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Gu X, Shen H, Zhu G, Li X, Zhang Y, Zhang R, Su F, Wang Z. Prognostic Model and Tumor Immune Microenvironment Analysis of Complement-Related Genes in Gastric Cancer. J Inflamm Res 2023; 16:4697-4711. [PMID: 37872955 PMCID: PMC10590588 DOI: 10.2147/jir.s422903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
Introduction The complement system is integral to the innate and adaptive immune response, helping antibodies eliminate pathogens. However, the potential role of complement and its modulators in the tumor microenvironment (TME) of gastric cancer (GC) remains unclear. Methods This study assessed the expression, frequency of somatic mutations, and copy number variations of complement family genes in GC derived from The Cancer Genome Atlas (TCGA). Lasso and Cox regression analyses were conducted to develop a prognostic model based on the complement genes family, with the training and validation sets taken from the TCGA-GC cohort (n=371) and the International Gene Expression Omnibus (GEO) cohort (n=433), correspondingly. The nomogram assessment model was used to predict patient outcomes. Additionally, the link between immune checkpoints, immune cells, and the prognostic model was investigated. Results In contrast to patients at low risk, those at high risk had a less favorable outcome. The prognostic model-derived risk score was shown to serve as a prognostic marker of GC independently, as per the multivariate Cox analysis. Nomogram assessment showed that the model had high reliability for predicting the survival of patients with GC in the 1, 3, 5 years. Additionally, the risk score was positively linked to the expression of immune checkpoints, notably CTLA4, LAG3, PDCD1, and CD274, according to an analysis of immune processes. The core gene C5aR1 in the prognostic model was found to be upregulated in GC tissues in contrast to adjoining normal tissues, and patients with elevated expressed levels of C5aR1 had lower 10-year overall survival (OS) rates. Conclusion Our work reveals that complement genes are associated with the diversity and complexity of TME. The complement prognosis model help improves our understanding of TME infiltration characteristics and makes immunotherapeutic strategies more effective.
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Affiliation(s)
- Xianhua Gu
- Department of Gynecology Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, People’s Republic of China
| | - Honghong Shen
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, People’s Republic of China
| | - Guangzheng Zhu
- Department of Surgical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, People’s Republic of China
| | - Xinwei Li
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, People’s Republic of China
| | - Yue Zhang
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, People’s Republic of China
| | - Rong Zhang
- Department of Gynecology Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, People’s Republic of China
| | - Fang Su
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, People’s Republic of China
| | - Zishu Wang
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, People’s Republic of China
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Dandekar T, Kunz M. Extremely Fast Sequence Comparisons Identify All the Molecules That Are Present in the Cell. Bioinformatics 2023. [DOI: 10.1007/978-3-662-65036-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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He X, Yan C, Zhao S, Zhao Y, Huang R, Li Y. The preventive effects of probiotic Akkermansia muciniphila on D-galactose/AlCl3 mediated Alzheimer's disease-like rats. Exp Gerontol 2022; 170:111959. [PMID: 36152776 DOI: 10.1016/j.exger.2022.111959] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 06/19/2022] [Accepted: 09/17/2022] [Indexed: 12/29/2022]
Abstract
AIMS We induced the AD-like rat models injected by AlCl3 and D-galactose, to explore the effects of an oral treatment of A. muciniphila on AD-like rats with periodontitis and its possible mechanism. MAIN METHODS We used Morris water maze test and micro-CT to assess the cognitive impairment and bone loss; Aβ1-42 deposition was tested by IHC; Serum LPS level and TG, HDL-C and AST/ALT levels were detected by LAL Test and biochemical tests; The gut microbiota was analyzed by 16S rRNA gene sequence. KEY FINDINGS We found that A. muciniphila could alleviate AD-like rats' cognitive impairment and mitigate ligature-induced periodontitis. Furthermore, A. muciniphila reduced Aβ1-42 deposition in the cortex and regions of the rats' brain, and altered TG, HDL-C and AST/ALT levels but had little ability to change circulating LPS level and cross the blood-brain barrier. Notably, A. muciniphila treatment could improve the abundance of some short chain fatty acid (SCFA)-producing or neurotransmitter-producing gut microbiome such as Blautia, Staphylococcus and Lactococcus, while the abundance of pathogenic Aerococcus and Streptococcus, which were associated inflammation, were decreased. SIGNIFICANCE Our findings suggested that A. muciniphila has a remissive effect on AD-like pathologies, potentially by regulating gut-brain axis through altering composition and function of gut microbial community or moderating peripheral circulation metabolism.
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Affiliation(s)
- Xiaoya He
- Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Caixia Yan
- Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Shuyang Zhao
- Queen Mary School of Medical College, Jiangxi Medical College, Qianhu Campus, Nanchang University, No. 1290 Xuefu Street, Jiangxi 330031, China
| | - Yuxi Zhao
- Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Ruijie Huang
- Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Yan Li
- Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
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An G, Feng L, Hou L, Li X, Bai J, He L, Gu S, Zhao X. A bioinformatics analysis of zinc finger protein family reveals potential oncogenic biomarkers in breast cancer. Gene 2022; 828:146471. [PMID: 35378249 DOI: 10.1016/j.gene.2022.146471] [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: 11/01/2021] [Revised: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Zinc finger protein family is the largest transcription factor family in the human genome. Studies have shown that the aberrant expression of zinc finger protein (ZNF) had a potential role in tumorigenesis. However, due to the high complexity of the ZNF family genes, the role of the ZNF family genes in breast cancer (BRCA) is still lacking in systematic understanding. AIM In the study, we aim to understand the expression profile, prognostic value, immune invasion pattern, tumor microenvironment, epigenetic and pathway relationships, and drug sensitivity of ZNFs using multi-omics data from public databases. RESULTS We focused on six members of ZNFs, which were upregulated in a variety of cancers. Notably, ZNF750 and ZNF224 were lower expressed in BRCA, and their expressions were significantly associated with BRCA prognosis. We confirmed the observations obtained by analyzing the clinic-pathological data. Otherwise, the expressions of ZNFs were significantly related to stromal and immune scores, and was significantly different among different immune subtypes in BRCA. Here, we found down-regulated methylation of ZNF217 and ZNF750. The relationship between methylation and survival showed the survival was worse for hypo-methylation of ZNF750 in BRCA, which is consistent with the correlation of high expression of ZNF750 in BRCA with worse survival. CONCLUSIONS Collectively, our results provide clues for a better understanding of the characterization of ZNF family genes in BRCA from a multi-omics perspective and show their potential for use as new tumor markers and therapeutic targets.
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Affiliation(s)
- Gaili An
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China; Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Lu Feng
- Department of Radiotherapy, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Lei Hou
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Xu Li
- Department of Oncology, Shaanxi Provincial Cancer Hospital, Xi'an 712000, Shaanxi, China
| | - Jun Bai
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Li He
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Shanzhi Gu
- Department of College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China.
| | - Xinhan Zhao
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China.
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Gene and prognostic value of N6-methyladenosine (m6A) modification regulatory factors in lung adenocarcinoma. Eur J Cancer Prev 2021; 31:354-362. [PMID: 34519693 DOI: 10.1097/cej.0000000000000717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Lung cancer is the leading cause of death worldwide, and its incidence continues to increase. The treatment of lung cancer is related to the subtypes and stages of cancer, but the therapeutic effect is still unsatisfactory. We found that 10 of the 13 genes were differentially expressed in lung cancer, YTHDF1, RBM15, HNRNPC, KIAA1429, METTL3 and YTHDF2 are high expression while METTL14, ZC3H13, FTO and WTAP are low expression. HNRNPC and METTL3 genes were associated with the risk and prognosis of LUAD and could regard as biomarkers for early diagnosis and treatment, which provides a theoretical basis for LUAD.
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He J, Tu Q, Ge Y, Qin Y, Cui B, Hu X, Wang Y, Deng Y, Wang K, Van Nostrand JD, Li J, Zhou J, Li Y, Zhou X. Taxonomic and Functional Analyses of the Supragingival Microbiome from Caries-Affected and Caries-Free Hosts. MICROBIAL ECOLOGY 2018; 75:543-554. [PMID: 28932895 DOI: 10.1007/s00248-017-1056-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Caries is one of the most prevalent and costly infectious diseases affecting humans of all ages. It is initiated by cariogenic supragingival dental plaques forming on saliva-coated tooth surfaces, yet the etiology remains elusive. To determine which microbial populations may predispose a patient to caries, we report here an in-depth and comprehensive view of the microbial community associated with supragingival dental plaque collected from the healthy teeth of caries patients and healthy adults. We found that microbial communities from caries patients had a higher evenness and inter-individual variations but simpler ecological networks compared to healthy controls despite the overall taxonomic structure being similar. Genera including Selenomonas, Treponema, Atopobium, and Bergeriella were distributed differently between the caries and healthy groups with disturbed co-occurrence patterns. In addition, caries and healthy subjects carried different Treponema, Atopobium, and Prevotella species. Moreover, distinct populations of 13 function genes involved in organic acid synthesis, glycan biosynthesis, complex carbohydrate degradation, amino acid synthesis and metabolism, purine and pyrimidine metabolism, isoprenoid biosynthesis, lipid metabolism, and co-factor biosynthesis were present in each of the healthy and caries groups. Our results suggested that the fundamental differences in dental plaque ecology partially explained the patients' susceptibility to caries, and could be used for caries risk prediction in the future.
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Affiliation(s)
- Jinzhi He
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Qichao Tu
- Department of Marine Sciences, Ocean College, Zhejiang University, Hangzhou, Zhejiang, China
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yichen Ge
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Bomiao Cui
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xiaoyu Hu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yuxia Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Ye Deng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kun Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Yan Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
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Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches. Sci Rep 2018; 8:2004. [PMID: 29386563 PMCID: PMC5792604 DOI: 10.1038/s41598-018-20366-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/17/2018] [Indexed: 11/25/2022] Open
Abstract
We used complementary morphological and DNA metabarcoding approaches to characterize soil nematode communities in three cropping systems, conventional till (CT), no-till (NT) and organic (ORG), from a long-term field experiment. We hypothesized that organic inputs to the ORG system would promote a more abundant nematode community, and that the NT system would show a more structured trophic system (higher Bongers MI) than CT due to decreased soil disturbance. The abundance of Tylenchidae and Cephalobidae both showed positive correlations to soil organic carbon and nitrogen, which were highest in the ORG system. The density of omnivore-predator and bacterial-feeding nematodes was reduced in NT soils compared to CT, while some plant-parasitic taxa increased. NT soils had similar Bongers MI values to CT, suggesting they contained nematode communities associated with soils experiencing comparable levels of disturbance. Metabarcoding revealed within-family differences in nematode diversity. Shannon and Simpson’s index values for the Tylenchidae and Rhabditidae were higher in the ORG system than CT. Compared to morphological analysis, metabarcoding over- or underestimated the prevalence of several nematode families and detected some families not observed based on morphology. Discrepancies between the techniques require further investigation to establish the accuracy of metabarcoding for characterization of soil nematode communities.
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Ankenbrand MJ, Terhoeven N, Hohlfeld S, Förster F, Keller A. biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format. F1000Res 2017; 5:2348. [PMID: 28105307 PMCID: PMC5224677 DOI: 10.12688/f1000research.9618.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/09/2017] [Indexed: 11/20/2022] Open
Abstract
The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277.
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Affiliation(s)
- Markus J Ankenbrand
- Department of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Würzburg, Germany
| | - Niklas Terhoeven
- Department of Plant Physiology and Biophysics (Botany I), University of Würzburg, Würzburg, Germany; Center for Computational and Theoretical Biology (CCTB), University of Würzburg, Würzburg, Germany
| | - Sonja Hohlfeld
- Department of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Würzburg, Germany
| | - Frank Förster
- Center for Computational and Theoretical Biology (CCTB), University of Würzburg, Würzburg, Germany; Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Würzburg, Germany
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Angly FE, Pantos O, Morgan TC, Rich V, Tonin H, Bourne DG, Mercurio P, Negri AP, Tyson GW. Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon. PeerJ 2016; 4:e1758. [PMID: 26989611 PMCID: PMC4793316 DOI: 10.7717/peerj.1758] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 02/13/2016] [Indexed: 11/25/2022] Open
Abstract
Diuron is a herbicide commonly used in agricultural areas where excess application causes it to leach into rivers, reach sensitive marine environments like the Great Barrier Reef (GBR) lagoon and pose risks to marine life. To investigate the impact of diuron on whole prokaryotic communities that underpin the marine food web and are integral to coral reef health, GBR lagoon water was incubated with diuron at environmentally-relevant concentration (8 µg/L), and sequenced at specific time points over the following year. 16S rRNA gene amplicon profiling revealed no significant short- or long-term effect of diuron on microbiome structure. The relative abundance of prokaryotic phototrophs was not significantly altered by diuron, which suggests that they were largely tolerant at this concentration. Assembly of a metagenome derived from waters sampled at a similar location in the GBR lagoon did not reveal the presence of mutations in the cyanobacterial photosystem that could explain diuron tolerance. However, resident phages displayed several variants of this gene and could potentially play a role in tolerance acquisition. Slow biodegradation of diuron was reported in the incubation flasks, but no correlation with the relative abundance of heterotrophs was evident. Analysis of metagenomic reads supports the hypothesis that previously uncharacterized hydrolases carried by low-abundance species may mediate herbicide degradation in the GBR lagoon. Overall, this study offers evidence that pelagic phototrophs of the GBR lagoon may be more tolerant of diuron than other tropical organisms, and that heterotrophs in the microbial seed bank may have the potential to degrade diuron and alleviate local anthropogenic stresses to inshore GBR ecosystems.
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Affiliation(s)
- Florent E. Angly
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Olga Pantos
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
- Global Change Institute, The University of Queensland, St Lucia, Queensland, Australia
| | - Thomas C. Morgan
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Virginia Rich
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States of America
- Microbiology Department, The Ohio State University, Columbus, OH, United States of America
| | - Hemerson Tonin
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - David G. Bourne
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Philip Mercurio
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- National Research Centre for Environmental Toxicology, The University of Queensland, Coopers Plains, Queensland, Australia
| | - Andrew P. Negri
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
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Angly FE, Heath C, Morgan TC, Tonin H, Rich V, Schaffelke B, Bourne DG, Tyson GW. Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events. PeerJ 2016; 4:e1511. [PMID: 26839738 PMCID: PMC4734448 DOI: 10.7717/peerj.1511] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/25/2015] [Indexed: 12/15/2022] Open
Abstract
The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR), with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae) and Synechococcales (e.g., Prochlorococcus), and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010–11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics.
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Affiliation(s)
- Florent E Angly
- Australian Centre for Ecogenomics, University of Queensland , St Lucia, Queensland , Australia
| | - Candice Heath
- Australian Centre for Ecogenomics, University of Queensland , St Lucia, Queensland , Australia
| | - Thomas C Morgan
- Australian Centre for Ecogenomics, University of Queensland , St Lucia, Queensland , Australia
| | - Hemerson Tonin
- Australian Institute of Marine Science , Townsville, Queensland , Australia
| | - Virginia Rich
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States of America; Microbiology Department, Ohio State University, Columbus, OH, United States of America
| | - Britta Schaffelke
- Australian Institute of Marine Science , Townsville, Queensland , Australia
| | - David G Bourne
- Australian Institute of Marine Science , Townsville, Queensland , Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, University of Queensland , St Lucia, Queensland , Australia
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11
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Archaeal and bacterial communities across a chronosequence of drained lake basins in Arctic Alaska. Sci Rep 2015; 5:18165. [PMID: 26681584 PMCID: PMC4683534 DOI: 10.1038/srep18165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/13/2015] [Indexed: 11/21/2022] Open
Abstract
We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus ‘Methanoflorens stordalenmirensis’ were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the active layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus ‘M. stordalenmirensis’ across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures.
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Angly FE, Dennis PG, Skarshewski A, Vanwonterghem I, Hugenholtz P, Tyson GW. CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. MICROBIOME 2014; 2:11. [PMID: 24708850 PMCID: PMC4021573 DOI: 10.1186/2049-2618-2-11] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 02/17/2014] [Indexed: 05/13/2023]
Abstract
BACKGROUND Culture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between species. RESULTS Based on 2,900 sequenced reference genomes, we show that 16S rRNA gene copy number (GCN) is strongly linked to microbial phylogenetic taxonomy, potentially under-representing Archaea in amplicon microbial profiles. Using this relationship, we inferred the GCN of all bacterial and archaeal lineages in the Greengenes database within a phylogenetic framework. We created CopyRighter, new software which uses these estimates to correct 16S rRNA amplicon microbial profiles and associated quantitative (q)PCR total abundance. CopyRighter parses microbial profiles and, because GCN estimates are pre-computed for all taxa in the reference taxonomy, rapidly corrects GCN bias. Software validation with in silico and in vitro mock communities indicated that GCN correction results in more accurate estimates of microbial relative abundance and improves the agreement between metagenomic and amplicon profiles. Analyses of human-associated and anaerobic digester microbiomes illustrate that correction makes tangible changes to estimates of qPCR total abundance, α and β diversity, and can significantly change biological interpretation. For example, human gut microbiomes from twins were reclassified into three rather than two enterotypes after GCN correction. CONCLUSIONS The CopyRighter bioinformatic tools permits rapid correction of GCN in microbial surveys, resulting in improved estimates of microbial abundance, α and β diversity.
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Affiliation(s)
- Florent E Angly
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Paul G Dennis
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Current affiliation: School of Agriculture and Food Sciences, Level 3, Hartley Teakle Building (83), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Adam Skarshewski
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Advanced Water Management Center, Level 4, Gehrmann Laboratories Building (60), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics/School of Chemistry and Molecular Biosciences/The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Advanced Water Management Center, Level 4, Gehrmann Laboratories Building (60), The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
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