Yoon Yap
- Clinical Trials and Research Unit, Changi General Hospital, Singapore
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor Campus, Selangor, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor Campus, Selangor, Malaysia
| | - Edmund Jon Deoon Lee
- Clinical Trials and Research Unit, Changi General Hospital, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tiing Leong Ang
- Department of Gastroenterology and Hepatology, Changi General Hospital, Singapore
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30
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Abstract
Discoveries in molecular genetics over the last two decades have broadened our information about the genomics of complex microbial communities. As in all other fields of medicine, there is an undeniable need to explore the microbiome and the way it is impacted by biological sex. A number, although small, of recent studies have demonstrated that women and men have striking differences in the species that constitute their microbiomes. This effects pathological physiology in fields such as hepatology, oncology, autoimmune disease (most notably diabetes mellitus), autism, and obstetrics. There is still an unfortunate lack of research being done on the “microgenderome”: the interaction between microbiota, sex hormones, and the immune system. This review will highlight some of the main areas to be affected by microgenderome physiology, with an in depth focus on obstetrics.
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Affiliation(s)
- Gali Levy
- Rambam Health Care Campus, Technion Faculty of Medicine, Haifa, Israel
| | - Ido Solt
- Rambam Health Care Campus, Technion Faculty of Medicine, Haifa, Israel
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31
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Xu J, Chen N, Wu Z, Song Y, Zhang Y, Wu N, Zhang F, Ren X, Liu Y. 5-Aminosalicylic Acid Alters the Gut Bacterial Microbiota in Patients With Ulcerative Colitis. Front Microbiol 2018; 9:1274. [PMID: 29951050 PMCID: PMC6008376 DOI: 10.3389/fmicb.2018.01274] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/24/2018] [Indexed: 12/15/2022] Open
Abstract
Background: The aim of this study was to clarify the effect of 5-aminosalicylic acid (5-ASA) treatment on gut bacterial microbiota in patients with ulcerative colitis (UC). Methods: A total of 57 UC patients, including 20 untreated and 37 5-ASA-treated, were recruited into an exploration cohort. We endoscopically collected both non-inflamed and inflamed mucosal samples from all patients, and compared the gut bacterial profiles using 16S rDNA sequencing. Ten untreated UC patients were then treated with 5-ASA and subsequently recruited for an independent validation study to confirm the acquired data. Results: In untreated UC patients, compared with those in non-inflamed mucosae, Firmicutes (such as Enterococcus) were decreased and Proteobacteria (e.g., Escherichia–Shigella) were increased in the inflamed mucosae. Compared with the inflamed mucosae of untreated UC patients, there was a higher abundance of Firmicutes (e.g., Enterococcus) and lower Proteobacteria (Escherichia–Shigella) in the inflamed mucosae of 5-ASA treated UC patients. In the validation cohort, after administration of 5-ASA, bacterial alteration was consistent with these data. Furthermore, there was a skewed negative correlation between Escherichia–Shigella and bacterial genera of Firmicutes in the inflamed mucosae. 5-ASA treatment decreased the strength of bacterial correlation and weakened the skewed negative correlation pattern. Conclusion: The microbial dysbiosis (mainly characterized by an increased abundance in the Escherichia–Shigella genus) and the skewed negative correlation between Escherichia–Shigella and bacterial genera of Firmicutes are two characteristics of the inflamed mucosae of UC patients. 5-ASA treatment decreases Escherichia–Shigella and weakens the skewed correlations, which may be related to its treatment efficiency.
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Affiliation(s)
- Jun Xu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Ning Chen
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Zhe Wu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yang Song
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yifan Zhang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Na Wu
- Institute of Clinical Molecular Biology and Central Laboratory, Peking University People's Hospital, Beijing, China
| | - Feng Zhang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Xinhua Ren
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yulan Liu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
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32
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Flynn KJ, Ruffin MT, Turgeon DK, Schloss PD. Spatial Variation of the Native Colon Microbiota in Healthy Adults. Cancer Prev Res (Phila) 2018; 11:393-402. [PMID: 29636352 DOI: 10.1158/1940-6207.capr-17-0370] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/16/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
The microbiome has been implicated in the development of colorectal cancer and inflammatory bowel diseases. The specific traits of these diseases vary along the axis of the digestive tract. Further, variation in the structure of the gut microbiota has been associated with both diseases. We profiled the microbiota of the healthy proximal and distal mucosa and lumen to better understand how bacterial populations vary along the colon. We used a two-colonoscope approach to sample proximal and distal mucosal and luminal contents from the colons of 20 healthy subjects that had not undergone any bowel preparation procedure. The biopsies and home-collected stool were subjected to 16S rRNA gene sequencing, and random forest classification models were built using taxa abundance and location to identify microbiota specific to each site. The right mucosa and lumen had the most similar community structures of the five sites we considered from each subject. The distal mucosa had higher relative abundance of Finegoldia, Murdochiella, Peptoniphilus, Porphyromonas, and Anaerococcus The proximal mucosa had more of the genera Enterobacteriaceae, Bacteroides, and Pseudomonas The classification model performed well when classifying mucosal samples into proximal or distal sides (AUC = 0.808). Separating proximal and distal luminal samples proved more challenging (AUC = 0.599), and specific microbiota that differentiated the two were hard to identify. By sampling the unprepped colon, we identified distinct bacterial populations native to the proximal and distal sides. Further investigation of these bacteria may elucidate if and how these groups contribute to different disease processes on their respective sides of the colon. Cancer Prev Res; 11(7); 393-402. ©2018 AACR.
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Affiliation(s)
- Kaitlin J Flynn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mack T Ruffin
- Department of Family and Community Medicine, College of Medicine, Pennsylvania State University, Hershey, Pennsylvania
| | - D Kim Turgeon
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan.
| | - Patrick D Schloss
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan.
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33
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Mullineaux-Sanders C, Suez J, Elinav E, Frankel G. Sieving through gut models of colonization resistance. Nat Microbiol 2018; 3:132-140. [PMID: 29358683 DOI: 10.1038/s41564-017-0095-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/08/2017] [Indexed: 12/24/2022]
Abstract
The development of innovative high-throughput genomics and metabolomics technologies has considerably expanded our understanding of the commensal microorganisms residing within the human body, collectively termed the microbiota. In recent years, the microbiota has been reported to have important roles in multiple aspects of human health, pathology and host-pathogen interactions. One function of commensals that has attracted particular interest is their role in protection against pathogens and pathobionts, a concept known as colonization resistance. However, pathogens are also able to sense and exploit the microbiota during infection. Therefore, obtaining a holistic understanding of colonization resistance mechanisms is essential for the development of microbiome-based and microbiome-targeting therapies for humans and animals. Achieving this is dependent on utilizing physiologically relevant animal models. In this Perspective, we discuss the colonization resistance functions of the gut microbiota and sieve through the advantages and limitations of murine models commonly used to study such mechanisms within the context of enteric bacterial infection.
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Affiliation(s)
- Caroline Mullineaux-Sanders
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Jotham Suez
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Gad Frankel
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK.
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34
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Smith-Brown P, Morrison M, Krause L, Davies PSW. Male-specific Association Between Fat-Free Mass Index and Fecal Microbiota in 2- to 3-Year-Old Australian Children. J Pediatr Gastroenterol Nutr 2018; 66:147-151. [PMID: 29045349 DOI: 10.1097/mpg.0000000000001780] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVES Maturation of the gut microbiota has been shown to influence childhood growth, whereas alterations in microbiota composition are proposed to be causally related to the development of overweight and obesity. The objective of this study is to explore the association between microbiota profile, body size, and body composition in young children. METHODS Fecal microbiota was examined by 16S rRNA gene sequencing, whereas body composition was assessed using the deuterium oxide dilution technique in a cohort of 37 well-nourished 2- to 3-year-old Australian children. RESULTS Microbiota composition (weighted UniFrac distance) was shown to be significantly associated with FFMI (fat-free mass index) z score (P = 0.027, adonis) in boys but not girls. In boys, FFMI z score was significantly correlated with the relative abundance of an OUT (Operational Taxonomic Unit) belonging to the Ruminococcaceae family (Rho = 0.822, P < 0.001, pFDR (false discovery rate adjusted P value) = 0.002, n = 18). At a FDR <0.2, FFMI z score in boys was positively associated with the relative abundance of OTU related to Dorea formicigenerans and Faecalibacterium prausnitzii and negatively correlated to an OTU related to Bacteroides cellulosilyticus. CONCLUSIONS These results suggest that previously reported associations between microbiota composition and body size may be driven by an association with fat-free mass, particularly in males.
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Affiliation(s)
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Queensland, Australia
| | - Lutz Krause
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Queensland, Australia
| | - Peter S W Davies
- Children's Nutrition Research Centre, Child Health Research Centre
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O’ Donnell MM, Harris HMB, Ross RP, O'Toole PW. Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals. Microbiologyopen 2017; 6:e00509. [PMID: 28834331 PMCID: PMC5635170 DOI: 10.1002/mbo3.509] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/21/2022] Open
Abstract
In this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.
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Affiliation(s)
- Michelle M. O’ Donnell
- Food Biosciences DepartmentTeagasc Food Research CentreCorkIreland
- Department of MicrobiologyUniversity College CorkCorkIreland
| | | | - R. Paul Ross
- Food Biosciences DepartmentTeagasc Food Research CentreCorkIreland
- Department of MicrobiologyUniversity College CorkCorkIreland
| | - Paul W. O'Toole
- Department of MicrobiologyUniversity College CorkCorkIreland
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Abstract
Recently, several lines of evidence that indicate a strong link between the development of colorectal cancer (CRC) and aspects of the gut microbiota have become apparent. However, it remains unclear how changes in the gut microbiota might influence carcinogenesis or how regional organization of the gut might influence the microbiota. In this review, we discuss several leading theories that connect gut microbial dysbiosis with CRC and set this against a backdrop of what is known about proximal-distal gut physiology and the pathways of CRC development and progression. Finally, we discuss the potential for gut microbial modulation therapies, for example, probiotics, antibiotics, and others, to target and improve gut microbial dysbiosis as a strategy for the prevention or treatment of CRC.
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Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota. mSystems 2017; 2:mSystems00086-17. [PMID: 28904999 PMCID: PMC5585691 DOI: 10.1128/msystems.00086-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/02/2017] [Indexed: 12/20/2022] Open
Abstract
The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention. The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention. Author Video: An author video summary of this article is available.
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Zhang S, Cao X, Huang H. Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research. Front Cell Infect Microbiol 2017; 7:51. [PMID: 28286741 PMCID: PMC5323387 DOI: 10.3389/fcimb.2017.00051] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/10/2017] [Indexed: 12/12/2022] Open
Abstract
Identifying intestinal microbiota is arguably an important task that is performed to determine the pathogenesis of inflammatory bowel diseases (IBD); thus, it is crucial to collect and analyze intestinally-associated microbiota. Analyzing a single niche to categorize individuals does not enable researchers to comprehensively study the spatial variations of the microbiota. Therefore, characterizing the spatial community structures of the inflammatory bowel disease microbiome is critical for advancing our understanding of the inflammatory landscape of IBD. However, at present there is no universally accepted consensus regarding the use of specific sampling strategies in different biogeographic locations. In this review, we discuss the spatial distribution when screening sample collections in IBD microbiota research. Here, we propose a novel model, a three-dimensional spatial community structure, which encompasses the x-, y-, and z-axis distributions; it can be used in some sampling sites, such as feces, colonoscopic biopsy, the mucus gel layer, and oral cavity. On the basis of this spatial model, this article also summarizes various sampling and processing strategies prior to and after DNA extraction and recommends guidelines for practical application in future research.
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Affiliation(s)
- Shaocun Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital; Tianjin Medical University Tianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
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Cuív PÓ, Begun J, Keely S, Lewindon PJ, Morrison M. Towards an integrated understanding of the therapeutic utility of exclusive enteral nutrition in the treatment of Crohn's disease. Food Funct 2017; 7:1741-51. [PMID: 26948398 DOI: 10.1039/c5fo01196e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Crohn's disease (CD) is a chronic disease characterized by episodic and disabling inflammation of the gastrointestinal tract in genetically susceptible individuals. The incidence and prevalence of CD is rising rapidly across the world emphasising that disease risk is also influenced by environmental and lifestyle factors, as well as the microbial community resident in the gut. Childhood-onset CD is associated with an aggressive disease course that can adversely impact patient growth and development. There is no cure for CD however new onset and recurrent cases of paediatric CD are often responsive to exclusive enteral nutrition (EEN) treatment. EEN treatment involves the exclusive consumption of an elemental or polymeric formula for several weeks and it is well established as a primary intervention strategy. EEN treatments typically achieve remission rates of over 80% and importantly they are associated with a high rate of mucosal healing, far superior to steroids, which is prognostic of improved long-term health outcomes. Furthermore, they are safe, have few side effects, and improve nutritional status and linear growth. Surprisingly, despite the utility of EEN our understanding of the host-microbe-diet interactions that underpin clinical remission and mucosal healing are limited. Here, we review the current state of knowledge and propose that the induction of autophagy, in addition to modulation of the microbiota and coordinated effects on inflammation and epithelial cell biology, may be critical for the therapeutic effects associated with EEN. A better understanding of EEN treatment will provide new opportunities to restore gut homeostasis and prolong periods of remission, as well as provide new insights into the factors that trigger and perhaps prevent CD.
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Affiliation(s)
- Páraic Ó Cuív
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Jakob Begun
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia and School of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia and Department of Gastroenterology, Mater Health Services, Brisbane, Australia
| | - Simon Keely
- School of Biomedical Science and Pharmacy, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia and Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Peter J Lewindon
- The University of Queensland, Department of Paediatrics and Child Health, Lady Cilento Children's Hospital, QLD 4101, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia.
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40
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Shanahan ER, Holtmann G, Morrison M. Life in the small intestine: the forgotten microbiome? MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The gastrointestinal (GI) microbiota is now widely accepted to be an important modulator of our health and well-being. The microbes colonising the GI tract aid in promoting gut and immune homeostasis, while alterations in the composition and/or density of these microbes, often referred to as dysbiosis, have been implicated in many intestinal and extra-intestinal disorders. As a result, the GI microbiota is of increasing interest as a therapeutic target. This is particularly the case in the context of GI disorders linked to chronic inflammation of the mucosa. In this article, we focus on the small intestinal microbiota, which in many senses can be considered the ‘forgotten' gut microbiome.
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Aguirre M, Venema K. Challenges in simulating the human gut for understanding the role of the microbiota in obesity. Benef Microbes 2016; 8:31-53. [PMID: 27903093 DOI: 10.3920/bm2016.0113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is an elevated incidence of cases of obesity worldwide. Therefore, the development of strategies to tackle this condition is of vital importance. This review focuses on the necessity of optimising in vitro systems to model human colonic fermentation in obese subjects. This may allow to increase the resolution and the physiological relevance of the information obtained from this type of studies when evaluating the potential role that the human gut microbiota plays in obesity. In light of the parameters that are currently used for the in vitro simulation of the human gut (which are mostly based on information derived from healthy subjects) and the possible difference with an obese condition, we propose to revise and improve specific standard operating procedures.
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Affiliation(s)
- M Aguirre
- 1 Top Institute of Food and Nutrition, P.O. Box 557, 6700 AA Wageningen, the Netherlands.,2 Department of Human Biology, Faculty of Health, Medicine and Life Sciences, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands.,3 The Netherlands Organization for Applied Scientific Research (TNO), P.O. Box 360, 3700 AJ Zeist, the Netherlands
| | - K Venema
- 1 Top Institute of Food and Nutrition, P.O. Box 557, 6700 AA Wageningen, the Netherlands.,2 Department of Human Biology, Faculty of Health, Medicine and Life Sciences, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands.,4 Beneficial Microbes Consultancy, Johan Karschstraat 3, 6709 TN Wageningen, the Netherlands
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Budden KF, Gellatly SL, Wood DLA, Cooper MA, Morrison M, Hugenholtz P, Hansbro PM. Emerging pathogenic links between microbiota and the gut-lung axis. Nat Rev Microbiol 2016; 15:55-63. [PMID: 27694885 DOI: 10.1038/nrmicro.2016.142] [Citation(s) in RCA: 870] [Impact Index Per Article: 108.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The microbiota is vital for the development of the immune system and homeostasis. Changes in microbial composition and function, termed dysbiosis, in the respiratory tract and the gut have recently been linked to alterations in immune responses and to disease development in the lungs. In this Opinion article, we review the microbial species that are usually found in healthy gastrointestinal and respiratory tracts, their dysbiosis in disease and interactions with the gut-lung axis. Although the gut-lung axis is only beginning to be understood, emerging evidence indicates that there is potential for manipulation of the gut microbiota in the treatment of lung diseases.
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Affiliation(s)
- Kurtis F Budden
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia
| | - Shaan L Gellatly
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia
| | - David L A Wood
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland 4072, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, and the Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia; and The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, Queensland 4102, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia
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Nagel R, Traub RJ, Allcock RJN, Kwan MMS, Bielefeldt-Ohmann H. Comparison of faecal microbiota in Blastocystis-positive and Blastocystis-negative irritable bowel syndrome patients. MICROBIOME 2016; 4:47. [PMID: 27580855 PMCID: PMC5007835 DOI: 10.1186/s40168-016-0191-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 08/09/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND We investigated whether the carriage of Blastocystis in IBS patients was associated with differences in the faecal microbiota. Forty patients with diarrhoea-predominant IBS (26 Blastocystis-positive and 14 Blastocystis-negative) and 57 healthy controls (HC) (42 Blastocystis-positive and 15 Blastocystis-negative) submitted faecal samples for metataxonomic analysis of the 16S ribosomal RNA gene. Differences in the relative abundance of bacteria in these IBS and HC groups were evaluated from phylum to genus level. RESULTS Significant changes were observed in two dominant phyla in IBS patients, regardless of Blastocystis infection status, namely a rise in Firmicutes and a statistically significant reduction in relative abundance of Bacteroidetes (with a threefold increase in the Firmicutes to Bacteoridetes ratio). Significant differences at genus level in IBS subjects compared to HC were also observed for many bacterial species. However, further clinical subgroup analysis of Blastocystis-positive and Blastocystis-negative subjects, regardless of symptoms, showed no significant differences at the phylum or genus level in IBS-P compared to IBS-N. CONCLUSIONS Significant differences in the faecal microbiota between diarrhoea-predominant IBS patients and healthy controls were confirmed, but the carriage of Blastocystis did not significantly alter the faecal microbiota. If Blastocystis-positive patients represent a separate clinical subtype of IBS, this group is not identified by changes in the microbiota.
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Affiliation(s)
- Robyn Nagel
- School of Veterinary Science, The University of Queensland, Gatton Campus, Brisbane, Queensland 4343 Australia
- Toowoomba Gastroenterology Clinic, Suite 105 Medici Medical Centre, 15 Scott St, Toowoomba, QLD 4350 Australia
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, Victoria 3052 Australia
| | - Richard J. N. Allcock
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia 6009 Australia
| | - Marcella M. S. Kwan
- Rural Clinical School, School of Medicine, The University of Queensland, Toowoomba, 4350 Australia
| | - Helle Bielefeldt-Ohmann
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland 4072 Australia
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Abstract
The relevance of biogeography to the distal gut microbiota has been investigated in both health and inflammatory bowel disease (IBD), however multiple factors, including sample type and methodology, microbiota characterization and interpersonal variability make the construction of a core model of colonic biogeography challenging. In addition, how phylogenetic classification relates to immunogenicity and whether consistent alterations in the microbiota are associated with ulcerative colitis (UC) remain open questions. This addendum seeks to review the human colonic microbiota in health and UC as currently understood, in the broader context of the human microbiome.
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Affiliation(s)
- Aonghus Lavelle
- School of Medicine and Medical Science,
University College Dublin, Dublin, Ireland,Centre for Colorectal Disease, St.
Vincent's University Hospital, Dublin,
Ireland
| | - Grainne Lennon
- School of Medicine and Medical Science,
University College Dublin, Dublin, Ireland,Centre for Colorectal Disease, St.
Vincent's University Hospital, Dublin,
Ireland
| | - Desmond C. Winter
- School of Medicine and Medical Science,
University College Dublin, Dublin, Ireland,Centre for Colorectal Disease, St.
Vincent's University Hospital, Dublin,
Ireland
| | - P. Ronan O'Connell
- School of Medicine and Medical Science,
University College Dublin, Dublin, Ireland,Centre for Colorectal Disease, St.
Vincent's University Hospital, Dublin,
Ireland
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Shanahan ER, Zhong L, Talley NJ, Morrison M, Holtmann G. Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures. Aliment Pharmacol Ther 2016; 43:1186-96. [PMID: 27086880 DOI: 10.1111/apt.13622] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 03/09/2016] [Accepted: 03/22/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND The mucosa-associated microbiota appears to be highly relevant to host-microbe interactions in the gastrointestinal (GI) tract. Thus, precise characterisation of the mucosa-associated microbiota may provide important insights for diagnostic and therapeutic development. However, for technical reasons, mucosal biopsies taken during standard endoscopic procedures are potentially contaminated by GI luminal contents. AIM To develop and validate a biopsy device that minimises contamination during sampling of the mucosa-associated microbiota. METHODS A new, encased biopsy forceps was developed, the Brisbane Aseptic Biopsy Device (BABD). This comprises sterile forceps encased by a sheath with a plug at the tip, allowing targeted, aseptic sampling of the mucosa. Matched duodenal biopsies were obtained using the BABD, standard biopsy forceps, and a sterile brush, from patients undergoing upper GI endoscopy for iron deficiency (n = 6). Total genomic deoxyribonucleic acid (gDNA) was extracted from samples and bacterial 16S rRNA gene libraries sequenced to investigate the mucosa-associated microbiota. RESULTS Microbial DNA was recovered from biopsies obtained by the BABD, confirming the presence of a duodenal mucosa-associated microbiota. This microbiota was dominated by the genus Streptococcus, with lower levels of Prevotella, Veillonella and Neisseria. At the individual patient level, substantial differences were observed between matched samples obtained using the different devices. A greater degree of bacterial diversity was observed in samples collected using the standard forceps, indicating the BABD affords collection of samples more representative of the mucosa-associated microbiota, by precluding luminal cross-contamination. CONCLUSIONS Cross-contamination can occur when mucosal biopsies are taken during standard endoscopic procedures. Utilising the novel Brisbane Aseptic Biopsy Device can reduce cross-contamination, and it offers improved opportunities to more precisely examine host-mucosa-associated microbiota interactions.
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Affiliation(s)
- E R Shanahan
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, and Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - L Zhong
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, and Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - N J Talley
- Faculty of Health, The University of Newcastle, Callaghan, NSW, Australia
| | - M Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - G Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, and Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
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The Impact of Lactobacillus casei on the Composition of the Cecal Microbiota and Innate Immune System Is Strain Specific. PLoS One 2016; 11:e0156374. [PMID: 27244133 PMCID: PMC4887021 DOI: 10.1371/journal.pone.0156374] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 05/13/2016] [Indexed: 02/07/2023] Open
Abstract
The probiotic function to impact human health is thought to be related to their ability to alter the composition of the gut microbiota and modulate the human innate immune system. The ability to function as a probiotic is believed to be strain specific. Strains of Lactobacillus casei are commonly utilized as probiotics that when consumed alter the composition of the gut microbiota and modulate the host immune response. L. casei strains are known to differ significantly in gene content. The objective of this study was to investigate seven different L. casei strains for their ability to alter the murine gut microbiota and modulate the murine immune system. C57BL/6 mice were fed L. casei strains at a dose of 108 CFU/day/mouse for seven days and sacrificed 3.5h after the last administration. The cecal content and the ileum tissue were collected for microbiota analysis and immune profiling, respectively. While 5 of the L. casei strains altered the gut microbiota in a strain specific manner, two of the strains did not alter the overall cecal microbiota composition. The observed changes cluster into three groups containing between 1 and 2 strains. Two strains that did not affect the gut microbiota composition cluster together with the control in their impact on pattern recognition receptors (PRRs) expression, suggesting that the ability to alter the cecal microbiota correlates with the ability to alter PRR expression. They also cluster together in their impact on the expression of intestinal antimicrobial peptides (AMPs). This result suggests that a relationship exists between the capability of a L. casei strains to alter the composition of the gut microbiota, PRR regulation, and AMP regulation.
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Selak M, Rivière A, Moens F, Van den Abbeele P, Geirnaert A, Rogelj I, Leroy F, De Vuyst L. Inulin-type fructan fermentation by bifidobacteria depends on the strain rather than the species and region in the human intestine. Appl Microbiol Biotechnol 2016; 100:4097-107. [PMID: 26861055 DOI: 10.1007/s00253-016-7351-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/08/2016] [Accepted: 01/23/2016] [Indexed: 01/01/2023]
Abstract
Inulin-type fructans (ITF) are known to cause a health-promoting bifidogenic effect, although the ITF degradation capacity of bifidobacteria in different intestinal regions remains unclear. The present study aims at offering new insights into this link, making use of a collection of 190 bifidobacterial strains, encompassing strains from gut biopsies (terminal ileum and proximal colon; mucosa-associated strains) and the simulator of the human intestinal microbial ecosystem (SHIME®; proximal and distal colon vessels; lumen-associated strains). A multivariate data analysis of all fermentation data revealed four clusters corresponding with different types of ITF degradation fingerprints, which were not correlated with the region in the intestine, suggesting that the degradation of ITF is uniform along the human intestine. Strains from cluster 1 consumed fructose, while strains from cluster 2 consumed more oligofructose than fructose. Higher fructose and oligofructose consumption was characteristic for clusters 3 and 4 strains, which degraded inulin too. In general, the mucosa-associated strains from biopsy origin seemed to be more specialized in the consumption of fructose and oligofructose, while the lumen-associated strains from SHIME origin displayed a higher degradation degree of inulin. Further, intra-species variability in ITF degradation was found, indicating strain-specific variations. The coexistence of different bifidobacterial strains with different ITF degradation fingerprints within the same intestinal region suggests cooperation for the degradation of ITF, with opportunities for cross-feeding on strain and/or species level.
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Affiliation(s)
- Marija Selak
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Audrey Rivière
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Frédéric Moens
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Pieter Van den Abbeele
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Annelies Geirnaert
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Irena Rogelj
- Institute of Dairy Science and Probiotics, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230, Domžale, Slovenia
| | - Frédéric Leroy
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.
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Khanafer N, Barbut F, Eckert C, Perraud M, Demont C, Luxemburger C, Vanhems P. Factors predictive of severe Clostridium difficile infection depend on the definition used. Anaerobe 2016; 37:43-8. [DOI: 10.1016/j.anaerobe.2015.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 08/14/2015] [Accepted: 08/24/2015] [Indexed: 12/16/2022]
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Aktas B, De Wolfe TJ, Tandee K, Safdar N, Darien BJ, Steele JL. The Effect of Lactobacillus casei 32G on the Mouse Cecum Microbiota and Innate Immune Response Is Dose and Time Dependent. PLoS One 2015; 10:e0145784. [PMID: 26714177 PMCID: PMC4705108 DOI: 10.1371/journal.pone.0145784] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/08/2015] [Indexed: 01/12/2023] Open
Abstract
Lactobacilli have been associated with a variety of immunomodulatory effects and some of these effects have been related to changes in gastrointestinal microbiota. However, the relationship between probiotic dose, time since probiotic consumption, changes in the microbiota, and immune system requires further investigation. The objective of this study was to determine if the effect of Lactobacillus casei 32G on the murine gastrointestinal microbiota and immune function are dose and time dependent. Mice were fed L. casei 32G at doses of 106, 107, or 108 CFU/day/mouse for seven days and were sacrificed 0.5h, 3.5h, 12h, or 24h after the last administration. The ileum tissue and the cecal content were collected for immune profiling by qPCR and microbiota analysis, respectively. The time required for L. casei 32G to reach the cecum was monitored by qPCR and the 32G bolus reaches the cecum 3.5h after the last administration. L. casei 32G altered the cecal microbiota with the predominance of Lachnospiraceae IS, and Oscillospira decreasing significantly (p < 0.05) in the mice receiving 108 CFU/mouse 32G relative to the control mice, while a significant (p < 0.05) increase was observed in the prevalence of lactobacilli. The lactobacilli that increased were determined to be a commensal lactobacilli. Interestingly, no significant difference in the overall microbiota composition, regardless of 32G doses, was observed at the 12h time point. A likely explanation for this observation is the level of feed derived-nutrients resulting from the 12h light/dark cycle. 32G results in consistent increases in Clec2h expression and reductions in TLR-2, alpha-defensins, and lysozyme. Changes in expression of these components of the innate immune system are one possible explanation for the observed changes in the cecal microbiota. Additionally, 32G administration was observed to alter the expression of cytokines (IL-10rb and TNF-α) in a manner consistent with an anti-inflammatory response.
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Affiliation(s)
- Busra Aktas
- Department of Food Science, University of Wisconsin, Madison, WI, United States of America
| | - Travis J. De Wolfe
- Department of Food Science, University of Wisconsin, Madison, WI, United States of America
| | - Kanokwan Tandee
- Food Science and Technology, Maejo University, Chiangmai, Thailand
| | - Nasia Safdar
- Infectious Diseases Division, Department of Medicine, University of Wisconsin, Madison, WI, United States of America
- William S. Middleton Veterans Affairs Hospital, Madison, WI, United States of America
| | - Benjamin J. Darien
- Animal Health and Biomedical Sciences, University of Wisconsin, Madison, WI, United States of America
| | - James L. Steele
- Department of Food Science, University of Wisconsin, Madison, WI, United States of America
- * E-mail:
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