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Ruiz A, Torrecillas S, Kashinskaya E, Andree KB, Solovyev M, Gisbert E. Comparative study of the gut microbial communities collected by scraping and swabbing in a fish model: a comprehensive guide to promote non-lethal procedures for gut microbial studies. Front Vet Sci 2024; 11:1374803. [PMID: 38585300 PMCID: PMC10997143 DOI: 10.3389/fvets.2024.1374803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
In the present study, we propose the use of swabs in non-lethal sampling procedures to collect the mucosa-adhered gut microbiota from the posterior intestine of fish, and therefore, we compare the bacterial communities collected by conventional scraping and by swabbing methods. For this purpose, samples of the posterior intestine of rainbow trout (Oncorhynchus mykiss) were collected first using the swabbing approach, and after fish euthanasia, by mucosa scraping. Finally, bacterial communities were compared by 16S rRNA gene Illumina sequencing. Results from the current study revealed that similar values of bacterial richness and diversity were found for both sampling procedures. Similarly, there were no differences between procedures when using qualitative metrics (Jaccard and unweighted UniFrac) for estimating inter-individual diversity, but the quantitative metrics (Bray-Curtis and weighted UniFrac) showed a higher dispersion when samples were obtained by swabbing compared to scraping. In terms of bacterial composition, there were differences in abundance for the phyla Firmicutes and Proteobacteria. The cause of these differential abundances may be the inability of the swab to access to certain areas, such as the basal region of the intestinal villi. Moreover, swabbing allowed a higher representation of low abundant taxa, which may also have an important role in host microbiome regardless of their low abundance. Overall, our results demonstrate that the sampling method is a factor to be considered in experimental design when studying gut bacterial communities to avoid potential biases in the interpretation or comparison of results from different studies. In addition, the advantages and disadvantages of each procedure (swabbing vs scraping) are discussed in detail, concluding that swabbing can be implemented as a reliable and non-lethal procedure for posterior gut microbiota studies, which is of particular interest for animal welfare and the 3Rs principle, and may offer a wide range of novel applications.
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Affiliation(s)
- Alberto Ruiz
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
| | - Silvia Torrecillas
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
| | - Elena Kashinskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Karl B. Andree
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
| | - Mikhail Solovyev
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- Biological Institute, Tomsk State University, Tomsk, Russia
| | - Enric Gisbert
- Aquaculture Program, Centre de La Ràpita, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), La Ràpita, Spain
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Xu C, Shao J. High-throughput omics technologies in inflammatory bowel disease. Clin Chim Acta 2024; 555:117828. [PMID: 38355001 DOI: 10.1016/j.cca.2024.117828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China
| | - Jing Shao
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China; Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China.
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3
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Brown G, Hoedt EC, Keely S, Shah A, Walker MM, Holtmann G, Talley NJ. Role of the duodenal microbiota in functional dyspepsia. Neurogastroenterol Motil 2022; 34:e14372. [PMID: 35403776 PMCID: PMC9786680 DOI: 10.1111/nmo.14372] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/04/2022] [Accepted: 03/14/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Functional dyspepsia (FD) is a common and debilitating gastrointestinal disorder attributed to altered gut-brain interactions. While the etiology of FD remains unknown, emerging research suggests the mechanisms are likely multifactorial and heterogenous among patient subgroups. Small bowel motor disturbances, visceral hypersensitivity, chronic microinflammation, and increased intestinal tract permeability have all been linked to the pathogenesis of FD. Recently, alterations to the gut microbiome have also been implicated to play an important role in the disease. Changes to the duodenal microbiota may either trigger or be a consequence of immune and neuronal disturbances observed in the disease, but the mechanisms of influence of small intestinal flora on gastrointestinal function and symptomatology are unknown. PURPOSE This review summarizes and synthesizes the literature on the link between the microbiota, low-grade inflammatory changes in the duodenum and FD. This review is not intended to provide a complete overview of FD or the small intestinal microbiota, but instead outline some of the key conceptual advances in understanding the interactions between altered gastrointestinal bacterial communities; dietary factors; host immune activation; and stimulation of the gut-brain axes in patients with FD versus controls. Current and emerging treatment approaches such as dietary interventions and antibiotic or probiotic use that have demonstrated symptom benefits for patients are reviewed, and their role in modulating the host-microbiota is discussed. Finally, suggested opportunities for diagnostic and therapeutic improvements for patients with this condition are presented.
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Affiliation(s)
- Georgia Brown
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia
| | - Emily C. Hoedt
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,School of Biomedical Sciences and PharmacyUniversity of NewcastleNewcastleNew South WalesAustralia,Hunter Medical Research InstituteNew Lambton HeightsNewcastleNew South WalesAustralia
| | - Simon Keely
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,School of Biomedical Sciences and PharmacyUniversity of NewcastleNewcastleNew South WalesAustralia,Hunter Medical Research InstituteNew Lambton HeightsNewcastleNew South WalesAustralia
| | - Ayesha Shah
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,Faculty of Medicine and Faculty of Health and Behavioural SciencesThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Marjorie M. Walker
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia
| | - Gerald Holtmann
- AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,Faculty of Medicine and Faculty of Health and Behavioural SciencesThe University of QueenslandSt. LuciaQueenslandAustralia,Department of Gastroenterology & HepatologyPrincess Alexandra HospitalWoolloongabbaQueenslandAustralia
| | - Nicholas J. Talley
- School of Medicine and Public HealthUniversity of NewcastleNewcastleNew South WalesAustralia,AGIRA (Australian Gastrointestinal Research Alliance)NewcastleNew South WalesAustralia,NHMRC Centre of Research Excellence in Digestive HealthNewcastleNew South WalesAustralia,Hunter Medical Research InstituteNew Lambton HeightsNewcastleNew South WalesAustralia
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4
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Su W, Du Y, Lian F, Wu H, Zhang X, Yang W, Duan Y, Pan Y, Liu W, Wu A, Zhao B, Wu C, Wu S. Standards for Collection, Preservation, and Transportation of Fecal Samples in TCM Clinical Trials. Front Cell Infect Microbiol 2022; 12:783682. [PMID: 35521221 PMCID: PMC9065286 DOI: 10.3389/fcimb.2022.783682] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/28/2022] [Indexed: 12/21/2022] Open
Abstract
Background Unlike chemical drugs with a single or a few kinds of active compounds, traditional Chinese medicines (TCMs)uses herbal formulas composed of numerous kinds of chemical constituents. Therefore, TCM clinical trials require unique and stricter standards for collecting, preserving, and transporting fecal samples than those used for chemical drugs. Unfortunately, there are no special standards for processing fecal samples in TCM clinical trials. Methods We invited interdisciplinary experts within TCM clinical trials and gut microbiome research to help formulate this standard. After more than a year’s in-depth discussion and amendments, we achieved a standard via expert interviews, literature research, questionnaire surveys, and public opinion solicitation. This standard has been reviewed and approved by the Standards Office of China of the Association of Chinese medicine. Results We established a sample information processing method prior to TCM clinical sample collection, which is adapted to the unique features of TCM. The method formulates detailed processing requirements for TCM information in addition to the factors that may disturb the gut microbiome. We also constructed a set of methods for collecting, preserving, and transporting fecal samples that meet the characteristics of TCM. These methods formulate detailed operating specifications on the collection approaches, storage conditions, transportation requirements, and management of fecal samples. Conclusions This standard guides the information processing prior to sample collection and the standard operating procedures for the collection, preservation, and transportation of fecal samples in TCM clinical trials, which also can be used as a reference by clinicians and researchers in modern medicines.
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Affiliation(s)
- Wenquan Su
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yawei Du
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Fengmei Lian
- Department of Endocrinology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hui Wu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinrong Zhang
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Wenli Yang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yunfeng Duan
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuanming Pan
- The 7th Medical Center, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Weijng Liu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Aiming Wu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Bowen Zhao
- Beijing QuantiHealth Technology Co, Ltd, Beijing, China
| | - Chongming Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Shengxian Wu, ; Chongming Wu,
| | - Shengxian Wu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Shengxian Wu, ; Chongming Wu,
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5
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Sardelli L, Perottoni S, Tunesi M, Boeri L, Fusco F, Petrini P, Albani D, Giordano C. Technological tools and strategies for culturing human gut microbiota in engineered in vitro models. Biotechnol Bioeng 2021; 118:2886-2905. [PMID: 33990954 PMCID: PMC8361989 DOI: 10.1002/bit.27816] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 03/29/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022]
Abstract
The gut microbiota directly impacts the pathophysiology of different human body districts. Consequently, microbiota investigation is an hot topic of research and its in vitro culture has gained extreme interest in different fields. However, the high sensitivity of microbiota to external stimuli, such as sampling procedure, and the physicochemical complexity of the gut environment make its in vitro culture a challenging task. New engineered microfluidic gut-on-a-chip devices have the potential to model some important features of the intestinal structure, but they are usually unable to sustain culture of microbiota over an extended period of time. The integration of gut-on-a-chip devices with bioreactors for continuous bacterial culture would lead to fast advances in the study of microbiota-host crosstalk. In this review, we summarize the main technologies for the continuous culture of microbiota as upstream systems to be coupled with microfluidic devices to study bacteria-host cells communication. The engineering of integrated microfluidic platforms, capable of sustaining both anaerobic and aerobic cultures, would be the starting point to unveil complex biological phenomena proper of the microbiota-host crosstalks, paving to way to multiple research and technological applications.
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Affiliation(s)
- Lorenzo Sardelli
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Simone Perottoni
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Marta Tunesi
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Lucia Boeri
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Federica Fusco
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Paola Petrini
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Diego Albani
- Department of NeuroscienceIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
| | - Carmen Giordano
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
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6
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Zhai S, Zhu Y, Feng P, Li M, Wang W, Yang L, Yang Y. Ochratoxin A: its impact on poultry gut health and microbiota, an overview. Poult Sci 2021; 100:101037. [PMID: 33752074 PMCID: PMC8005833 DOI: 10.1016/j.psj.2021.101037] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/24/2020] [Accepted: 01/02/2021] [Indexed: 12/25/2022] Open
Abstract
Ochratoxin A (OTA) is a widespread mycotoxin, that has strong thermal stability, and is difficult to remove from feed. OTA is nephrotoxic, hepatotoxic, teratogenic, immunotoxic, and enterotoxic to several species of animals. The gut is the first defense barrier against various types of mycotoxins present in feed that enter the body, and it is closely connected to other tissues through enterohepatic circulation. Compared with mammals, poultry is more sensitive to OTA and has a lower absorption rate. Therefore, the gut is an important target tissue for OTA in poultry. This review comprehensively discusses the role of OTA in gut health and the gut microbiota of poultry, focusing on the effect of OTA on digestive and absorptive processes, intestinal barrier integrity, intestinal histomorphology, gut immunity, and gut microbiota. According to the studies described to date, OTA can affect gut dysbiosis, including increasing gut permeability, immunity, and bacterial translocation, and can eventually lead to gut and other organ injury. Although there are many studies investigating the effects of OTA on the gut health of poultry, further studies are needed to better characterize the underlying mechanisms of action and develop preventative or therapeutic interventions for mycotoxicosis in poultry.
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Affiliation(s)
- Shuangshuang Zhai
- College of Animal Science, Yangtze University, Jingzhou 434000, China
| | - Yongwen Zhu
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou 510000, China
| | - Peishi Feng
- Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Macheng Li
- Research and Development department, Hunan Microorganism & Herb Biological Feed Technology Co., Ltd., Xiangtan 411100, China
| | - Wence Wang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou 510000, China
| | - Lin Yang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou 510000, China
| | - Ye Yang
- College of Animal Science, Yangtze University, Jingzhou 434000, China.
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7
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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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8
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Raftery AL, Tsantikos E, Harris NL, Hibbs ML. Links Between Inflammatory Bowel Disease and Chronic Obstructive Pulmonary Disease. Front Immunol 2020; 11:2144. [PMID: 33042125 PMCID: PMC7517908 DOI: 10.3389/fimmu.2020.02144] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
Inflammatory bowel disease (IBD) and chronic obstructive pulmonary disease (COPD) are chronic inflammatory diseases of the gastrointestinal and respiratory tracts, respectively. These mucosal tissues bear commonalities in embryology, structure and physiology. Inherent similarities in immune responses at the two sites, as well as overlapping environmental risk factors, help to explain the increase in prevalence of IBD amongst COPD patients. Over the past decade, a tremendous amount of research has been conducted to define the microbiological makeup of the intestine, known as the intestinal microbiota, and determine its contribution to health and disease. Intestinal microbial dysbiosis is now known to be associated with IBD where it impacts upon intestinal epithelial barrier integrity and leads to augmented immune responses and the perpetuation of chronic inflammation. While much less is known about the lung microbiota, like the intestine, it has its own distinct, diverse microflora, with dysbiosis being reported in respiratory disease settings such as COPD. Recent research has begun to delineate the interaction or crosstalk between the lung and the intestine and how this may influence, or be influenced by, the microbiota. It is now known that microbial products and metabolites can be transferred from the intestine to the lung via the bloodstream, providing a mechanism for communication. While recent studies indicate that intestinal microbiota can influence respiratory health, intestinal dysbiosis in COPD has not yet been described although it is anticipated since factors that lead to dysbiosis are similarly associated with COPD. This review will focus on the gut-lung axis in the context of IBD and COPD, highlighting the role of environmental and genetic factors and the impact of microbial dysbiosis on chronic inflammation in the intestinal tract and lung.
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Affiliation(s)
- April L Raftery
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Evelyn Tsantikos
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Nicola L Harris
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Margaret L Hibbs
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
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9
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Guo XY, Liu XJ, Hao JY. Gut microbiota in ulcerative colitis: insights on pathogenesis and treatment. J Dig Dis 2020; 21:147-159. [PMID: 32040250 DOI: 10.1111/1751-2980.12849] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/16/2020] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
Gut microbiota constitute the largest reservoir of the human microbiome and are an abundant and stable ecosystem-based on its diversity, complexity, redundancy, and host interactions This ecosystem is indispensable for human development and health. The integrity of the intestinal mucosal barrier depends on its interactions with gut microbiota. The commensal bacterial community is implicated in the pathogenesis of inflammatory bowel disease (IBD), including ulcerative colitis (UC). The dysbiosis of microbes is characterized by reduced biodiversity, abnormal composition of gut microbiota, altered spatial distribution, as well as interactions among microbiota, between different strains of microbiota, and with the host. The defects in microecology, with the related metabolic pathways and molecular mechanisms, play a critical role in the innate immunity of the intestinal mucosa in UC. Fecal microbiota transplantation (FMT) has been used to treat many diseases related to gut microbiota, with the most promising outcome reported in antibiotic-associated diarrhea, followed by IBD. This review evaluated the results of various reports of FMT in UC. The efficacy of FMT remains highly controversial, and needs to be regularized by integrated management, standardization of procedures, and individualization of treatment.
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Affiliation(s)
- Xiao Yan Guo
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xin Juan Liu
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jian Yu Hao
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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10
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Flux MC, Lowry CA. Finding intestinal fortitude: Integrating the microbiome into a holistic view of depression mechanisms, treatment, and resilience. Neurobiol Dis 2020; 135:104578. [PMID: 31454550 PMCID: PMC6995775 DOI: 10.1016/j.nbd.2019.104578] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 06/27/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023] Open
Abstract
Depression affects at least 322 million people globally, or approximately 4.4% of the world's population. While the earnestness of researchers and clinicians to understand and treat depression is not waning, the number of individuals suffering from depression continues to increase over and above the rate of global population growth. There is a sincere need for a paradigm shift. Research in the past decade is beginning to take a more holistic approach to understanding depression etiology and treatment, integrating multiple body systems into whole-body conceptualizations of this mental health affliction. Evidence supports the hypothesis that the gut microbiome, or the collective trillions of microbes inhabiting the gastrointestinal tract, is an important factor determining both the risk of development of depression and persistence of depressive symptoms. This review discusses recent advances in both rodent and human research that explore bidirectional communication between the gut microbiome and the immune, endocrine, and central nervous systems implicated in the etiology and pathophysiology of depression. Through interactions with circulating inflammatory markers and hormones, afferent and efferent neural systems, and other, more niche, pathways, the gut microbiome can affect behavior to facilitate the development of depression, exacerbate current symptoms, or contribute to treatment and resilience. While the challenge of depression may be the direst mental health crisis of our age, new discoveries in the gut microbiome, when integrated into a holistic perspective, hold great promise for the future of positive mental health.
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Affiliation(s)
- M C Flux
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Christopher A Lowry
- Department of Integrative Physiology, Center for Neuroscience, and Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO 80309, USA; Department of Physical Medicine & Rehabilitation and Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO 80045, USA; Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO 80045, USA; Senior Fellow, VIVO Planetary Health, Worldwide Universities Network (WUN), West New York, NJ 07093, USA.
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11
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Comparison of the fecal, cecal, and mucus microbiome in male and female mice after TNBS-induced colitis. PLoS One 2019; 14:e0225079. [PMID: 31703107 PMCID: PMC6839838 DOI: 10.1371/journal.pone.0225079] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/28/2019] [Indexed: 12/15/2022] Open
Abstract
Crohn’s Disease and Ulcerative Colitis are chronic, inflammatory conditions of the digestive tract, collectively known as Inflammatory Bowel Disease (IBD). The combined influence of lifestyle factors, genetics, and the gut microbiome contribute to IBD pathogenesis. Studies of the gut microbiome have shown significant differences in its composition between healthy individuals and those with IBD. Due to the high inter-individual microbiome variation seen in humans, mouse models of IBD are often used to investigate potential IBD mechanisms and their interplay between host, microbial, and environmental factors. While fecal samples are the predominant material used for microbial community analysis, they may not be the ideal sample to use for analysis of the microbiome of mice with experimental colitis, such as that induced by 2, 4, 6 trinitrobenzesulfonic acid (TNBS). As TNBS is administered intrarectally to induce colitis and inflammation is confined to the colon in this model, we hypothesized that the microbiome of the colonic mucus would most closely correlate with TNBS colitis severity. Based on our previous research, we also hypothesized that sex would be associated with both disease severity and microbial differences in mice with chronic TNBS colitis. We examined and compared the fecal, cecal content, and colonic mucus microbiota of 8-week old male and female C57BL/6J wild-type mice prior to and after the induction of TNBS colitis via 16S rRNA gene sequencing. We found that the colonic mucus microbiome was more closely correlated with disease severity than were alterations in the fecal and cecal microbiomes. We also found that the microbiomes of the feces, cecum, and mucus were distinct, but found no significant differences that were associated with sex in either compartment. Our findings highlight the importance of sampling colonic mucus in TNBS-induced colitis. Moreover, consideration of the differential impact of sex on the microbiome across mouse strains may be critical for the appropriate application of TNBS colitis models and robust comparisons across studies in the future.
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Abulizi N, Quin C, Brown K, Chan YK, Gill SK, Gibson DL. Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids. Nutrients 2019; 11:nu11020418. [PMID: 30781503 PMCID: PMC6412740 DOI: 10.3390/nu11020418] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/01/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023] Open
Abstract
The dynamics of the tripartite relationship between the host, gut bacteria and diet in the gut is relatively unknown. An imbalance between harmful and protective gut bacteria, termed dysbiosis, has been linked to many diseases and has most often been attributed to high-fat dietary intake. However, we recently clarified that the type of fat, not calories, were important in the development of murine colitis. To further understand the host-microbe dynamic in response to dietary lipids, we fed mice isocaloric high-fat diets containing either milk fat, corn oil or olive oil and performed 16S rRNA gene sequencing of the colon microbiome and mass spectrometry-based relative quantification of the colonic metaproteome. The corn oil diet, rich in omega-6 polyunsaturated fatty acids, increased the potential for pathobiont survival and invasion in an inflamed, oxidized and damaged gut while saturated fatty acids promoted compensatory inflammatory responses involved in tissue healing. We conclude that various lipids uniquely alter the host-microbe interaction in the gut. While high-fat consumption has a distinct impact on the gut microbiota, the type of fatty acids alters the relative microbial abundances and predicted functions. These results support that the type of fat are key to understanding the biological effects of high-fat diets on gut health.
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Affiliation(s)
- Nijiati Abulizi
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
| | - Candice Quin
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
| | - Kirsty Brown
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
| | - Yee Kwan Chan
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
| | - Sandeep K Gill
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
| | - Deanna L Gibson
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver V6T 1Z3, Canada.
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Heintz-Buschart A, Wilmes P. Human Gut Microbiome: Function Matters. Trends Microbiol 2018; 26:563-574. [DOI: 10.1016/j.tim.2017.11.002] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/29/2017] [Accepted: 11/03/2017] [Indexed: 12/16/2022]
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Russo E, Bacci G, Chiellini C, Fagorzi C, Niccolai E, Taddei A, Ricci F, Ringressi MN, Borrelli R, Melli F, Miloeva M, Bechi P, Mengoni A, Fani R, Amedei A. Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study. Front Microbiol 2018; 8:2699. [PMID: 29375539 PMCID: PMC5770402 DOI: 10.3389/fmicb.2017.02699] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/26/2017] [Indexed: 12/15/2022] Open
Abstract
In this study Next-Generation Sequencing (NGS) was used to analyze and compare human microbiota from three different compartments, i.e., saliva, feces, and cancer tissue (CT), of a selected cohort of 10 Italian patients with colorectal cancer (CRC) vs. 10 healthy controls (saliva and feces). Furthermore, the Fusobacterium nucleatum abundance in the same body site was investigated through real-time quantitative polymerase chain reaction (qPCR) to assess the association with CRC. Differences in bacterial composition, F. nucleatum abundance in healthy controls vs. CRC patients, and the association of F. nucleatum with clinical parameters were observed. Taxonomic analysis based on 16S rRNA gene, revealed the presence of three main bacterial phyla, which includes about 80% of reads: Firmicutes (39.18%), Bacteroidetes (30.36%), and Proteobacteria (10.65%). The results highlighted the presence of different bacterial compositions; in particular, the fecal samples of CRC patients seemed to be enriched with Bacteroidetes, whereas in the fecal samples of healthy controls Firmicutes were one of the major phyla detected though these differences were not statistically significant. The CT samples showed the highest alpha diversity values. These results emphasize a different taxonomic composition of feces from CRC compared to healthy controls. Despite the low number of samples included in the study, these results suggest the importance of microbiota in the CRC progression and could pave the way to the development of therapeutic interventions and novel microbial-related diagnostic tools in CRC patients.
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Affiliation(s)
- Edda Russo
- Immunology, Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, Florence, Italy
| | | | - Camilla Fagorzi
- Department of Biology, University of Florence, Florence, Italy
| | - Elena Niccolai
- Immunology, Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Antonio Taddei
- Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Federica Ricci
- Immunology, Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Maria N Ringressi
- Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Rossella Borrelli
- Immunology, Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Filippo Melli
- Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Manouela Miloeva
- Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Paolo Bechi
- Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Florence, Italy
| | - Amedeo Amedei
- Immunology, Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy.,Neuromusculoskeletal Department (Interdisciplinary Internal Medicine), Azienda Ospedaliera Universitaria Careggi, Florence, Italy
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Kodukula K, Faller DV, Harpp DN, Kanara I, Pernokas J, Pernokas M, Powers WR, Soukos NS, Steliou K, Moos WH. Gut Microbiota and Salivary Diagnostics: The Mouth Is Salivating to Tell Us Something. Biores Open Access 2017; 6:123-132. [PMID: 29098118 PMCID: PMC5665491 DOI: 10.1089/biores.2017.0020] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The microbiome of the human body represents a symbiosis of microbial networks spanning multiple organ systems. Bacteria predominantly represent the diversity of human microbiota, but not to be forgotten are fungi, viruses, and protists. Mounting evidence points to the fact that the "microbial signature" is host-specific and relatively stable over time. As our understanding of the human microbiome and its relationship to the health of the host increases, it is becoming clear that many and perhaps most chronic conditions have a microbial involvement. The oral and gastrointestinal tract microbiome constitutes the bulk of the overall human microbial load, and thus presents unique opportunities for advancing human health prognosis, diagnosis, and therapy development. This review is an attempt to catalog a broad diversity of recent evidence and focus it toward opportunities for prevention and treatment of debilitating illnesses.
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Affiliation(s)
- Krishna Kodukula
- Bridgewater College, Bridgewater, Virginia
- ShangPharma Innovation, Inc., South San Francisco, California
- PhenoMatriX, Inc., Natick, Massachusetts
| | - Douglas V. Faller
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Cancer Research Center, Boston University School of Medicine, Boston, Massachusetts
| | - David N. Harpp
- Department of Chemistry, McGill University, Montreal, Canada
| | | | - Julie Pernokas
- Advanced Dental Associates of New England, Woburn, Massachusetts
| | - Mark Pernokas
- Advanced Dental Associates of New England, Woburn, Massachusetts
| | - Whitney R. Powers
- Department of Health Sciences, Boston University, Boston, Massachusetts
- Department of Anatomy, Boston University School of Medicine, Boston, Massachusetts
| | - Nikolaos S. Soukos
- Dana Research Center, Department of Physics, Northeastern University, Boston, Massachusetts
| | - Kosta Steliou
- PhenoMatriX, Inc., Natick, Massachusetts
- Cancer Research Center, Boston University School of Medicine, Boston, Massachusetts
| | - Walter H. Moos
- ShangPharma Innovation, Inc., South San Francisco, California
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, California
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