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McPhail MN, Wu M, Tague K, Wajeeh H, Demory Beckler M, Kesselman MM. A Scoping Review of the Positive and Negative Bacteria Associated With the Gut Microbiomes of Systemic Lupus Erythematosus Patients. Cureus 2024; 16:e57512. [PMID: 38707123 PMCID: PMC11067397 DOI: 10.7759/cureus.57512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that affects multiple systems of the body. Recent research on the gut microbiota dysbiosis associated with SLE patients has gained traction and warranted further exploration. It has not been determined whether the change in the gut microbiota is a cause of SLE or a symptom of SLE. However, based on the physiological and pathophysiological role of the bacteria in the gut microbiome, as levels of the bacteria rise or fall, symptomatology in SLE patients could be affected. This review analyzes the recent studies that examined the changes in the gut microbiota of SLE patients and highlights the correlations between gut dysbiosis and the clinical manifestations of SLE. A systematic search strategy was developed by combining the terms "SLE," "systemic lupus erythematosus," and "gut microbiome." Biomedical Reference Collection, CINAHL, Medline ProQuest, and PubMed Central databases were searched by combining the appropriate keywords with "AND." Only full-text, English-language articles were searched. The articles were restricted from 2013 to 2023. Only peer-reviewed controlled studies with both human and animal trials were included in this scoping review. Review articles, non-English articles, editorials, case studies, and duplicate articles from the four databases were excluded. Various species of bacteria were found to be positively or negatively associated with SLE gut microbiomes. Among the bacterial species increased were Clostridium, Lactobacilli, Streptococcus, Enterobacter, and Klebsiella. The bacterial species that decreased were Bifidobacteria, Prevotella, and the Firmicutes/Bacteroidetes ratio. Literature shows that Clostridium is one of several bacteria found in abundance, from pre-disease to the diseased state of SLE. Lachnospiraceae and Ruminococcaceae are both part of the family of butyrate-producing anaerobes that are known for their role in strengthening the skin barrier function and, therefore, may explain the cutaneous manifestations of SLE patients. Studies have also shown that the Firmicutes/Bacteroidetes ratio is significantly depressed, which may lead to appetite changes and weight loss seen in SLE patients. Based on the established role of these bacteria within the gut microbiome, the disruption in the gut ecosystem could explain the symptomatology common in SLE patients. By addressing these changes, our scoping review encourages further research to establish a true causal relationship between the bacterial changes in SLE patients as well as furthering the scope of microbiota changes in other systems and autoimmune diseases.
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Affiliation(s)
- Marissa N McPhail
- Osteopathic Medicine, Nova Southeastern University Dr. Kiran C. Patel College of Osteopathic Medicine, Fort Lauderdale, USA
| | - Michael Wu
- Osteopathic Medicine, Nova Southeastern University Dr. Kiran C. Patel College of Osteopathic Medicine, Fort Lauderdale, USA
| | - Kelsey Tague
- Osteopathic Medicine, Nova Southeastern University Dr. Kiran C. Patel College of Osteopathic Medicine, Fort Lauderdale, USA
| | - Hassaan Wajeeh
- Osteopathic Medicine, Nova Southeastern University Dr. Kiran C. Patel College of Osteopathic Medicine, Fort Lauderdale, USA
| | - Michelle Demory Beckler
- Microbiology and Immunology, Nova Southeastern University Dr. Kiran C. Patel College of Allopathic Medicine, Fort Lauderdale, USA
| | - Marc M Kesselman
- Rheumatology, Nova Southeastern University Dr. Kiran C. Patel College of Osteopathic Medicine, Davie, USA
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2
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Zhang M, Zhou Y, Cui X, Zhu L. The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis. Microorganisms 2024; 12:713. [PMID: 38674657 PMCID: PMC11051890 DOI: 10.3390/microorganisms12040713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.
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Affiliation(s)
| | | | | | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210098, China; (M.Z.); (Y.Z.); (X.C.)
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Hotchkiss MZ, Forrest JRK, Poulain AJ. Exposure to a fungicide for a field-realistic duration does not alter bumble bee fecal microbiota structure. Appl Environ Microbiol 2024; 90:e0173923. [PMID: 38240563 PMCID: PMC10880609 DOI: 10.1128/aem.01739-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/25/2023] [Indexed: 02/22/2024] Open
Abstract
Social bees are frequently exposed to pesticides when foraging on nectar and pollen. Recent research has shown that pesticide exposure not only impacts social bee host health but can also alter the community structure of social bee gut microbiotas. However, most research on pesticide-bee gut microbiota interactions has been conducted in honey bees; bumble bees, native North American pollinators, have received less attention and, due to differences in their ecology, may be exposed to certain pesticides for shorter durations than honey bees. Here, we examine how exposure to the fungicide chlorothalonil for a short, field-realistic duration alters bumble bee fecal microbiotas (used as a proxy for gut microbiotas) and host performance. We expose small groups of Bombus impatiens workers (microcolonies) to field-realistic chlorothalonil concentrations for 5 days, track changes in fecal microbiotas during the exposure period and a recovery period, and compare microcolony offspring production between treatments at the end of the experiment. We also assess the use of fecal microbiotas as a gut microbiota proxy by comparing community structures of fecal and gut microbiotas. We find that chlorothalonil exposure for a short duration does not alter bumble bee fecal microbiota structure or affect microcolony production at any concentration but that fecal and gut microbiotas differ significantly in community structure. Our results show that, at least when exposure durations are brief and unaccompanied by other stressors, bumble bee microbiotas are resilient to fungicide exposure. Additionally, our work highlights the importance of sampling gut microbiotas directly, when possible.IMPORTANCEWith global pesticide use expected to increase in the coming decades, studies on how pesticides affect the health and performance of animals, including and perhaps especially pollinators, will be crucial to minimize negative environmental impacts of pesticides in agriculture. Here, we find no effect of exposure to chlorothalonil for a short, field-realistic period on bumble bee fecal microbiota community structure or microcolony production regardless of pesticide concentration. Our results can help inform pesticide use practices to minimize negative environmental impacts on the health and fitness of bumble bees, which are key native, commercial pollinators in North America. We also find that concurrently sampled bumble bee fecal and gut microbiotas contain similar microbes but differ from one another in community structure and consequently suggest that using fecal microbiotas as a proxy for gut microbiotas be done cautiously; this result contributes to our understanding of proxy use in gut microbiota research.
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Liu X, Li K, Yang Y, Cao D, Xu X, He Z, Wu W. Gut resistome profiling reveals high diversity and fluctuations in pancreatic cancer cohorts. Front Cell Infect Microbiol 2024; 14:1354234. [PMID: 38384305 PMCID: PMC10879602 DOI: 10.3389/fcimb.2024.1354234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
Background Pancreatic cancer is one of the deadliest cancer, with a 5-year overall survival rate of 11%. Unfortunately, most patients are diagnosed with advanced stage by the time they present with symptoms. In the past decade, microbiome studies have explored the association of pancreatic cancer with the human oral and gut microbiomes. However, the gut microbial antibiotic resistance genes profiling of pancreatic cancer patients was never reported compared to that of the healthy cohort. Results In this study, we addressed the gut microbial antibiotic resistance genes profile using the metagenomic data from two online public pancreatic cancer cohorts. We found a high degree of data concordance between the two cohorts, which can therefore be used for cross-sectional comparisons. Meanwhile, we used two strategies to predict antibiotic resistance genes and compared the advantages and disadvantages of these two approaches. We also constructed microbe-antibiotic resistance gene networks and found that most of the hub nodes in the networks were antibiotic resistance genes. Conclusions In summary, we describe the panorama of antibiotic resistance genes in the gut microbes of patients with pancreatic cancer. We hope that our study will provide new perspectives on treatment options for the disease.
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Affiliation(s)
- Xudong Liu
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Kexin Li
- School of Engineering Medicine, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, China
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology- Hans Knöll Institute, Jena, Germany
| | - Yun Yang
- School of Engineering Medicine, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, China
| | - Dingyan Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xinjie Xu
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Zilong He
- School of Engineering Medicine, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, China
| | - Wenming Wu
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
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Seppi M, Pasqualini J, Facchin S, Savarino EV, Suweis S. Emergent Functional Organization of Gut Microbiomes in Health and Diseases. Biomolecules 2023; 14:5. [PMID: 38275746 PMCID: PMC10813293 DOI: 10.3390/biom14010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Continuous and significant progress in sequencing technologies and bioinformatics pipelines has revolutionized our comprehension of microbial communities, especially for human microbiomes. However, most studies have focused on studying the taxonomic composition of the microbiomes and we are still not able to characterize dysbiosis and unveil the underlying ecological consequences. This study explores the emergent organization of functional abundances and correlations of gut microbiomes in health and disease. Leveraging metagenomic sequences, taxonomic and functional tables are constructed, enabling comparative analysis. First, we show that emergent taxonomic and functional patterns are not useful to characterize dysbiosis. Then, through differential abundance analyses applied to functions, we reveal distinct functional compositions in healthy versus unhealthy microbiomes. In addition, we inquire into the functional correlation structure, revealing significant differences between the healthy and unhealthy groups, which may significantly contribute to understanding dysbiosis. Our study demonstrates that scrutinizing the functional organization in the microbiome provides novel insights into the underlying state of the microbiome. The shared data structure underlying the functional and taxonomic compositions allows for a comprehensive macroecological examination. Our findings not only shed light on dysbiosis, but also underscore the importance of studying functional interrelationships for a nuanced understanding of the dynamics of the microbial community. This research proposes a novel approach, bridging the gap between microbial ecology and functional analyses, promising a deeper understanding of the intricate world of the gut microbiota and its implications for human health.
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Affiliation(s)
- Marcello Seppi
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
| | - Jacopo Pasqualini
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
| | - Sonia Facchin
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Via Giustiniani 2, 35121 Padua, Italy; (S.F.); (E.V.S.)
| | - Edoardo Vincenzo Savarino
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Via Giustiniani 2, 35121 Padua, Italy; (S.F.); (E.V.S.)
| | - Samir Suweis
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
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Peng YC, Xu JX, You XM, Huang YY, Ma L, Li LQ, Qi LN. Specific gut microbiome signature predicts hepatitis B virus-related hepatocellular carcinoma patients with microvascular invasion. Ann Med 2023; 55:2283160. [PMID: 38112540 PMCID: PMC10986448 DOI: 10.1080/07853890.2023.2283160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND We aimed to assess differences in intestinal microflora between patients with operable hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) with microvascular invasion (MVI) and those without MVI. Additionally, we investigated the potential of the microbiome as a non-invasive biomarker for patients with MVI. METHODS We analyzed the preoperative gut microbiomes (GMs) of two groups, the MVI (n = 46) and non-MVI (n = 56) groups, using 16S ribosomal RNA gene sequencing data. At the operational taxonomic unit level, we employed random forest models to predict MVI risk and validated the results in independent validation cohorts [MVI group (n = 17) and non-MVI group (n = 15)]. RESULTS β diversity analysis, utilizing weighted UniFrac distances, revealed a significant difference between the MVI and non-MVI groups, as indicated by non-metric multidimensional scaling and principal coordinate analysis. We also observed a significant correlation between the characteristic intestinal microbial communities at the genus level and their main functions. Nine optimal microbial markers were identified, with an area under the curve of 79.76% between 46 MVI and 56 non-MVI samples and 79.80% in the independent verification group. CONCLUSION This pioneering analysis of the GM in patients with operable HBV-HCC with and without MVI opens new avenues for treating HBV-HCC with MVI. We successfully established a diagnostic model and independently verified microbial markers for patients with MVI. As preoperative targeted biomarkers, GM holds potential as a non-invasive tool for patients with HBV-HCC with MVI.
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Affiliation(s)
- Yu-Chong Peng
- Department of General Surgery, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Jing-Xuan Xu
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
| | - Xue-Mei You
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
| | - Yi-Yue Huang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
| | - Liang Ma
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
| | - Le-Qun Li
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
- Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning, China
| | - Lu-Nan Qi
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Nanning, China
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Garbisu C, Alkorta I. A case for the importance of following antibiotic resistant bacteria throughout the soil food web. Bioessays 2023; 45:e2300153. [PMID: 37987191 DOI: 10.1002/bies.202300153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/17/2023] [Accepted: 10/04/2023] [Indexed: 11/22/2023]
Abstract
It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.
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Affiliation(s)
- Carlos Garbisu
- NEIKER - Basque Institute for Agricultural Research and Development, Derio, Spain
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
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Schwarz M, Beza-Beza CF, Mikaelyan A. Wood fibers are a crucial microhabitat for cellulose- and xylan- degrading bacteria in the hindgut of the wood-feeding beetle Odontotaenius disjunctus. Front Microbiol 2023; 14:1173696. [PMID: 37448580 PMCID: PMC10338082 DOI: 10.3389/fmicb.2023.1173696] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction Wood digestion in insects relies on the maintenance of a mosaic of numerous microhabitats, each colonized by distinct microbiomes. Understanding the division of digestive labor between these microhabitats- is central to understanding the physiology and evolution of symbiotic wood digestion. A microhabitat that has emerged to be of direct relevance to the process of lignocellulose digestion is the surface of ingested plant material. Wood particles in the guts of some termites are colonized by a specialized bacterial fiber-digesting microbiome, but whether this represents a widespread strategy among insect lineages that have independently evolved wood-feeding remains an open question. Methods In this study, we investigated the bacterial communities specifically associated with wood fibers in the gut of the passalid beetle Odontotaenius disjunctus. We developed a Percoll-based centrifugation method to isolate and enrich the wood particles from the anterior hindgut, allowing us to access the wood fibers and their associated microbiome. We then performed assays of enzyme activity and used short-read and long-read amplicon sequencing of the 16S rRNA gene to identify the composition of the fiber-associated microbiome. Results Our assays demonstrated that the anterior hindgut, which houses a majority of the bacterial load, is an important site for lignocellulose digestion. Wood particles enriched from the anterior hindgut contribute to a large proportion of the total enzyme activity. The sequencing revealed that O. disjunctus, like termites, harbors a distinct fiber-associated microbiome, but notably, its community is enriched in insect-specific groups of Lactococcus and Turicibacter. Discussion Our study underscores the importance of microhabitats in fostering the complex symbiotic relationships between wood-feeding insects and their microbiomes. The discovery of distinct fiber-digesting symbionts in O. disjunctus, compared to termites, highlights the diverse evolutionary paths insects have taken to adapt to a challenging diet.
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Affiliation(s)
| | | | - Aram Mikaelyan
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
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Karki S, Mainali A, Pandey S, Uprety N, Panigrahi K, Adhikari S. Veillonella Bacteremia in a Patient With Metastatic Colorectal Carcinoma. Cureus 2023; 15:e41152. [PMID: 37519587 PMCID: PMC10386893 DOI: 10.7759/cureus.41152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2023] [Indexed: 08/01/2023] Open
Abstract
Colorectal carcinoma has increasingly been reported to be associated with gut microbial dysbiosis. Bacteroides, Fusobacterium, Faecalibacterium, Blautia, etc., are gut microbes commonly associated with colorectal carcinoma. Gut microbial dysregulation secondary to infectious, inflammatory, toxin exposure or change in dietary habits coupled with the disruption of the inner mucosal layer overlying the luminal epithelium is hypothesized as the inciting events leading to microbial invasion and subsequent tumorigenesis. Although the precise mechanism is unclear, disruption of normal host responses like inflammation, apoptosis, cellular proliferation, free radical injury, production of oncogenic toxins, etc., is postulated to play a role. We report a case of Veillonella bacteremia in a patient with metastatic colorectal carcinoma without a preceding history of periodontal disease. The patient was managed with ampicillin-sulbactam, which was followed by subsequent negative blood cultures. This case report signifies the association of gut microbiota like Veillonella with colorectal carcinoma and the importance of subsequent screening for colorectal cancer following Veillonella bacteremia.
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Affiliation(s)
- Sailesh Karki
- Internal Medicine, One Brooklyn Health-Interfaith Medical Center, Brooklyn, USA
| | - Arjun Mainali
- Internal Medicine, One Brooklyn Health-Interfaith Medical Center, Brooklyn, USA
| | - Sagar Pandey
- Internal Medicine, One Brooklyn Health-Interfaith Medical Center, Brooklyn, USA
| | - Navodita Uprety
- Internal Medicine, One Brooklyn Health-Interfaith Medical Center, Brooklyn, USA
| | - Kalpana Panigrahi
- Internal Medicine, One Brooklyn Health-Interfaith Medical Center, Brooklyn, USA
| | - Samaj Adhikari
- Internal Medicine, One Brooklyn Health-Interfaith Medical Center, Brooklyn, USA
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Paramsothy J, Gutlapalli SD, Ganipineni VDP, Okorie IJ, Ugwendum D, Piccione G, Ducey J, Kouyate G, Onana A, Emmer L, Arulthasan V, Otterbeck P, Nfonoyim J. Understanding Auto-Brewery Syndrome in 2023: A Clinical and Comprehensive Review of a Rare Medical Condition. Cureus 2023; 15:e37678. [PMID: 37206535 PMCID: PMC10189828 DOI: 10.7759/cureus.37678] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2023] [Indexed: 05/21/2023] Open
Abstract
Auto-brewery syndrome (ABS) occurs when the gastrointestinal tract produces excessive endogenous ethanol. This article examines various aspects of ABS such as its epidemiology, underlying etiology, diagnostic difficulties, management strategies, and social implications. By synthesizing the existing medical literature, we hope to identify understanding gaps, pave the way for further research, and ultimately improve detection, treatment, and awareness. The databases we used are PubMed, PubMed Central, and Google Scholar. We carefully screened all published articles from inception till date and narrowed down 24 relevant articles. We at Richmond University Medical Center and Mount Sinai are one of the leading medical centers for diagnosing and treating this rare condition in the United States.
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Affiliation(s)
- Jananthan Paramsothy
- Internal Medicine, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
| | - Sai Dheeraj Gutlapalli
- Internal Medicine, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
- Internal Medicine Clinical Research, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Vijay Durga Pradeep Ganipineni
- General Medicine, SRM Medical College Hospital and Research Center, Chennai, IND
- General Medicine, Andhra Medical College/King George Hospital, Visakhapatnam, IND
- Internal Medicine, Thomas Hospital Infirmary Health, Fairhope, USA
| | - Ikpechukwu J Okorie
- Internal Medicine, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
| | - Derek Ugwendum
- Internal Medicine, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
| | - GianPaolo Piccione
- Internal Medicine, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
| | - James Ducey
- Internal Medicine, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
| | - Gnama Kouyate
- Internal Medicine, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
| | - Arnold Onana
- Internal Medicine, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
| | - Louis Emmer
- Internal Medicine, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
| | - Vaithilingam Arulthasan
- Internal Medicine, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
| | - Philip Otterbeck
- Endocrinology, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
| | - Jay Nfonoyim
- Pulmonary and Critical Care, Richmond University Medical Center Affiliated with Mount Sinai Health System and Icahn School of Medicine at Mount Sinai, Staten Island, USA
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11
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Ul-Haq A, Lee KA, Seo H, Kim S, Jo S, Ko KM, Moon SJ, Kim YS, Choi JR, Song HY, Kim HS. Characteristic alterations of gut microbiota in uncontrolled gout. J Microbiol 2022; 60:1178-1190. [PMID: 36422845 DOI: 10.1007/s12275-022-2416-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Microbiome research has been on the rise recently for a more in-depth understanding of gout. Meanwhile, there is a need to understand the gut microbiome related to uric acid-lowering drug resistance. In this study, 16S rRNA gene-based microbiota analysis was performed for a total of 65 stool samples from 17 healthy controls and 48 febuxostat-treated gout patients (including 28 controlled subjects with decreased uric acid levels and 20 uncontrolled subjects with non-reduced uric acid levels). Alpha diversity of bacterial community decreased in the healthy control, controlled, and uncontrolled groups. In the case of beta diversity, the bacterial community was significantly different among groups (healthy control, controlled, and uncontrolled groups). Taxonomic biomarker analysis revealed the increased population of g-Bifidobacterium in healthy controls and g-Prevotella in uncontrolled patients. PCR further confirmed this result at the species level. Additionally, functional metagenomics predictions led to the exploration of various functional biomarkers, including purine metabolism. The results of this study can serve as a basis for developing potential new strategies for diagnosing and treating gout from microbiome prospects.
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Affiliation(s)
- Asad Ul-Haq
- Division of Rheumatology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, 04401, Republic of Korea
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Kyung-Ann Lee
- Division of Rheumatology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, 04401, Republic of Korea
| | - Hoonhee Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Republic of Korea
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 33151, Republic of Korea
| | - Sukyung Kim
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 33151, Republic of Korea
| | - Sujin Jo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Kyung Min Ko
- Division of Rheumatology, Department of Internal Medicine, International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon, 22711, Republic of Korea
| | - Su-Jin Moon
- Division of Rheumatology, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 07345, Republic of Korea
| | - Yun Sung Kim
- Division of Rheumatology, Department of Internal Medicine, Chosun University College of Medicine, Gwangju, 61452, Republic of Korea
| | - Jung Ran Choi
- Divison of Rheumatology, Department of Internal Medicine, Pohang St. Mary's Hospital, Pohang, 37661, Republic of Korea
| | - Ho-Yeon Song
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Republic of Korea.
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 33151, Republic of Korea.
| | - Hyun-Sook Kim
- Division of Rheumatology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, 04401, Republic of Korea.
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12
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Hotchkiss MZ, Poulain AJ, Forrest JRK. Pesticide-induced disturbances of bee gut microbiotas. FEMS Microbiol Rev 2022; 46:6517452. [PMID: 35107129 DOI: 10.1093/femsre/fuab056] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022] Open
Abstract
Social bee gut microbiotas play key roles in host health and performance. Worryingly, a growing body of literature shows that pesticide exposure can disturb these microbiotas. Most studies examine changes in taxonomic composition in Western honey bee (Apis mellifera) gut microbiotas caused by insecticide exposure. Core bee gut microbiota taxa shift in abundance after exposure but are rarely eliminated, with declines in Bifidobacteriales and Lactobacillus near melliventris abundance being the most common shifts. Pesticide concentration, exposure duration, season and concurrent stressors all influence whether and how bee gut microbiotas are disturbed. Also, the mechanism of disturbance-i.e. whether a pesticide directly affects microbial growth or indirectly affects the microbiota by altering host health-likely affects disturbance consistency. Despite growing interest in this topic, important questions remain unanswered. Specifically, metabolic shifts in bee gut microbiotas remain largely uninvestigated, as do effects of pesticide-disturbed gut microbiotas on bee host performance. Furthermore, few bee species have been studied other than A. mellifera, and few herbicides and fungicides have been examined. We call for these knowledge gaps to be addressed so that we may obtain a comprehensive picture of how pesticides alter bee gut microbiotas, and of the functional consequences of these changes.
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13
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Gu Y, Zhou G, Zhou F, Li Y, Wu Q, He H, Zhang Y, Ma C, Ding J, Hua K. Gut and Vaginal Microbiomes in PCOS: Implications for Women's Health. Front Endocrinol (Lausanne) 2022; 13:808508. [PMID: 35282446 PMCID: PMC8905243 DOI: 10.3389/fendo.2022.808508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/01/2022] [Indexed: 12/12/2022] Open
Abstract
PCOS is defined as a kind of endocrine and metabolic disorder which affects females at reproductive ages, is becoming much more common, nowadays. Microbiomes are known as microorganisms that inhabit the body to play a vital role in human health. In recent years, several basic and clinical studies have tried to investigate the correlation between the reproductive health/disorder and microbiomes (gut microbiomes and vaginal microbiomes). However, the mechanism is still unclear. In this review, we reviewed the relationship between PCOS and microbiomes, including gut/vaginal microbiomes compositions in PCOS, mechanism of microbiomes and PCOS, and then collectively focused on the recent findings on the influence of microbiomes on the novel insight regarding the therapeutic strategies for PCOS in the future clinical practice.
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Affiliation(s)
- Yuanyuan Gu
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, China
- Department of Gynecology, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Guannan Zhou
- Department of Gynecology, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Department of Gynecology, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Fangyue Zhou
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yao Li
- Department of Urology, Gongli Hospital of Shanghai Pudong New Area, Shanghai, China
| | - Qiongwei Wu
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, China
| | - Hongyu He
- Department of Intensive Care Unit, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yi Zhang
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, China
| | - Chengbin Ma
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, China
- *Correspondence: Chengbin Ma, ; Jingxin Ding, ; Keqin Hua,
| | - Jingxin Ding
- Department of Gynecology, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Department of Gynecology, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
- *Correspondence: Chengbin Ma, ; Jingxin Ding, ; Keqin Hua,
| | - Keqin Hua
- Department of Gynecology, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Department of Gynecology, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
- *Correspondence: Chengbin Ma, ; Jingxin Ding, ; Keqin Hua,
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14
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Zhu L, Zhang Y, Cui X, Zhu Y, Dai Q, Chen H, Liu G, Yao R, Yang Z. Host Bias in Diet-Source Microbiome Transmission in Wild Cohabitating Herbivores: New Knowledge for the Evolution of Herbivory and Plant Defense. Microbiol Spectr 2021; 9:e0075621. [PMID: 34406815 PMCID: PMC8552726 DOI: 10.1128/spectrum.00756-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
It is commonly understood that dietary nutrition will influence the composition and function of the animal gut microbiome. However, the transmission of organisms from the diet-source microbiome to the animal gut microbiome in the natural environment remains poorly understood, and elucidating this process may help in understanding the evolution of herbivores and plant defenses. Here, we investigated diet-source microbiome transmission across a range of herbivores (insects and mammals) living in both captive and wild environments. We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. IMPORTANCE We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. This study shed new light on the coevolution of herbivory and plant defense.
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Affiliation(s)
- Lifeng Zhu
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Yongyong Zhang
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Xinyuan Cui
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Yudong Zhu
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Qinlong Dai
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Hua Chen
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Guoqi Liu
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Ran Yao
- College of Life Sciences, Nanjing Norma University, Nanjing, China
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15
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Li A, Laville E, Tarquis L, Lombard V, Ropartz D, Terrapon N, Henrissat B, Guieysse D, Esque J, Durand J, Morgavi DP, Potocki-Veronese G. Analysis of the diversity of the glycoside hydrolase family 130 in mammal gut microbiomes reveals a novel mannoside-phosphorylase function. Microb Genom 2020; 6:mgen000404. [PMID: 32667876 PMCID: PMC7660257 DOI: 10.1099/mgen.0.000404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/20/2020] [Indexed: 12/04/2022] Open
Abstract
Mannoside phosphorylases are involved in the intracellular metabolization of mannooligosaccharides, and are also useful enzymes for the in vitro synthesis of oligosaccharides. They are found in glycoside hydrolase family GH130. Here we report on an analysis of 6308 GH130 sequences, including 4714 from the human, bovine, porcine and murine microbiomes. Using sequence similarity networks, we divided the diversity of sequences into 15 mostly isofunctional meta-nodes; of these, 9 contained no experimentally characterized member. By examining the multiple sequence alignments in each meta-node, we predicted the determinants of the phosphorolytic mechanism and linkage specificity. We thus hypothesized that eight uncharacterized meta-nodes would be phosphorylases. These sequences are characterized by the absence of signal peptides and of the catalytic base. Those sequences with the conserved E/K, E/R and Y/R pairs of residues involved in substrate binding would target β-1,2-, β-1,3- and β-1,4-linked mannosyl residues, respectively. These predictions were tested by characterizing members of three of the uncharacterized meta-nodes from gut bacteria. We discovered the first known β-1,4-mannosyl-glucuronic acid phosphorylase, which targets a motif of the Shigella lipopolysaccharide O-antigen. This work uncovers a reliable strategy for the discovery of novel mannoside-phosphorylases, reveals possible interactions between gut bacteria, and identifies a biotechnological tool for the synthesis of antigenic oligosaccharides.
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Affiliation(s)
- Ao Li
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Elisabeth Laville
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Laurence Tarquis
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Vincent Lombard
- AFMB, UMR 7257 CNRS, Aix-Marseille Université, F-13288 Marseille, France
- INRAE, USC 1408 AFMB, F-13288 Marseille, France
| | - David Ropartz
- INRAE, UR BIA, F-44316 Nantes, France
- INRAE, BIBS facility, F-44316 Nantes, France
| | - Nicolas Terrapon
- AFMB, UMR 7257 CNRS, Aix-Marseille Université, F-13288 Marseille, France
- INRAE, USC 1408 AFMB, F-13288 Marseille, France
| | - Bernard Henrissat
- AFMB, UMR 7257 CNRS, Aix-Marseille Université, F-13288 Marseille, France
- INRAE, USC 1408 AFMB, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Guieysse
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Jeremy Esque
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Julien Durand
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Diego P. Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
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16
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Abstract
The gut microbiota in humans communicates to the central nervous system through the gut-brain axis, and this communication functions in a bidirectional manner. The backbone of this axis is via the vagus nerve allowing the communication. Research on the functionality of the gut-brain axis is present; however, analysis of the diversity and stratification of the gut microbiota is in its infancy. Through the exploration of various studies focusing on the role of the gut microbiota and its effects on the efficacy of selective serotonin receptor inhibitors (SSRIs) in depression management, many promising alterations in constructive changes have emerged. It has become evident that a set of quantifiable microbial markers have been identified as consistent in the stools of depressive subjects that can be further used to determine the severity of disease progression - the presence of certain bacterial species being a common thread amongst the therapeutic bacteria for depression management. The vagus nerve's role in the gut-brain axis, which is vital to carry out any constructive alterations in the gut microbiota, has been strengthened through evidence of SSRIs depending on the vagus to execute therapeutic effects. This review will focus on the interaction between the diversity of the gut microbiota and investigate its link with depression.
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Affiliation(s)
- Saruja Nanthakumaran
- Department of Research, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Saijanakan Sridharan
- Department of Research, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Manoj R Somagutta
- Department of Research, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Ashley A Arnold
- Surgery, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Vanessa May
- Department of Research, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Sukrut Pagad
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Bilal Haider Malik
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
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17
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Dong J, Liu S, Zhang Y, Dai Y, Wu Q. A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas. Front Microbiol 2020; 11:1061. [PMID: 32612579 PMCID: PMC7309450 DOI: 10.3389/fmicb.2020.01061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 04/29/2020] [Indexed: 11/13/2022] Open
Abstract
The comparison of metagenomes is crucial for studying the relationship between microbial communities and environmental factors. One recently published alignment-free whole metagenome comparison method based on k-mer frequencies, Libra, showed higher resolutions than the present fastest method, Mash, on whole metagenomic sequencing reads, but it did not perform as well on the assembled contigs. Here, we developed a new alignment-free tool, KmerFreqCalc, for the comparison of the whole metagenomic data, which first calculated the frequencies of both forward and reverse complementary sequences of k-mers like Mash and then computed the cosine distance between the samples based on k-mer frequency vectors like Libra. We applied KmerFreqCalc on the assembled contigs of the gut microbiomes of wild giant pandas and compared the results to Libra and Mash. The results indicated that KmerFreqCalc was able to detect the subtle difference between giant panda samples caused by seasonal diet change, showing better clustering than Libra and Mash. Therefore, KmerFreqCalc has high resolution and accuracy for assembled contigs, being very suitable for comparison of samples with low dissimilarity.
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Affiliation(s)
- Jiuhong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuai Liu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China.,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yaran Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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18
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Fu S, Zhuang F, Guo L, Qiu Y, Xiong J, Ye C, Liu Y, Wu Z, Hou Y, Hu CAA. Effect of Baicalin-Aluminum Complexes on Fecal Microbiome in Piglets. Int J Mol Sci 2019; 20:ijms20102390. [PMID: 31091773 PMCID: PMC6566245 DOI: 10.3390/ijms20102390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome has important effects on gastrointestinal diseases. Diarrhea attenuation functions of baicalin (BA) is not clear. Baicalin-aluminum complexes (BBA) were synthesized from BA, but the BBA's efficacy on the diarrhea of piglets and the gut microbiomes have not been explored and the mechanism remains unclear. This study has explored whether BBA could modulate the composition of the gut microbiomes of piglets during diarrhea. The results showed that the diarrhea rate reduced significantly after treatment with BBA. BBA altered the overall structure of the gut microbiomes. In addition, the Gene Ontology (GO) enrichment analysis indicated that the functional differentially expressed genes, which were involved in the top 30 GO enrichments, were associated with hydrogenase (acceptor) activity, nicotinamide-nucleotide adenylyltransferase activity, and isocitrate lyase activity, belong to the molecular function. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that flagellar assembly, bacterial chemotaxis, lipopolysaccharide biosynthesis, ATP-binding cassette transporters (ABC) transporters, biosynthesis of amino acids, and phosphotransferase system (PTS) were the most enriched during BBA treatment process. Taken together, our results first demonstrated that BBA treatment could modulate the gut microbiomes composition of piglets with diarrhea, which may provide new potential insights on the mechanisms of gut microbiomes associated underlying the antimicrobial efficacy of BBA.
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Affiliation(s)
- Shulin Fu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Feng Zhuang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Ling Guo
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Yinsheng Qiu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Jianglin Xiong
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Chun Ye
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Yu Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Zhongyuan Wu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Yongqing Hou
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Chien-An Andy Hu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.
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19
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Yao R, Xu L, Lu G, Zhu L. Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation. Evol Bioinform Online 2019; 15:1176934319848438. [PMID: 31205409 PMCID: PMC6537485 DOI: 10.1177/1176934319848438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/15/2019] [Indexed: 11/16/2022] Open
Abstract
The relationship between animal conservation and the animal gut microbiome is a hot topic in current microbial ecology research. Our group has recently revealed that the occurrence of diverse combinations of gut microbial compositions and functions (metagenomics) in Père David's deer (Elaphurus davidianus) populations is likely to lead to increased evolutionary potential and resilience in response to environmental changes. Thus, considering the effects of diet on the gut microbiome and the importance of a stable gut microbial community to host health, we suggest that a transitional buffer period (with feeding on a regular diet and a diet from the translocation habitat) is needed before animal translocation. When the gut microbiome enters into relatively stable stages and adapts to the new diet from the translocation site, the time is suitable for translocation. Long-term monitoring of the gut microbiomes of translocated animals (by collecting fresh feces and carrying out next-generation sequencing) is still necessary after their translocation.
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Affiliation(s)
- Ran Yao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lianglaing Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guoqing Lu
- Department of Biology, University of Nebraska Omaha, Omaha, NE, USA
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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20
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Williams CL, Ybarra AR, Meredith AN, Durrant BS, Tubbs CW. Gut Microbiota and Phytoestrogen-Associated Infertility in Southern White Rhinoceros. mBio 2019; 10:e00311-19. [PMID: 30967461 PMCID: PMC6456749 DOI: 10.1128/mbio.00311-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 01/08/2023] Open
Abstract
With recent poaching of southern white rhinoceros (SWR [Ceratotherium simum simum]) reaching record levels, the need for a robust assurance population is urgent. However, the global captive SWR population is not currently self-sustaining due to the reproductive failure of captive-born females. Dietary phytoestrogens have been proposed to play a role in this phenomenon, and recent work has demonstrated a negative relationship between diet estrogenicity and fertility of captive-born female SWR. To further examine this relationship, we compared gut microbial communities, fecal phytoestrogens, and fertility of SWR to those of another rhinoceros species-the greater one-horned rhinoceros (GOHR [Rhinoceros unicornis]), which consumes a similar diet but exhibits high levels of fertility in captivity. Using 16S rRNA amplicon sequencing and mass spectrometry, we identified a species-specific fecal microbiota and three dominant fecal phytoestrogen profiles. These profiles exhibited various levels of estrogenicity when tested in an in vitro estrogen receptor activation assay for both rhinoceros species, with profiles dominated by the microbial metabolite equol stimulating the highest levels of receptor activation. Finally, we found that SWR fertility varies significantly not only with respect to phytoestrogen profile, but also with respect to the abundance of several bacterial taxa and microbially derived phytoestrogen metabolites. Taken together, these data suggest that in addition to species differences in estrogen receptor sensitivity to phytoestrogens, reproductive outcomes may be driven by the gut microbiota's transformation of dietary phytoestrogens in captive SWR females.IMPORTANCE Southern white rhinoceros (SWR) poaching has reached record levels, and captive infertility has rendered SWR assurance populations no longer self-sustaining. Previous work has identified dietary phytoestrogens as a likely cause of this problem. Here, we investigate the role of gut microbiota in this phenomenon by comparing two rhinoceros species to provide the first characterizations of gut microbiomes for any rhinoceros species. To our knowledge, our approach, combining parallel sequencing, mass spectrometry, and estrogen receptor activation assays, provides insight into the relationship between microbially mediated phytoestrogen metabolism and fertility that is novel for any vertebrate species. With this information, we plan to direct future work aimed at developing strategies to improve captive reproduction in the hope of alleviating their threat of extinction.
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Affiliation(s)
- Candace L Williams
- Institute for Conservation Research, San Diego Zoo Global, Escondido, California, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Alexis R Ybarra
- Institute for Conservation Research, San Diego Zoo Global, Escondido, California, USA
| | - Ashley N Meredith
- Mississippi State Chemical Laboratory, Mississippi State, Mississippi, USA
| | - Barbara S Durrant
- Institute for Conservation Research, San Diego Zoo Global, Escondido, California, USA
| | - Christopher W Tubbs
- Institute for Conservation Research, San Diego Zoo Global, Escondido, California, USA
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Watanabe K, Petri WA. Learning from the research on amebiasis and gut microbiome: Is stimulation by gut flora essential for effective neutrophil mediated protection from external pathogens? Gut Microbes 2018; 10:100-104. [PMID: 30252579 PMCID: PMC6363069 DOI: 10.1080/19490976.2018.1479626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 05/14/2018] [Indexed: 02/03/2023] Open
Abstract
Amebiasis, caused by intestinal infection with Entamoeba histolytica, is one of the leading causes of parasite infection-related mortality and morbidity globally. Although its pathogenesis, including determinant factors of infection outcome, remains unclear, recent clinical data indicate that the gut microbiome plays a role in determining the severity of amebiasis. Recently, we investigated the effects of the gut microbiome on neutrophil mediated protection from E. histolytica infection using a mouse model. We identified that surface expression of CXCR2 on neutrophils was diminished in mice with dysbiosis, which resulted in decreased neutrophil recruitment to the infection site, allowing more aggressive intestinal tissue damage by E. histolytica. Our results indicated that oxidase activity during E. histolytica infection was also diminished after dysbiosis, consistent with the results from prior research. Thus, the gut microbiome plays an important role in regulating neutrophil phenotype when fighting against external pathogens.
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Affiliation(s)
- Koji Watanabe
- a AIDS Clinical Center , National Center for Global Health and Medicine , Tokyo , Japan
| | - William A Petri
- b Division of Infectious Diseases and International Health , University of Virginia , Charlottesville , VA , USA
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Duranti S, Lugli GA, Mancabelli L, Turroni F, Milani C, Mangifesta M, Ferrario C, Anzalone R, Viappiani A, van Sinderen D, Ventura M. Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria. Appl Environ Microbiol 2017; 83:e02894-16. [PMID: 27864179 DOI: 10.1128/AEM.02894-16] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 11/17/2016] [Indexed: 12/11/2022] Open
Abstract
The microbiota of the human gastrointestinal tract (GIT) may regularly be exposed to antibiotics, which are used to prevent and treat infectious diseases caused by bacteria and fungi. Bacterial communities of the gut retain a reservoir of antibiotic resistance (AR) genes, and antibiotic therapy thus positively selects for those microorganisms that harbor such genetic features, causing microbiota modulation. During the first months following birth, bifidobacteria represent some of the most dominant components of the human gut microbiota, although little is known about their AR gene complement (or resistome). In the current study, we assessed the resistome of the Bifidobacterium genus based on phenotypic and genotypic data of members that represent all currently recognized bifidobacterial (sub)species. Moreover, a comparison between the bifidobacterial resistome and gut metagenome data sets from adults and infants shows that the bifidobacterial community present at the first week following birth possesses a reduced AR arsenal compared to that present in the infant bifidobacterial population in subsequent weeks of the first year of life. Our findings reinforce the concept that the early infant gut microbiota is more susceptible to disturbances by antibiotic treatment than the gut microbiota developed at a later life stage. IMPORTANCE The spread of resistance to antibiotics among bacterial communities has represented a major concern since their discovery in the last century. The risk of genetic transfer of resistance genes between microorganisms has been extensively investigated due to its relevance to human health. In contrast, there is only limited information available on antibiotic resistance among human gut commensal microorganisms such as bifidobacteria, which are widely exploited by the food industry as health-promoting microorganisms or probiotic ingredients. In the current study, we explored the occurrence of antibiotic resistance genes in the genomes of bifidobacteria and evaluated their genetic mobility to other human gut commensal microorganisms.
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