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Jiang H, Tian Y, Xu L, Chen X, Huang Y, Wu J, Wang T, Liu T, Wu X, Ye C, Wu H, Ye W, Fang L, Zhang Y. Alterations of the bile microbiome is associated with progression-free survival in pancreatic ductal adenocarcinoma patients. BMC Microbiol 2024; 24:235. [PMID: 38956452 PMCID: PMC11218221 DOI: 10.1186/s12866-024-03371-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Patients with pancreatic ductal adenocarcinoma (PDAC) display an altered oral, gastrointestinal, and intra-pancreatic microbiome compared to healthy individuals. However, knowledge regarding the bile microbiome and its potential impact on progression-free survival in PDACs remains limited. METHODS Patients with PDAC (n = 45), including 20 matched pairs before and after surgery, and benign controls (n = 16) were included prospectively. The characteristics of the microbiomes of the total 81 bile were revealed by 16 S-rRNA gene sequencing. PDAC patients were divided into distinct groups based on tumor marker levels, disease staging, before and after surgery, as well as progression free survival (PFS) for further analysis. Disease diagnostic model was formulated utilizing the random forest algorithm. RESULTS PDAC patients harbor a unique and diverse bile microbiome (PCoA, weighted Unifrac, p = 0.038), and the increasing microbial diversity is correlated with dysbiosis according to key microbes and microbial functions. Aliihoeflea emerged as the genus displaying the most significant alteration among two groups (p < 0.01). Significant differences were found in beta diversity of the bile microbiome between long-term PFS and short-term PFS groups (PCoA, weighted Unifrac, p = 0.005). Bacillota and Actinomycetota were identified as altered phylum between two groups associated with progression-free survival in all PDAC patients. Additionally, we identified three biomarkers as the most suitable set for the random forest model, which indicated a significantly elevated likelihood of disease occurrence in the PDAC group (p < 0.0001). The area under the receiver operating characteristic (ROC) curve reached 80.8% with a 95% confidence interval ranging from 55.0 to 100%. Due to the scarcity of bile samples, we were unable to conduct further external verification. CONCLUSION PDAC is characterized by an altered microbiome of bile ducts. Biliary dysbiosis is linked with progression-free survival in all PDACs. This study revealed the alteration of the bile microbiome in PDACs and successfully developed a diagnostic model for PDAC.
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Affiliation(s)
- Hang Jiang
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yitong Tian
- Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Linwei Xu
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
| | - Xing Chen
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
| | - Yurun Huang
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jia Wu
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, China
| | - Tingting Liu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, China
| | - Xitian Wu
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Chao Ye
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Hao Wu
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Wenkai Ye
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Luo Fang
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China.
| | - Yuhua Zhang
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, China.
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
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Wang P, Xie C. Identification and analysis of a clinically isolated strain of Halomonas based on whole-genome sequencing and comparative genomics. Lab Med 2024; 55:80-87. [PMID: 37210212 DOI: 10.1093/labmed/lmad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
OBJECTIVE The aim of this study was to identify the species of a Halomonas strain isolated from a neonatal blood sample and to understand the potential pathogenicity and characteristic genes of the strain. METHODS The genomic DNA of strain 18071143 (identified as Halomonas by matrix-assisted laser desorption-ionization time of flight-mass spectrometry and the 16S ribosomal RNA (rRNA) gene sequence) was sequenced using Nanopore PromethION platforms. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were calculated using the complete genome sequences of the strain. Comparative genomic analyses were performed on strain 18071143 and 3 strains of Halomonas (Halomonas stevensii S18214, Halomonas hamiltonii KCTC 22154, and Halomonas johnsoniae KCTC 22157) that were associated with human infections and had high genomic similarity to strain 18071143. RESULTS Phylogenetic, ANI, and dDDH similarity analyses based on genome sequence indicated that strain 18071143 belonged to the species H stevensii. Similarities exist between strain 18071143 and the other 3 Halomonas strains in terms of gene structure and protein function. Nonetheless, strain 18071143 has greater potential for DNA replication, recombination, repair, and horizontal transfer. CONCLUSION Whole-genome sequencing holds great promise for accurate strain identification in clinical microbiology. In addition, the results of this study provide data for understanding Halomonas from the perspective of pathogenic bacteria.
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Affiliation(s)
- Pinjia Wang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Chengbin Xie
- Department of Laboratory Medicine, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, China
- Department of Laboratory Medicine, Women's and Children's Hospital Affiliated to Chengdu Medical College, Chengdu, China
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He L, Yang BZ, Ma YJ, Wen L, Liu F, Zhang XJ, Liu TQ. Differences in clinical features and gut microbiota between individuals with methamphetamine casual use and methamphetamine use disorder. Front Cell Infect Microbiol 2023; 13:1103919. [PMID: 36909722 PMCID: PMC9996337 DOI: 10.3389/fcimb.2023.1103919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
Background The transition from methamphetamine (MA) casual use (MCU) to compulsive use is enigmatic as some MA users can remain in casual use, but some cannot. There is a knowledge gap if gut microbiota (GM) play a role in differing MCU from MA use disorder (MUD). We aimed to investigate the clinical features and GM differences between individuals with MCU and MUD. Method We recruited two groups of MA users -MCU and MUD - and matched them according to age and body mass index (n=21 in each group). Participants were accessed using the Semi-Structured Assessment for Drug Dependence and Alcoholism, and their fecal samples were undergone 16S ribosomal DNA sequencing. We compared the hosts' clinical features and GM diversity, composition, and structure (represented by enterotypes) between the two groups. We have identified differential microbes between the two groups and performed network analyses connecting GM and the clinical traits. Result Compared with the casual users, individuals with MUD had higher incidences of MA-induced neuropsychiatric symptoms (e.g., paranoia, depression) and withdrawal symptoms (e.g., fatigue, drowsiness, and increased appetite), as well as stronger cravings for and intentions to use MA, and increased MA tolerance. The GM diversity showed no significant differences between the two groups, but four genera (Halomonas, Clostridium, Devosia, and Dorea) were enriched in the individuals with MUD (p<0.05). Three distinct enterotypes were identified in all MA users, and Ruminococcus-driven enterotype 2 was dominant in individuals with MUD compared to the MCU (61.90% vs. 28.60%, p=0.03). Network analysis shows that Devosia is the hub genus (hub index = 0.75), which is not only related to the counts of the MUD diagnostic criteria (ρ=0.40; p=0.01) but also to the clinical features of MA users such as reduced social activities (ρ=0.54; p<0.01). Devosia is also associated with the increased intention to use MA (ρ=0.48; p<0.01), increased MA tolerance (ρ=0.38; p=0.01), craving for MA (ρ=0.37; p=0.01), and MA-induced withdrawal symptoms (p<0.05). Conclusion Our findings suggest that Ruminococcus-driven enterotype 2 and the genera Devosia might be two influential factors that differentiate MA casual use from MUD, but further studies are warranted.
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Affiliation(s)
- Li He
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Bao-Zhu Yang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
| | - Yue-Jiao Ma
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Li Wen
- Department of Internal Medicine, Section of Endocrinology & Core Laboratory of Yale Center for Clinical Investigation, Yale University School of Medicine, New Haven, CT, United States
| | - Feng Liu
- Compulsory Detoxification Center of Changsha Public Security Bureau, Changsha, Hunan, China
| | - Xiao-Jie Zhang
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Tie-Qiao Liu
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Kalaitzidou MP, Alvanou MV, Papageorgiou KV, Lattos A, Sofia M, Kritas SK, Petridou E, Giantsis IA. Pollution Indicators and HAB-Associated Halophilic Bacteria Alongside Harmful Cyanobacteria in the Largest Mussel Cultivation Area in Greece. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095285. [PMID: 35564680 PMCID: PMC9104808 DOI: 10.3390/ijerph19095285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/16/2022]
Abstract
Taking into consideration the essential contribution of Mytilus galloprovincialis farming, it is of rising importance to add knowledge regarding bacterial species occurrence in water samples from aquaculture zones from the point of view of both the organism and public health. In the present study, we investigated the bacterial community existing in water samples from six Mytilus galloprovincialis aquaculture areas in the Thermaikos gulf, northern Greece, that may provoke toxicity in aquatic organisms and humans and may indicate environmental pollution in mussel production as well as algal blooms. Bacterial species were identified molecularly by sequencing of a partial 16s rRNA segment and were analyzed phylogenetically for the confirmation of the bacterial taxonomy. The results obtained revealed the presence of four bacterial genera (Halomonas sp., Planococcus sp., Sulfitobacter sp., and Synechocystis sp.). Members of the Halomonas and Sulfitobacter genera have been isolated from highly polluted sites, Planococcus bacteria have been identified in samples derived directly from plastic debris, and Synechocystis bacteria are in line with microcystin detection. In this context, the monitoring of the bacteria community in mussel aquaculture water samples from the Thermaikos gulf, the largest mussel cultivation area in Greece, represents an indicator of water pollution, microplastics presence, algal blooms, and toxin presence.
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Affiliation(s)
- Maria P. Kalaitzidou
- National Reference Laboratory for Marine Biotoxins, Department of Food Microbiology, Biochemical Control, Residues, Marine Biotoxins and Other Water Toxins, Directorate of Veterinary Center of Thessaloniki, Ministry of Rural Development and Food, 54627 Thessaloniki, Greece;
| | - Maria V. Alvanou
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
| | - Konstantinos V. Papageorgiou
- 3rd Military Veterinary Hospital, General Staff, Hellenic Ministry of Defense, 15th Km Thessaloniki-Vasilika, 57001 Thessaloniki, Greece;
| | - Athanasios Lattos
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
| | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece;
| | - Spyridon K. Kritas
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.K.K.); (E.P.)
| | - Evanthia Petridou
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.K.K.); (E.P.)
| | - Ioannis A. Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
- Correspondence:
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Stevens DA, Johnson N. Mystery solved? Halomonas and dialysis infections. Diagn Microbiol Infect Dis 2017; 88:1-2. [DOI: 10.1016/j.diagmicrobio.2017.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/15/2017] [Accepted: 01/30/2017] [Indexed: 11/16/2022]
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Giannelli V, Di Gregorio V, Iebba V, Giusto M, Schippa S, Merli M, Thalheimer U. Microbiota and the gut-liver axis: Bacterial translocation, inflammation and infection in cirrhosis. World J Gastroenterol 2014; 20:16795-16810. [PMID: 25492994 PMCID: PMC4258550 DOI: 10.3748/wjg.v20.i45.16795] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/26/2014] [Accepted: 09/30/2014] [Indexed: 02/06/2023] Open
Abstract
Liver disease is associated with qualitative and quantitative changes in the intestinal microbiota. In cirrhotic patients the alteration in gut microbiota is characterized by an overgrowth of potentially pathogenic bacteria (i.e., gram negative species) and a decrease in autochthonous familiae. Here we summarize the available literature on the risk of gut dysbiosis in liver cirrhosis and its clinical consequences. We therefore described the features of the complex interaction between gut microbiota and cirrhotic host, the so called “gut-liver axis”, with a particular attention to the acquired risk of bacterial translocation, systemic inflammation and the relationship with systemic infections in the cirrhotic patient. Such knowledge might help to develop novel and innovative strategies for the prevention and therapy of gut dysbiosis and its complication in liver cirrhosis.
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Altered profile of human gut microbiome is associated with cirrhosis and its complications. J Hepatol 2014; 60:940-7. [PMID: 24374295 PMCID: PMC3995845 DOI: 10.1016/j.jhep.2013.12.019] [Citation(s) in RCA: 739] [Impact Index Per Article: 73.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 11/05/2013] [Accepted: 12/16/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The gut microbiome is altered in cirrhosis; however its evolution with disease progression is only partly understood. We aimed to study changes in the microbiome over cirrhosis severity, its stability over time and its longitudinal alterations with decompensation. METHODS Controls and age-matched cirrhotics (compensated/decompensated/hospitalized) were included. Their stool microbiota was quantified using multi-tagged pyrosequencing. The ratio of autochthonous to non-autochthonous taxa was calculated as the cirrhosis dysbiosis ratio (CDR); a low number indicating dysbiosis. Firstly, the microbiome was compared between controls and cirrhotic sub-groups. Secondly, for stability assessment, stool collected twice within 6months in compensated outpatients was analyzed. Thirdly, changes after decompensation were assessed using (a) longitudinal comparison in patients before/after hepatic encephalopathy development (HE), (b) longitudinal cohort of hospitalized infected cirrhotics MELD-matched to uninfected cirrhotics followed for 30days. RESULTS 244 subjects [219 cirrhotics (121 compensated outpatients, 54 decompensated outpatients, 44 inpatients) and 25 age-matched controls] were included. CDR was highest in controls (2.05) followed by compensated (0.89), decompensated (0.66), and inpatients (0.32, p<0.0001) and negatively correlated with endotoxin. Microbiota and CDR remained unchanged in stable outpatient cirrhotics (0.91 vs. 0.86, p=0.45). In patients studied before/after HE development, dysbiosis occurred post-HE (CDR: 1.2 to 0.42, p=0.03). In the longitudinal matched-cohort, microbiota were significantly different between infected/uninfected cirrhotics at baseline and a low CDR was associated with death and organ failures within 30days. CONCLUSIONS Progressive changes in the gut microbiome accompany cirrhosis and become more severe in the setting of decompensation. The cirrhosis dysbiosis ratio may be a useful quantitative index to describe microbiome alterations accompanying cirrhosis progression.
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Li K, Lin K, Li Z, Zhang Q, Song F, Che Z, Chen G, Xiang W. Spoilage and Pathogenic Bacteria Associated with Spoilage Process of Sichuan Pickle during the Spontaneous Fermentation. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2014. [DOI: 10.3136/fstr.20.899] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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