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Alhhazmi AA, Alhamawi RM, Almisned RM, Almutairi HA, Jan AA, Kurdi SM, Almutawif YA, Mohammed-Saeid W. Gut Microbial and Associated Metabolite Markers for Colorectal Cancer Diagnosis. Microorganisms 2023; 11:2037. [PMID: 37630597 PMCID: PMC10457972 DOI: 10.3390/microorganisms11082037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/29/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023] Open
Abstract
Globally, colorectal cancer (CRC) is the second most common cause of mortality worldwide. Considerable evidence indicates that dysbiosis of the gut microbial community and its metabolite secretions play a fundamental role in advanced adenoma (ADA) and CRC development and progression. This study is a systematic review that aims to assess the clinical association between gut microbial markers and/or gut and circulating metabolites with ADA and CRC. Five electronic databases were searched by four independent reviewers. Only controlled trials that compared ADA and/or CRC with healthy control (HC) using either untargeted (16s rRNA gene or whole genome sequencing) or targeted (gene-based real-time PCR) identification methods for gut microbiome profile, or untargeted or targeted metabolite profiling approaches from the gut or serum/plasma, were eligible. Three independent reviewers evaluated the quality of the studies using the Cochrane Handbook for Systematic Reviews of Interventions. Twenty-four studies were eligible. We identified strong evidence of two microbial markers Fusobacterium and Porphyromonas for ADA vs. CRC, and nine microbial markers Lachnospiraceae-Lachnoclostridium, Ruminococcaceae-Ruminococcus, Parvimonas spp., Parvimonas micra, Enterobacteriaceae, Fusobacterium spp., Bacteroides, Peptostreptococcus-Peptostreptococcus stomatis, Clostridia spp.-Clostridium hylemonae, Clostridium symbiosum, and Porphyromonas-Porphyromonas asaccharolytica for CRC vs. HC. The remaining metabolite marker evidence between the various groups, including ADA vs. HC, ADA vs. HC, and CRC vs. HC, was not of sufficient quality to support additional findings. The identified gut microbial markers can be used in a panel for diagnosing ADA and/or CRC. Further research in the metabolite markers area is needed to evaluate the possibility to use in diagnostic or prognostic markers for colorectal cancer.
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Affiliation(s)
- Areej A. Alhhazmi
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, P.O. Box 344, Al-Madinah Al-Munawarah 42353, Saudi Arabia; (R.M.A.); (S.M.K.); (Y.A.A.)
| | - Renad M. Alhamawi
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, P.O. Box 344, Al-Madinah Al-Munawarah 42353, Saudi Arabia; (R.M.A.); (S.M.K.); (Y.A.A.)
| | - Reema M. Almisned
- Seha Polyclinic, P.O. Box 150, Al-Madinah Al-Munawarah 41311, Saudi Arabia;
| | - Hanouf A. Almutairi
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), P.O. Box 6900, Thuwal 23955, Saudi Arabia;
| | - Ahdab A. Jan
- Abdulla Fouad Medical Supplies and Services (AFMS), P.O. Box 150, Al-Madinah Al-Munawarah 21414, Saudi Arabia;
| | - Shahad M. Kurdi
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, P.O. Box 344, Al-Madinah Al-Munawarah 42353, Saudi Arabia; (R.M.A.); (S.M.K.); (Y.A.A.)
| | - Yahya A. Almutawif
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, P.O. Box 344, Al-Madinah Al-Munawarah 42353, Saudi Arabia; (R.M.A.); (S.M.K.); (Y.A.A.)
| | - Waleed Mohammed-Saeid
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taibah University, P.O. Box 344, Al-Madinah Al-Munawarah 42353, Saudi Arabia;
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Peter TK, Withanage MHH, Comnick CL, Pendleton C, Dabdoub S, Ganesan S, Drake D, Banas J, Xie XJ, Zeng E. Systematic review and meta-analysis of oral squamous cell carcinoma associated oral microbiome. Front Microbiol 2022; 13:968304. [PMID: 36338051 PMCID: PMC9632422 DOI: 10.3389/fmicb.2022.968304] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/29/2022] [Indexed: 11/30/2022] Open
Abstract
The intersection between the human oral microbiome and oral health is an emerging area of study which has gained momentum over the last decade. This momentum has motivated a search for associations between the oral microbiome and oral cancer, in hopes of identifying possible biomarkers that facilitate earlier diagnosis and improved prognosis for patients with that disease. The present study examined the relationship between the microbiome in the human oral cavity and oral squamous cell carcinoma (OSCC). We searched the literature for case-control studies which focused on the relationship between the human oral microbiome and OSCC. We aggregated three types of data from these studies: bacteriome data at the genus level, predicted functional pathway data, and gene abundance data. From these data, we noted several microbial genera which may be associated with oral cancer status, including Fusobacterium. We also identified functional pathways which merit further investigation, including RNA degradation (ko03018) and primary immunodeficiency (ko05340). In addition, our analysis of gene abundance data identified the gene K06147 (ATP-binding cassette, subfamily B, bacterial) as being over abundant in OSCC samples. Our results are generalizations which identified some currents that we believe could guide further research. Our work faced several limitations related to the heterogeneity of the available data. Wide variation in methods for sample collection, methods for controlling for known behavioral risk factors, computing platform choice, and methods for case-control design all posed confounding factors in this work. We examined the current methods of data collection, data processing, and data reporting in order to offer suggestions toward the establishment of best practices within this field. We propose that these limitations should be addressed through the implementation of standardized data analytic practices that will conform to the rigor and reproducibility standards required of publicly funded research.
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Affiliation(s)
- Tabitha K. Peter
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Miyuraj H. H. Withanage
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Carissa L. Comnick
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Chandler Pendleton
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Shareef Dabdoub
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States,College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Sukirth Ganesan
- College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States,Department of Periodontics, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - David Drake
- College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Jeffrey Banas
- College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States,Department of Pediatric Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Xian Jin Xie
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States,College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States,Department of Preventative and Community Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, United States,College of Dentistry, Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, United States,Department of Preventative and Community Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, United States,*Correspondence: Erliang Zeng
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3
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Zhang J, Li W, Tang Y, Liu X, Zhang H, Zhou Y, Wang Y, Xiao W, Yu Y. Testing Two Somatic Cell Count Cutoff Values for Bovine Subclinical Mastitis Detection Based on Milk Microbiota and Peripheral Blood Leukocyte Transcriptome Profile. Animals (Basel) 2022; 12:ani12131694. [PMID: 35804592 PMCID: PMC9264859 DOI: 10.3390/ani12131694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022] Open
Abstract
Somatic cell count (SCC) is an important indicator of the health state of bovine udders. However, the exact cut-off value used for differentiating the cows with healthy quarters from the cows with subclinical mastitis remains controversial. Here, we collected composite milk (milk from four udder quarters) and peripheral blood samples from individual cows in two different dairy farms and used 16S rRNA gene sequencing combined with RNA-seq to explore the differences in the milk microbial composition and transcriptome of cows with three different SCC levels (LSCC: <100,000 cells/mL, MSCC: 100,000−200,000 cells/mL, HSCC: >200,000 cells/mL). Results showed that the milk microbial profiles and gene expression profiles of samples derived from cows in the MSCC group were indeed relatively easily discriminated from those from cows in the LSCC group. Discriminative analysis also uncovered some differentially abundant microbiota at the genus level, such as Bifidobacterium and Lachnospiraceae_AC2044_group, which were more abundant in milk samples from cows with SCC below 100,000 cells/mL. As for the transcriptome profiling, 79 differentially expressed genes (DEGs) were found to have the same direction of regulation in two sites, and functional analyses also showed that biological processes involved in inflammatory responses were more active in MSCC and HSCC cows. Overall, these results showed a similarity between the milk microbiota and gene expression profiles of MSCC and HSCC cows, which presented further evidence that 100,000 cells/ml is a more optimal cut-off value than 200,000 cells/mL for intramammary infection detection at the cow level.
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Affiliation(s)
- Jinning Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (J.Z.); (W.L.); (Y.T.); (X.L.); (H.Z.); (Y.Z.); (Y.W.)
| | - Wenlong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (J.Z.); (W.L.); (Y.T.); (X.L.); (H.Z.); (Y.Z.); (Y.W.)
| | - Yongjie Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (J.Z.); (W.L.); (Y.T.); (X.L.); (H.Z.); (Y.Z.); (Y.W.)
| | - Xueqin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (J.Z.); (W.L.); (Y.T.); (X.L.); (H.Z.); (Y.Z.); (Y.W.)
| | - Hailiang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (J.Z.); (W.L.); (Y.T.); (X.L.); (H.Z.); (Y.Z.); (Y.W.)
| | - Yueling Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (J.Z.); (W.L.); (Y.T.); (X.L.); (H.Z.); (Y.Z.); (Y.W.)
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (J.Z.); (W.L.); (Y.T.); (X.L.); (H.Z.); (Y.Z.); (Y.W.)
| | - Wei Xiao
- Beijing Animal Husbandry Station, Beijing 100029, China
- Correspondence: (W.X.); (Y.Y.)
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (J.Z.); (W.L.); (Y.T.); (X.L.); (H.Z.); (Y.Z.); (Y.W.)
- Correspondence: (W.X.); (Y.Y.)
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El Khoury S, Gauthier J, Bouslama S, Cheaib B, Giovenazzo P, Derome N. Dietary Contamination with a Neonicotinoid (Clothianidin) Gradient Triggers Specific Dysbiosis Signatures of Microbiota Activity along the Honeybee ( Apis mellifera) Digestive Tract. Microorganisms 2021; 9:microorganisms9112283. [PMID: 34835409 PMCID: PMC8619528 DOI: 10.3390/microorganisms9112283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Pesticides are increasing honeybee (Apis mellifera) death rates globally. Clothianidin neonicotinoid appears to impair the microbe–immunity axis. We conducted cage experiments on newly emerged bees that were 4–6 days old and used a 16S rRNA metataxonomic approach to measure the impact of three sublethal clothianidin concentrations (0.1, 1 and 10 ppb) on survival, sucrose syrup consumption and gut microbiota community structure. Exposure to clothianidin significantly increased mortality in the three concentrations compared to controls. Interestingly, the lowest clothianidin concentration was associated with the highest mortality, and the medium concentration with the highest food intake. Exposure to clothianidin induced significant variation in the taxonomic distribution of gut microbiota activity. Co-abundance network analysis revealed local dysbiosis signatures specific to each gut section (midgut, ileum and rectum) were driven by specific taxa. Our findings confirm that exposure to clothianidin triggers a reshuffling of beneficial strains and/or potentially pathogenic taxa within the gut, suggesting a honeybee’s symbiotic defense systems’ disruption, such as resistance to microbial colonization. This study highlights the role of weak transcriptional activity taxa in maintaining a stable honeybee gut microbiota. Finally, the early detection of gut dysbiosis in honeybees is a promising biomarker in hive management for assessing the impact exposure to sublethal xenobiotics.
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Affiliation(s)
- Sarah El Khoury
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (S.E.K.); (J.G.); (S.B.); (P.G.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
| | - Jeff Gauthier
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (S.E.K.); (J.G.); (S.B.); (P.G.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
| | - Sidki Bouslama
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (S.E.K.); (J.G.); (S.B.); (P.G.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
| | - Bachar Cheaib
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Pierre Giovenazzo
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (S.E.K.); (J.G.); (S.B.); (P.G.)
| | - Nicolas Derome
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (S.E.K.); (J.G.); (S.B.); (P.G.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
- Correspondence:
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Wei LQ, Cheong IH, Yang GH, Li XG, Kozlakidis Z, Ding L, Liu NN, Wang H. The Application of High-Throughput Technologies for the Study of Microbiome and Cancer. Front Genet 2021; 12:699793. [PMID: 34394190 PMCID: PMC8355622 DOI: 10.3389/fgene.2021.699793] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022] Open
Abstract
Human gut microbiome research, especially gut microbiome, has been developing at a considerable pace over the last decades, driven by a rapid technological advancement. The emergence of high-throughput technologies, such as genomics, transcriptomics, and others, has afforded the generation of large volumes of data, and in relation to specific pathologies such as different cancer types. The current review identifies high-throughput technologies as they have been implemented in the study of microbiome and cancer. Four main thematic areas have emerged: the characterization of microbial diversity and composition, microbial functional analyses, biomarker prediction, and, lastly, potential therapeutic applications. The majority of studies identified focus on the microbiome diversity characterization, which is reaching technological maturity, while the remaining three thematic areas could be described as emerging.
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Affiliation(s)
- Lu Qi Wei
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Io Hong Cheong
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Huan Yang
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Guang Li
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zisis Kozlakidis
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Lei Ding
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ning Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhang L, Zhang J, Wei Y, Hu W, Liu G, Zeng H, Shi H. Microbiome-wide association studies reveal correlations between the structure and metabolism of the rhizosphere microbiome and disease resistance in cassava. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:689-701. [PMID: 33095967 PMCID: PMC8051613 DOI: 10.1111/pbi.13495] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/18/2020] [Indexed: 05/07/2023]
Abstract
Cassava is one of the most important staple food crops in tropical regions. To date, an understanding of the relationship between microbial communities and disease resistance in cassava has remained elusive. In order to explore the relationship among microbiome and phenotypes for further targeted design of microbial community, 16S rRNA and ITS of microbiome of ten cassava varieties were analysed, and a distinctive microbial community in the rhizosphere showed significant interdependence with disease resistance. Shotgun metagenome sequencing was performed to elucidate the structure of microbiomes of cassava rhizosphere. Comprehensive microbiome studies were performed to assess the correlation between the rhizosphere microbiome and disease resistance. Subsequently, the metagenome of rhizosphere microbiome was annotated to obtain taxonomic information at species level and identify metabolic pathways that were significantly associated with cassava disease resistance. Notably, cassava disease resistance was significantly associated with Lactococcus sp., which specifically produces nisin. To definitively explain the role of nisin and underlying mechanism, analysis of nisin biosynthesis-associated genes together with in vitro and in vivo experiments highlighted the effect of nisin on inhibiting the growth of Xanthomonas axonopodis pv. manihotis (Xam) and activating immune response in cassava. The new insights between cassava rhizosphere microbiome especially Lactococcus sp. and disease resistance provide valuable information into further control of cassava disease.
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Affiliation(s)
- Lin Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Jiachao Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Hongqiu Zeng
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
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7
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Gut microbiome analysis as a predictive marker for the gastric cancer patients. Appl Microbiol Biotechnol 2021; 105:803-814. [PMID: 33404833 DOI: 10.1007/s00253-020-11043-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/24/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023]
Abstract
Gut microbiota have been implicated in the development of cancer. Colorectal and gastric cancers, the major gastrointestinal tract cancers, are closely connected with the gut microbiome. Nevertheless, the characteristics of gut microbiota composition that correlate with gastric cancer are unclear. In this study, we investigated gut microbiota alterations during the progression of gastric cancer to identify the most relevant taxa associated with gastric cancer and evaluated the potential of the microbiome as an indicator for the diagnosis of gastric cancer. Compared with the healthy group, gut microbiota composition and diversity shifted in patients with gastric cancer. Different bacteria were used to design a random forest model, which provided an area under the curve value of 0.91. Verification samples achieved a true positive rate of 0.83 in gastric cancer. Principal component analysis showed that gastritis shares some microbiome characteristics of gastric cancer. Chemotherapy reduced the elevated bacteria levels in gastric cancer by more than half. More importantly, we found that the genera Lactobacillus and Megasphaera were associated with gastric cancer.Key Points• Gut microbiota has high sensitivity and specificity in distinguishing patients with gastric cancer from healthy individuals, indicating that gut microbiota is a potential noninvasive tool for the diagnosis of gastric cancer.• Gastritis shares some microbiota features with gastric cancer, and chemotherapy reduces the microbial abundance and diversity in gastric cancer patients.• Two bacterial taxa, namely, Lactobacillus and Megasphaera, are predictive markers for gastric cancer.
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Liao H, Li C, Ai Y, Kou Y. Gut microbiome is more stable in males than in females during the development of colorectal cancer. J Appl Microbiol 2020; 131:435-448. [PMID: 33245828 DOI: 10.1111/jam.14943] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Abstract
AIMS Gut microbial alterations have great potential to predict the development of colorectal cancer (CRC); however, how gut microbes respond to the development of CRC in males and females at the community level is unknown. We aim to investigate the differences of gut microbiota between the male and female. METHODS AND RESULTS We reanalysed the dataset in a published project from a sex perspective at the community level by characterizing the gut microbiome in patients (including males and females) from three clinical groups representative of the stages of CRC development: healthy, adenoma, and carcinoma. The results indicated that the microbial α-diversity showed no significant difference in the male gut but had decreased significantly in the female gut with the development of CRC. In males, a significant difference in the microbial β-diversity was only observed between the healthy and carcinoma subgroups. However, significant community deviations were detected with the development of CRC in females. The microbial community assembly processes changed from deterministic to stochastic in males, whereas they became increasingly deterministic in females with the development of CRC. Moreover microbial co-occurrence associations tended to be more complicated in males; rare species were enriched in the co-occurrence network of the male gut, whereas key species loss was observed in the co-occurrence network of the female gut. CONCLUSIONS The microbial communities in the male gut were more stable than those in the female gut, and microbial community assembly in the gut was sex dependent with the development of CRC. Our study suggests that sexual dimorphism needs to be considered to better predict the risk of CRC based on microbial shifts. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this is the first report showing how gut microbes respond to the development of CRC in males and females at the community scale.
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Affiliation(s)
- H Liao
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - C Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Y Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Y Kou
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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9
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Zhou C, Zhou X, Wen Z, Liu L, Yang Z, Yang L, Li P, Guo X, Mei X. Compound Fu brick tea modifies the intestinal microbiome composition in high-fat diet-induced obesity mice. Food Sci Nutr 2020; 8:5508-5520. [PMID: 33133553 PMCID: PMC7590332 DOI: 10.1002/fsn3.1850] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/17/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022] Open
Abstract
Compound Fu Brick Tea (CFBT), which is from Duyun city in China, is a traditional Chinese dark tea, Fu Brick Tea, mixed with six herbal medicine. It is consumed by local people for reducing weight, but the mechanism is not clear. The disorder of intestinal microbiome caused by long-term high-fat diet (HFD) is one of the inducements of obesity and related metabolic syndrome. In this study, mice were fed with HFD to establish a high-fat model. Fifty mice were randomly divided into six groups: normal control (CK), HFD model control (NK), positive control with medicine (YK), CFBT groups with low, middle, and high dose (FL, FM, FH). The V3-V4 DNA region of fecal microbiome from mouse intestine was sequenced. The results showed that the diversity of intestinal microflora was highest in CK and lowest in NK. Compared with CK, the dominant bacterium Firmicutes was increased and Bacteroidetes decreased at phylum level in NK. Compared with NK, the abundance of microbiome in CFBT groups was significantly higher and the composition was changed: Muribaculaceae, Bacteroidaceae, and Prevotellaceae increased and Lachnospiraceae decreased in CFBT groups at family level, while at the genus level, Bacteroides increased and Lactobacillus decreased. These results conclude that CFBT can increase the abundance of intestinal microbiome in mice, promote the growth of beneficial bacteria and reduce the number of pathogenic bacteria, and restore the imbalance of intestinal microbiome caused by poor diet.
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Affiliation(s)
- Caibi Zhou
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Xiaolu Zhou
- College of Horticulture and Landscape ArchitectureHunan Agricultural UniversityChangshaChina
| | - Zhirui Wen
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Liming Liu
- College of Horticulture and Landscape ArchitectureHunan Agricultural UniversityChangshaChina
| | - Zaibo Yang
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Lu Yang
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Ping Li
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Xiying Guo
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Xin Mei
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
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Brandon-Mong GJ, Shaw GTW, Chen WH, Chen CC, Wang D. A network approach to investigating the key microbes and stability of gut microbial communities in a mouse neuropathic pain model. BMC Microbiol 2020; 20:295. [PMID: 32998681 PMCID: PMC7525972 DOI: 10.1186/s12866-020-01981-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background Neuropathic pain is an abnormally increased sensitivity to pain, especially from mechanical or thermal stimuli. To date, the current pharmacological treatments for neuropathic pain are still unsatisfactory. The gut microbiota reportedly plays important roles in inducing neuropathic pain, so probiotics have also been used to treat it. However, the underlying questions around the interactions in and stability of the gut microbiota in a spared nerve injury-induced neuropathic pain model and the key microbes (i.e., the microbes that play critical roles) involved have not been answered. We collected 66 fecal samples over 2 weeks (three mice and 11 time points in spared nerve injury-induced neuropathic pain and Sham groups). The 16S rRNA gene was polymerase chain reaction amplified, sequenced on a MiSeq platform, and analyzed using a MOTHUR- UPARSE pipeline. Results Here we show that spared nerve injury-induced neuropathic pain alters gut microbial diversity in mice. We successfully constructed reliable microbial interaction networks using the Metagenomic Microbial Interaction Simulator (MetaMIS) and analyzed these networks based on 177,147 simulations. Interestingly, at a higher resolution, our results showed that spared nerve injury-induced neuropathic pain altered both the stability of the microbial community and the key microbes in a gut micro-ecosystem. Oscillospira, which was classified as a low-abundance and core microbe, was identified as the key microbe in the Sham group, whereas Staphylococcus, classified as a rare and non-core microbe, was identified as the key microbe in the spared nerve injury-induced neuropathic pain group. Conclusions In summary, our results provide novel experimental evidence that spared nerve injury-induced neuropathic pain reshapes gut microbial diversity, and alters the stability and key microbes in the gut.
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Affiliation(s)
- Guo-Jie Brandon-Mong
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Grace Tzun-Wen Shaw
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan
| | - Wei-Hsin Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chien-Chang Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan
| | - Daryi Wang
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan. .,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.
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