151
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Zeng S, Zhou R, Bao S, Li X, Deng Z, Hou D, Weng S, He J, Huang Z. Identification of Multigene Biomarker for Shrimp White Feces Syndrome by Full-Length Transcriptome Sequencing. Front Genet 2020; 11:71. [PMID: 32133029 PMCID: PMC7040362 DOI: 10.3389/fgene.2020.00071] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 11/23/2019] [Accepted: 01/22/2020] [Indexed: 12/23/2022] Open
Abstract
The pacific white shrimp, Litopenaeus vannamei, with the largest shrimp industry production in the world, is currently threatened by a severe disease, white feces syndrome (WFS), which cause devastating losses globally, while its causal agents remain largely unknown. Herein, compared to the Control shrimp by metagenomic analysis, we firstly investigated that the altered functions of intestinal microbial community in WFS shrimp were the enrichment of bacterial chemotaxis and flagellar assembly pathways, hinting at a potential role of pathogenic bacteria for growth and development, which might be related to WFS occurrence. Single-molecule real-time (SMRT) sequencing was to further identify the gene structure and gene regulation for more clues in WFS aetiology. Totally 50,049 high quality transcripts were obtained, capturing 39,995 previously mapped and 10,054 newly detected transcripts, which were annotated to 30,554 genes. A total of 158 differentially expressed genes (DEGs) were characterized in WFS shrimp. These DEGs were strongly associated with various immune related genes that regulated the expression of multiple antimicrobial peptides (e.g., antilipopolysaccharide factors, penaeidins, and crustin), which were further experimentally validated using quantitative PCR on transcript level. Collectively, multigene biomarkers were identified to be closely associated with WFS, especially those functional alterations in microbial community and the upregulated immune related gene with antibacterial activities. Our finding not only inspired our cogitation on WFS aetiology from both microbial and host immune response perspectives with combined metagenomic and full-length transcriptome sequencing, but also provided valuable information for enhancing shrimp aquaculture.
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Affiliation(s)
- Shenzheng Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center, Sun Yat-sen University, Guangzhou, China
| | - Renjun Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shicheng Bao
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xuanting Li
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhixuan Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center, Sun Yat-sen University, Guangzhou, China
| | - Zhijian Huang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center, Sun Yat-sen University, Guangzhou, China
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152
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Worsley-Tonks KEL, Miller EA, Gehrt SD, McKenzie SC, Travis DA, Johnson TJ, Craft ME. Characterization of antimicrobial resistance genes in Enterobacteriaceae carried by suburban mesocarnivores and locally owned and stray dogs. Zoonoses Public Health 2020; 67:460-466. [PMID: 32034890 DOI: 10.1111/zph.12691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 06/07/2019] [Revised: 12/16/2019] [Accepted: 01/08/2020] [Indexed: 11/28/2022]
Abstract
The role of wildlife in the dissemination of antimicrobial-resistant bacteria and antimicrobial resistance genes (ARGs) in the environment is of increasing concern. We investigated the occurrence, richness and transmissibility potential of ARGs detected in the faeces of three mesocarnivore species: the coyote (Canis latrans), raccoon (Procyon lotor) and Virginia opossum (Didelphis virginiana), and of stray and owned dogs in suburban Chicago, IL, USA. Rectal swabs were collected from live-captured coyotes (n = 32), raccoons (n = 31) and Virginia opossums (n = 22). Fresh faecal samples were collected from locally owned (n = 13) and stray dogs (n = 18) and from the live-captured mesocarnivores, when available. Faecal samples and rectal swabs were enriched to select for Enterobacteriaceae and pooled by mesocarnivore species and dog type (owned or stray). Pooled enriched samples were then analysed for the presence of ARGs using shotgun sequencing. The three mesocarnivore and stray dog samples had twice as many unique ARGs compared to the owned dog sample, which was partly driven by a greater richness of beta-lactamase genes (genes conferring resistance to penicillins and cephalosporins). Raccoon and stray dog samples had the most ARGs in common, suggesting possible exposure to similar environmental sources of ARGs. In addition to identifying clinically relevant ARGs (e.g. blaCMY and qnrB), some ARGs were linked to the class 1 integrase gene, intI1, which may indicate anthropogenic origin. Findings from this pilot investigation suggest that the microbial communities of suburban mesocarnivores and stray dogs can host ARGs that can confer resistance to several antimicrobials used in human and veterinary medicine.
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Affiliation(s)
| | - Elizabeth A Miller
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Falcon Heights, MN, USA
| | - Stanley D Gehrt
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | | | - Dominic A Travis
- Department of Veterinary Population Medicine, University of Minnesota, Falcon Heights, MN, USA
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Falcon Heights, MN, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, Falcon Heights, MN, USA
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153
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Zhang M, Hill JE, Godson DL, Ngeleka M, Fernando C, Huang Y. The pulmonary virome, bacteriological and histopathological findings in bovine respiratory disease from western Canada. Transbound Emerg Dis 2019; 67:924-934. [PMID: 31715071 PMCID: PMC7168541 DOI: 10.1111/tbed.13419] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 08/28/2019] [Revised: 10/10/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022]
Abstract
The aetiology and pathogenesis of bovine respiratory disease (BRD) are complex and involve the interplay of infectious agents, management and environmental factors. Previous studies of BRD focused on ante‐mortem samples from the upper respiratory tract and identified several unconventional viruses. The lung, however, is the primary location where significant BRD lesions are usually found and is a common post‐mortem diagnostic specimen. In this study, results of high‐throughput virome sequencing, bacterial culture, targeted real‐time PCR and histological examination of 130 bovine pneumonic lungs from western Canadian cattle were combined to explore associations of microorganisms with different types of pneumonia. Fibrinous bronchopneumonia (FBP) was the predominant type of pneumonia (46.2%, 60/130) and was associated with the detection of Mannheimia haemolytica. Detection of Histophilus somni and Pasteurella multocida was associated with suppurative bronchopneumonia (SBP) and concurrent bronchopneumonia and bronchointerstitial pneumonia (BP&BIP), respectively. Sixteen viruses were identified, of which bovine parvovirus 2 (BPV2) was the most prevalent (11.5%, 15/130) followed by ungulate tetraparvovirus 1 (UTPV1, 8.5%, 11/130) and bovine respiratory syncytial virus (BRSV, 8.5%, 11/130). None of these viruses, however, were significantly associated with a particular type of pneumonia. Unconventional viruses such as influenza D virus (IDV) and bovine rhinitis B virus (BRBV) were detected, although sparsely, consistent with our previous findings in upper respiratory tract samples. Taken together, our results show that while virus detection in post‐mortem lung samples is of relatively little diagnostic value, the strong associations of H. somni and M. haemolytica with SBP and FBP, respectively, indicate that histopathology can be useful in differentiating bacterial aetiologies.
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Affiliation(s)
- Maodong Zhang
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dale L Godson
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Prairie Diagnostic Services Inc., Saskatoon, SK, Canada
| | - Musangu Ngeleka
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Prairie Diagnostic Services Inc., Saskatoon, SK, Canada
| | - Champika Fernando
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yanyun Huang
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Prairie Diagnostic Services Inc., Saskatoon, SK, Canada
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154
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Chan WS, Au CH, Leung HCM, Ho DN, Li D, Chan TL, Lam TW, Ma ESK, Tang BSF. Potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis. Future Cardiol 2019; 15:411-424. [PMID: 31691592 DOI: 10.2217/fca-2018-0088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: To explore potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis (IE) caused by fastidious bacteria. Materials & methods: Plasma and heart valves of two patients, who were diagnosed with IE caused by Bartonella quintana and Propionibacterium species, were sequenced by using Illumina MiSeq and Nanopore MinION. Results: For patient 1, B. quintana was detected in the plasma pool collected 4 days before valvular replacement surgery. For patient 2, Propionibacterium sp. oral taxon 193 was detected in the plasma sample collected on hospital day 1. Nearly complete bacterial genomes (>98%) were retrieved from resected heart valves of both patients, enabling detection of antibiotic resistance-associated features. Real-time sequencing of heart valves identified both pathogens within the first 16 min of sequencing runs. Conclusion: Metagenomic sequencing may be a helpful supplement to IE diagnostic workflow, especially when conventional tests fail to yield a diagnosis.
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Affiliation(s)
- Wai-Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
| | - Chun-Hang Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
| | - Henry Chi-Ming Leung
- Department of Computer Science, The University of Hong Kong, Hong Kong, PR China.,L3 Bioinformatics Limited, Hong Kong, PR China
| | - Dona N Ho
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
| | - Dinghua Li
- Department of Computer Science, The University of Hong Kong, Hong Kong, PR China
| | - Tsun-Leung Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
| | - Tak-Wah Lam
- Department of Computer Science, The University of Hong Kong, Hong Kong, PR China.,L3 Bioinformatics Limited, Hong Kong, PR China
| | - Edmond Shiu-Kwan Ma
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
| | - Bone Siu-Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, PR China
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155
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Xue F, Sun F, Jiang L, Hua D, Wang Y, Nan X, Zhao Y, Xiong B. Effects of Partial Replacment of Dietary Forage Using Kelp Powder ( Thallus laminariae) on Ruminal Fermentation and Lactation Performances of Dairy Cows. Animals (Basel) 2019; 9:E852. [PMID: 31652562 PMCID: PMC6826980 DOI: 10.3390/ani9100852] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/09/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Kelp powder, which was rich in novel oligosaccharides and iodine might be utilized by the rumen microbiome, promoted the ruminal fermentation and finally enhanced the lactation performance of dairy cows. Therefore, the purpose of this study was to investigate the effects of kelp powder partially replacing dietary forage on rumen fermentation and lactation performance of dairy cows. (2) Methods: In the present study, 20 Chinese Holstein dairy cows were randomly divided into two treatments, a control diet (CON) and a kelp powder replacing diet (Kelp) for a 35-d long trial. Dry matter intake (DMI), milk production, milk quality, ruminal fermentable parameters, and rumen microbiota were measured to investigate the effects of kelp powder feeding on dairy cows. (3) Results: On the lactation performance, kelp significantly increased milk iodine content and effectively enhanced milk production and milk fat content. On the fermentable aspects, kelp significantly raised TVFA while reducing the ammonia-N content. On the rumen microbial aspect, kelp feeding significantly promoted the proliferation of Firmicutes and Proteobacteria while suppressing Bacteroidetes. (4) Conclusion: kelp powder as an ingredient of feedstuff might promote the rumen fermentation ability and effectively increase milk fat and iodine content, and consequently improve the milk nutritional value.
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Affiliation(s)
- Fuguang Xue
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Fuyu Sun
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Linshu Jiang
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing University of Agriculture, Beijing 102206, China.
| | - Dengke Hua
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yue Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xuemei Nan
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yiguang Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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156
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Strubbia S, Schaeffer J, Oude Munnink BB, Besnard A, Phan MVT, Nieuwenhuijse DF, de Graaf M, Schapendonk CME, Wacrenier C, Cotten M, Koopmans MPG, Le Guyader FS. Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters. Front Microbiol 2019; 10:2394. [PMID: 31681246 PMCID: PMC6811496 DOI: 10.3389/fmicb.2019.02394] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 07/24/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were used to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in environmental samples. Family-specific viral contigs were classified and sorted by SLIM and final norovirus contigs were genotyped using the online Norovirus genotyping tool v2.0. From sewage samples, 14 norovirus genogroup I sequences were identified of which six were complete genomes. For norovirus genogroup II, nine sequences were identified and three of them comprised more than half of the genome. In oyster samples bioaccumulated with these sewage samples, only the use of an enrichment step during library preparation allowed successful identification of nine different sequences of norovirus genogroup I and four for genogroup II (>500 bp). This study demonstrates the importance of method development to increase virus recovery, and the interest of a capture-based approach to be able to identify viruses present at low concentrations.
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Affiliation(s)
- Sofia Strubbia
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Julien Schaeffer
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Alban Besnard
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - My V T Phan
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Candice Wacrenier
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Matthew Cotten
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
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157
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Abstract
PURPOSE OF REVIEW Posttransplantation infections are common. It is anticipated that infection will be no less common in xenotransplantation recipients. Prolonged xenograft survivals have resulted from advances in immunosuppressive strategies and development of swine that decrease host immune responses via genetic manipulation, notably CRISPR/cas9 manipulation. As prospects for clinical trials improve, consideration of the unique infectious risks posed by xenotransplantation reemerge. RECENT FINDINGS Organisms likely to cause infection in human recipients of porcine xenografts are unknown in advance of clinical trials. Microbiological screening of swine intended as xenograft donors can be more intensive than is currently feasible for human allograft donors. Monitoring infection in recipients will also be more intensive. Key opportunities in infectious diseases of xenotransplantation include major technological advances in evaluation of the microbiome by unbiased metagenomic sequencing, assessments of some risks posed by porcine endogenous retroviruses (PERVs) including antiretroviral susceptibilities, availability of swine with deletion of genomic PERVs, and recognition of the rapidly changing epidemiology of infection in swine worldwide. SUMMARY Unknown infectious risks in xenotransplantation requires application of advanced microbiological techniques to discern and prevent infection in graft recipients. Clinical trials will provide an opportunity to advance the safety of all of organ transplantation.
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Affiliation(s)
- Jay A Fishman
- Transplantation Infectious Disease and Compromised Host Program, Infectious Disease Division and MGH Transplant Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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158
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Saa P, Chiu C, Grimm K, Yu G, Benjamin RJ, Corash L, Stramer SL. Acute Zika virus infection in an asymptomatic blood donor at the onset of the Puerto Rico epidemic. Transfusion 2019; 59:3164-3170. [PMID: 31407817 PMCID: PMC6785374 DOI: 10.1111/trf.15484] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 05/03/2019] [Revised: 07/14/2019] [Accepted: 07/14/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Zika virus (ZIKV) spread to Puerto Rico likely originated from southeastern Brazil approximately 8.5 months earlier than blood donation screening for ZIKV was initiated, but the time of ZIKV introduction in the blood donor population remains unknown. METHODS To better understand when arboviral infections first appeared in the blood donor pool in Puerto Rico, we retrospectively screened for ZIKV RNA (as well as chikungunya [CHIKV] and dengue [DENV] viral RNA) a repository of 1186 linked blood donor and recipient samples collected from February 2015 to May 2016 as an endpoint efficacy measure following the introduction of platelet pathogen reduction (PR). Phylogenetic analysis identified relatedness of donor strain to other circulating strains, and molecular clock analysis identified the estimated time of introduction. RESULTS An asymptomatic donor collected in December 2015 was ZIKV RNA confirmed positive, 4 months BEFORE investigational nucleic acid testing (NAT) implementation in April 2016, coincident and related to the first reported autochthonous cases. No CHIKV RNA or DENV RNA reactives were identified in donors or recipients, and no adverse events were reported from PR use in recipients. Phylogenetic analysis confirmed the molecular relatedness of the donor ZIKV strain to the Puerto Rico lineage likely introduced approximately 4.5 months earlier. CONCLUSION This study identified an asymptomatic ZIKV infection in a blood donor occurring before those previously recognized by blood donation screening. NAT and PR continue to be used as acceptable strategies to prevent transfusion-transmitted arboviral infections worldwide; however, repeated arboviral outbreaks warrant consideration of PR as a more proactive approach.
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Affiliation(s)
- Paula Saa
- American Red Cross, Scientific Affairs, Gaithersburg, MD 20877
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, CA 94107
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 91407
| | - Kacie Grimm
- American Red Cross, Scientific Affairs, Gaithersburg, MD 20877
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, CA 94107
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 91407
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159
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Kufner V, Plate A, Schmutz S, Braun DL, Günthard HF, Capaul R, Zbinden A, Mueller NJ, Trkola A, Huber M. Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases. Genes (Basel) 2019; 10:genes10090661. [PMID: 31470675 PMCID: PMC6770117 DOI: 10.3390/genes10090661] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 07/31/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 01/28/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) can capture the full spectrum of viral pathogens in a specimen and has the potential to become an all-in-one solution for virus diagnostics. To date, clinical application is still in an early phase and limitations remain. Here, we evaluated the impact of viral mNGS for cases analyzed over two years in a tertiary diagnostics unit. High throughput mNGS was performed upon request by the treating clinician in cases where the etiology of infection remained unknown or the initial differential diagnosis was very broad. The results were compared to conventional routine testing regarding outcome and workload. In total, 163 specimens from 105 patients were sequenced. The main sample types were cerebrospinal fluid (34%), blood (33%) and throat swabs (10%). In the majority of the cases, viral encephalitis/meningitis or respiratory infection was suspected. In parallel, conventional virus diagnostic tests were performed (mean 18.5 individually probed targets/patients). mNGS detected viruses in 34 cases (32%). While often confirmatory, in multiple cases, the identified viruses were not included in the selected routine diagnostic tests. Two years of mNGS in a tertiary diagnostics unit demonstrated the advantages of a single, untargeted approach for comprehensive, rapid and efficient virus diagnostics, confirming the utility of mNGS in complementing current routine tests.
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Affiliation(s)
- Verena Kufner
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plate
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Dominique L Braun
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Huldrych F Günthard
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Nicolas J Mueller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland.
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.
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160
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Aarnoutse R, Ziemons J, Penders J, Rensen SS, de Vos-Geelen J, Smidt ML. The Clinical Link between Human Intestinal Microbiota and Systemic Cancer Therapy. Int J Mol Sci 2019; 20:ijms20174145. [PMID: 31450659 PMCID: PMC6747354 DOI: 10.3390/ijms20174145] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 07/31/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 02/07/2023] Open
Abstract
Clinical interest in the human intestinal microbiota has increased considerably. However, an overview of clinical studies investigating the link between the human intestinal microbiota and systemic cancer therapy is lacking. This systematic review summarizes all clinical studies describing the association between baseline intestinal microbiota and systemic cancer therapy outcome as well as therapy-related changes in intestinal microbiota composition. A systematic literature search was performed and provided 23 articles. There were strong indications for a close association between the intestinal microbiota and outcome of immunotherapy. Furthermore, the development of chemotherapy-induced infectious complications seemed to be associated with the baseline microbiota profile. Both chemotherapy and immunotherapy induced drastic changes in gut microbiota composition with possible consequences for treatment efficacy. Evidence in the field of hormonal therapy was very limited. Large heterogeneity concerning study design, study population, and methods used for analysis limited comparability and generalization of results. For the future, longitudinal studies investigating the predictive ability of baseline intestinal microbiota concerning treatment outcome and complications as well as the potential use of microbiota-modulating strategies in cancer patients are required. More knowledge in this field is likely to be of clinical benefit since modulation of the microbiota might support cancer therapy in the future.
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Affiliation(s)
- Romy Aarnoutse
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands.
- Department of Surgery, Maastricht University Medical Center+, 6202 AZ Maastricht, The Netherlands.
| | - Janine Ziemons
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands
- Department of Surgery, Maastricht University Medical Center+, 6202 AZ Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, Maastricht University Medical Center+, 6202 AZ Maastricht, The Netherlands
- NUTRIM - School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands
| | - Sander S Rensen
- Department of Surgery, Maastricht University Medical Center+, 6202 AZ Maastricht, The Netherlands
- NUTRIM - School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands
| | - Judith de Vos-Geelen
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands
- Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Center+, 6202 AZ Maastricht, The Netherlands
| | - Marjolein L Smidt
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands
- Department of Surgery, Maastricht University Medical Center+, 6202 AZ Maastricht, The Netherlands
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161
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Wu L, Zeng T, Zinellu A, Rubino S, Kelvin DJ, Carru C. A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians. mSystems 2019; 4:4/4/e00325-19. [PMID: 31289141 PMCID: PMC6616150 DOI: 10.1128/msystems.00325-19] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 06/18/2019] [Indexed: 02/05/2023] Open
Abstract
Sardinia, Italy, has a high prevalence of residents who live more than 100 years. The reasons for longevity in this isolated region are currently unknown. Gut microbiota may hold a clue. To explore the role gut microbiota may play in healthy aging and longevity, we used metagenomic sequencing to determine the compositional and functional differences in gut microbiota associated with populations of different ages in Sardinia. Our data revealed that the gut microbiota of both young and elderly Sardinians shared similar taxonomic and functional profiles. A different pattern was found in centenarians. Within the centenarian group, the gut microbiota was correlated with the functional independence measurement of the host. Centenarians had a higher diversity of core microbiota species and microbial genes than those in the young and elderly. We found that the gut microbiota in Sardinian centenarians displayed a rearranged taxonomic pattern compared with those of the young and elderly, featured by depletion of Faecalibacterium prausnitzii and Eubacterium rectale and enriched for Methanobrevibacter smithii and Bifidobacterium adolescentis Moreover, functional analysis revealed that the microbiota in centenarians had high capacity for central metabolism, especially glycolysis and fermentation to short-chain fatty acids (SCFAs), although the gut microbiota in centenarians was low in genes encoding enzymes involved in degradation of carbohydrates, including fibers and galactose.IMPORTANCE The gut microbiota has been proposed as a promising determinant for human health. Centenarians as a model for extreme aging may help us understand the correlation of gut microbiota with healthy aging and longevity. Here we confirmed that centenarians had microbiota elements usually associated with benefits to health. Our finding of a high capacity of glycolysis and related SCFA production represented a healthy microbiome and environment that is regarded as beneficial for host gut epithelium. The low abundance of genes encoding components of pathways involved in carbohydrate degradation was also found in the gut microbiota of Sardinian centenarians and is often associated with poor gut health. Overall, our study here represents an expansion of previous research investigating the age-related changes in gut microbiota. Furthermore, our study provides a new prospective for potential targets for gut microbiota intervention directed at limiting gut inflammation and pathology and enhancing a healthy gut barrier.
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Affiliation(s)
- Lu Wu
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Tiansheng Zeng
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - David J Kelvin
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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162
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Zhang M, Hill JE, Fernando C, Alexander TW, Timsit E, van der Meer F, Huang Y. Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease. Transbound Emerg Dis 2019; 66:1379-1386. [PMID: 30873724 PMCID: PMC7168561 DOI: 10.1111/tbed.13172] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 11/30/2018] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 12/23/2022]
Abstract
Bovine respiratory disease (BRD) causes considerable economic losses in North America. The pathogenesis involves interactions between bacteria, viruses, environment and management factors. Primary viral infection can increase the risk of secondary fatal bacterial infection. The objective of this study was to use metagenomic sequencing to characterize the respiratory viromes of paired nasal swabs and tracheal washes from western Canadian feedlot cattle, with or without BRD. A total of 116 cattle (116 nasal swabs and 116 tracheal washes) were analysed. The presence of influenza D virus (IDV), bovine rhinitis A virus (BRAV), bovine rhinitis B virus (BRBV), bovine coronavirus (BCV) and bovine respiratory syncytial virus (BRSV) was associated with BRD. Agreement between identification of viruses in nasal swabs and tracheal washes was generally weak, indicating that sampling location may affect detection of infection. This study reported several viruses for the first time in Canada and provides a basis for further studies investigating candidate viruses important to the prevention of BRD.
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Affiliation(s)
- Maodong Zhang
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Champika Fernando
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Trevor W Alexander
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Edouard Timsit
- Department of Production Animal Health, University of Calgary, Calgary, AB, Canada.,Simpson Ranch Chair in Beef Cattle Health and Wellness, University of Calgary, Calgary, AB, Canada.,Feedlot Health Management Services, Okotoks, AB, Canada
| | - Frank van der Meer
- Department of Ecosystem and Public Health, University of Calgary, Calgary, AB, Canada
| | - Yanyun Huang
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Prairie Diagnostic Services Inc, Saskatoon, SK, Canada
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163
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Hu Y, Feng Y, Wu J, Liu F, Zhang Z, Hao Y, Liang S, Li B, Li J, Lv N, Xu Y, Zhu B, Sun Z. The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients. Front Cell Infect Microbiol 2019; 9:90. [PMID: 31001490 PMCID: PMC6456665 DOI: 10.3389/fcimb.2019.00090] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [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: 11/29/2018] [Accepted: 03/14/2019] [Indexed: 11/13/2022] Open
Abstract
Cross talk occurs between the human gut and the lung through a gut-lung axis involving the gut microbiota. However, the signatures of the human gut microbiota after active Mycobacterium tuberculosis infection have not been fully understood. Here, we investigated changes in the gut microbiota in tuberculosis (TB) patients by shotgun sequencing the gut microbiomes of 31 healthy controls and 46 patients. We observed a dramatic changes in gut microbiota in tuberculosis patients as reflected by significant decreases in species number and microbial diversity. The gut microbiota of TB patients were mostly featured by the striking decrease of short-chain fatty acids (SCFAs)-producingbacteria as well as associated metabolic pathways. A classification model based on the abundance of three species, Haemophilus parainfluenzae, Roseburia inulinivorans, and Roseburia hominis, performed well for discriminating between healthy and diseased patients. Additionally, the healthy and diseased states can be distinguished by SNPs in the species of B. vulgatus. We present a comprehensive profile of changes in the microbiota in clinical TB patients. Our findings will shed light on the design of future diagnoses and treatments for M. tuberculosis infections.
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Affiliation(s)
- Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuqing Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiannan Wu
- Translational Medicine Research Center, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Fei Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiguo Zhang
- Department of Laboratory Medicine, Tuberculosis Control Institute in Changping District, Beijing, China
| | - Yanan Hao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shihao Liang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Boxing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Na Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuhui Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Zhaogang Sun
- Translational Medicine Research Center, Beijing Chest Hospital, Capital Medical University, Beijing, China
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164
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Wang H, Yan Y, Yi X, Duan Y, Wang J, Li S, Luo L, Huang T, Inglis B, Li X, Ji W, Tan T, Si W. Histopathological Features and Composition of Gut Microbiota in Rhesus Monkey of Alcoholic Liver Disease. Front Microbiol 2019; 10:165. [PMID: 30800107 PMCID: PMC6375900 DOI: 10.3389/fmicb.2019.00165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 09/20/2018] [Accepted: 01/22/2019] [Indexed: 12/25/2022] Open
Abstract
Alcohol-induced chronic liver disease (ALD) is becoming the most common liver disease in the world. However, there are no effective, universally accepted therapies for ALD. The etiology of ALD remains blurry so far. Historical evidence has demonstrated a link between the liver and gut microbiota. But it is difficult to distinguish the effect of gut microbiota changes caused by alcohol consumption in humans since the microbiota change detected in humans is complicated by diet and environmental factors. Due to the genetic, physiological, metabolic, and behavioral similarities to humans, the rhesus monkey provides excellent translational validity in preclinical studies, and the diet and environmental conditions can be controlled well in rhesus monkey. In our study, we explored the relationship between ALD and the gut microbiome in the rhesus monkeys with alcoholic liver steatosis. Our results showed that there was a change of the bacterial community structure in monkeys with ALD. Differences of the relative abundances of gut microbiota at phylum, order, family, genus, and species levels were observed between control monkeys and monkeys with ALD, and different pathways enriched in the monkeys with ALD were identified by metagenomic function analysis. Firmicutes, Proteobacteria, Verrucomicrobia tended to increase whereas Bacteroidetes and Actinobacteria decreased in the fecal microbiota of ALD group compared to the control group. Lactobacillales and Lactobacillus significantly decreased in ALD monkeys compared with normal monkeys, Streptococcus was lower in the ALD group compared with the control group. The non-human primate model of ALD will be useful for exploration of the microbiome markers as diagnosis and potentially prognosis for ALD. The ALD model will benefit the development of new therapeutic procedures for treating ALD and provide safety and efficacy evaluation for clinical application.
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Affiliation(s)
- Hong Wang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yaping Yan
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Xiaoyan Yi
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanchao Duan
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Junfeng Wang
- Department of Hepatic and Bile Duct Surgery, The First People's Hospital of Yunnan Province, Kunming, China
| | - Shanshan Li
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Lilin Luo
- Department of Pathology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Tianzhuang Huang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Briauna Inglis
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Xi Li
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Weizhi Ji
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Tao Tan
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Wei Si
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
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165
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Liew WPP, Mohd-Redzwan S, Than LTL. Gut Microbiota Profiling of Aflatoxin B1-Induced Rats Treated with Lactobacillus casei Shirota. Toxins (Basel) 2019; 11:E49. [PMID: 30658400 PMCID: PMC6357033 DOI: 10.3390/toxins11010049] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 12/20/2018] [Accepted: 01/10/2019] [Indexed: 12/21/2022] Open
Abstract
Aflatoxin B1 (AFB1) is a ubiquitous carcinogenic food contaminant. Gut microbiota is of vital importance for the host's health, regrettably, limited studies have reported the effects of xenobiotic toxins towards gut microbiota. Thus, the present study aims to investigate the interactions between AFB1 and the gut microbiota. Besides, an AFB1-binding microorganism, Lactobacillus casei Shirota (Lcs) was tested on its ability to ameliorate the changes on gut microbiota induced by AFB1. The fecal contents of three groups of rats included an untreated control group, an AFB1 group, as well as an Lcs + AFB1 group, were analyzed. Using the MiSeq platform, the PCR products of 16S rDNA gene extracted from the feces were subjected to next-generation sequencing. The alpha diversity index (Shannon) showed that the richness of communities increased significantly in the Lcs + AFB1 group compared to the control and AFB1 groups. Meanwhile, beta diversity indices demonstrated that AFB1 group significantly deviated from the control and Lcs + AFB1 groups. AFB1-exposed rats were especially high in Alloprevotella spp. abundance. Such alteration in the bacterial composition might give an insight on the interactions of AFB1 towards gut microbiota and how Lcs plays its role in detoxification of AFB1.
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Affiliation(s)
- Winnie-Pui-Pui Liew
- Department of Nutrition and Dietetics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Sabran Mohd-Redzwan
- Department of Nutrition and Dietetics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Leslie Thian Lung Than
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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166
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Wang JC, Bergeron M, Andersen H, Tikhtman R, Haslam D, Hunter T, Herr AB, de Alarcon A. Feasibility of shotgun metagenomics to assess microbial ecology of pediatric tracheostomy tubes. Laryngoscope 2018; 129:317-323. [PMID: 30565684 DOI: 10.1002/lary.27356] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Biofilm formation on medical devices such as tracheostomy tubes (TTs) is a serious problem. The clinical impact of biofilms on the airway is still unclear. Biofilms may play a role in granulation tissue development, recurrent airway infections, and failure of laryngotracheal reconstructions. The microbial ecology on TTs has yet to be elucidated. The purpose of this study was to determine the feasibility of shotgun metagenomics to assess the biodistribution of microorganisms on TTs. METHODS Four TTs were collected from pediatric patients (1.4-10.2 years) with (n = 2) and without (n = 2) granulation tissue formation. Duration of TT placement prior to retrieval from patients ranged from 5 to 365 days. DNA extraction was performed using the MO BIO UltraClean Microbial Isolation (Mo Bio Laboratories, Carlsbad, CA). Library generation using Nextera XT adapters (Illumina Inc., San Diego, CA) and metagenomic shotgun sequencing was performed using the Illumina NextSeq500 (Illumina Inc, San Diego, CA). Salinibacter ruber, a species not found in mammalian microbiome communities, was used as a DNA standard and represented 0.7% to 5.7% of the microbiome, ensuring good quality and abundance of sample DNA. RESULTS Metagenomic shotgun sequencing was successful for all patients. In TTs associated with granuloma, Fusobacterium nucleatum, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae were predominant, most of which are considered pathogens. From TTs without granulomas, Neisseria mucosa, Neisseria sicca, Acinetobacter baumannii, and Haemophilus parainfluenzae were identified, primarily consistent with respiratory microbiome. CONCLUSION This study reveals that metagenomic shotgun sequencing of biofilms formed on pediatric TTs is feasible with an apparent difference in microbiome for patients with granulation tissue. Further studies are necessary to elucidate the pathogenesis of microbial ecology and its role in airway disease in patients with TTs. LEVEL OF EVIDENCE 2c Laryngoscope, 129:317-323, 2019.
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Affiliation(s)
- James C Wang
- Department of Otolaryngology-Head and Neck Surgery, Cincinnati, OH, U.S.A.,Division of Pediatric Otolaryngology-Head and Neck Surgery, Cincinnati, OH, U.S.A
| | - Mathieu Bergeron
- Division of Pediatric Otolaryngology-Head and Neck Surgery, Cincinnati, OH, U.S.A
| | | | - Raisa Tikhtman
- School of Medicine, University of Cincinnati Medical Center, Cincinnati, OH, U.S.A
| | - David Haslam
- Division of Pediatric Otolaryngology-Head and Neck Surgery, Cincinnati, OH, U.S.A
| | - Tammy Hunter
- School of Medicine, University of Cincinnati Medical Center, Cincinnati, OH, U.S.A.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, U.S.A
| | - Andrew B Herr
- Division of Infectious Diseases, Cincinnati, OH, U.S.A
| | - Alessandro de Alarcon
- Department of Otolaryngology-Head and Neck Surgery, Cincinnati, OH, U.S.A.,Division of Pediatric Otolaryngology-Head and Neck Surgery, Cincinnati, OH, U.S.A
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167
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Liang H, Chen H, Ji C, Lin X, Zhang W, Li L. Dynamic and Functional Characteristics of Predominant Species in Industrial Paocai as Revealed by Combined DGGE and Metagenomic Sequencing. Front Microbiol 2018; 9:2416. [PMID: 30356774 PMCID: PMC6189446 DOI: 10.3389/fmicb.2018.02416] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 06/08/2018] [Accepted: 09/20/2018] [Indexed: 01/12/2023] Open
Abstract
The microbial community during the fermentation of industrial paocai, a lactic acid fermented vegetable food, was investigated via combined denaturing gradient gel electrophoresis (DGGE) and metagenomic sequencing. Firmicutes and Proteobacteria were identified as the dominant phyla during the fermentation. DGGE results of the bacterial community analysis showed that many genera were observed during the fermentation of industrial paocai, but the same predominant genus and species were observed: Lactobacillus and Lactobacillus (L.) alimentarius/L. paralimentarius. The abundance of L. alimentarius/L. paralimentarius increased fast during the initial stage of fermentation and approximately remained constant during the later stage. Metagenomic sequencing was used to finally identify the predominant species and their genetic functions. Metabolism was the primary functions of the microbial community in industrial paocai fermentation, including carbohydrate metabolism (CM), overview (OV), amino acid metabolism (AAM), nucleotide metabolism (NM), energy metabolism (EM), etc. The predominant species L. alimentarius and L. paralimentarius were involved in plenty of pathways in metabolism and played different roles in the metabolism of carbohydrate, amino acid, lipid to form flavor compounds during industrial paocai fermentation. This study provided valuable information about the predominant species in industrial paocai and its functional properties, which could enable us to advance our understanding of the fermentation mechanism during fermentation of industrial paocai. Our results will advance the understanding of the microbial roles in the industrial paocai fermentation and provide a theoretical basis for improving the quality of industrial paocai products.
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Affiliation(s)
- Huipeng Liang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Huiying Chen
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Chaofan Ji
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Xinping Lin
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Wenxue Zhang
- Food Eco-engineering and Biotechnology Lab, College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, China
| | - Li Li
- College of Biotechnology Engineering, Sichuan University of Science and Engineering, Zigong, China
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168
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Yang S, Gao X, Meng J, Zhang A, Zhou Y, Long M, Li B, Deng W, Jin L, Zhao S, Wu D, He Y, Li C, Liu S, Huang Y, Zhang H, Zou L. Metagenomic Analysis of Bacteria, Fungi, Bacteriophages, and Helminths in the Gut of Giant Pandas. Front Microbiol 2018; 9:1717. [PMID: 30108570 PMCID: PMC6080571 DOI: 10.3389/fmicb.2018.01717] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [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: 02/01/2018] [Accepted: 07/10/2018] [Indexed: 11/13/2022] Open
Abstract
To obtain full details of gut microbiota, including bacteria, fungi, bacteriophages, and helminths, in giant pandas (GPs), we created a comprehensive microbial genome database and used metagenomic sequences to align against the database. We delineated a detailed and different gut microbiota structures of GPs. A total of 680 species of bacteria, 198 fungi, 185 bacteriophages, and 45 helminths were found. Compared with 16S rRNA sequencing, the dominant bacterium phyla not only included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria but also Cyanobacteria and other eight phyla. Aside from Ascomycota, Basidiomycota, and Glomeromycota, Mucoromycota, and Microsporidia were the dominant fungi phyla. The bacteriophages were predominantly dsDNA Myoviridae, Siphoviridae, Podoviridae, ssDNA Inoviridae, and Microviridae. For helminths, phylum Nematoda was the dominant. In addition to previously described parasites, another 44 species of helminths were found in GPs. Also, differences in abundance of microbiota were found between the captive, semiwild, and wild GPs. A total of 1,739 genes encoding cellulase, β-glucosidase, and cellulose β-1,4-cellobiosidase were responsible for the metabolism of cellulose, and 128,707 putative glycoside hydrolase genes were found in bacteria/fungi. Taken together, the results indicated not only bacteria but also fungi, bacteriophages, and helminths were diverse in gut of giant pandas, which provided basis for the further identification of role of gut microbiota. Besides, metagenomics revealed that the bacteria/fungi in gut of GPs harbor the ability of cellulose and hemicellulose degradation.
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Affiliation(s)
- Shengzhi Yang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xin Gao
- Department of Nutrition and Food Science, University of Maryland, College Park, College Park, MD, United States
| | - Jianghong Meng
- Department of Nutrition and Food Science, University of Maryland, College Park, College Park, MD, United States
| | - Anyun Zhang
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Yingmin Zhou
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Mei Long
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Bei Li
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Wenwen Deng
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lei Jin
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Siyue Zhao
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Daifu Wu
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Yongguo He
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Caiwu Li
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya’an, China
| | - Yan Huang
- The China Conservation and Research Center for the Giant Panda, Wolong, China
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), Wolong, China
| | - Hemin Zhang
- The China Conservation and Research Center for the Giant Panda, Wolong, China
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), Wolong, China
| | - Likou Zou
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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169
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Thézé J, Li T, du Plessis L, Bouquet J, Kraemer MUG, Somasekar S, Yu G, de Cesare M, Balmaseda A, Kuan G, Harris E, Wu CH, Ansari MA, Bowden R, Faria NR, Yagi S, Messenger S, Brooks T, Stone M, Bloch EM, Busch M, Muñoz-Medina JE, González-Bonilla CR, Wolinsky S, López S, Arias CF, Bonsall D, Chiu CY, Pybus OG. Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico. Cell Host Microbe 2018; 23:855-864.e7. [PMID: 29805095 PMCID: PMC6006413 DOI: 10.1016/j.chom.2018.04.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [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: 02/16/2018] [Revised: 03/27/2018] [Accepted: 04/26/2018] [Indexed: 02/06/2023]
Abstract
The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures.
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Affiliation(s)
- Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - Tony Li
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Jerome Bouquet
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK; Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Harvard University, Boston, MA, USA
| | - Sneha Somasekar
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Mariateresa de Cesare
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Angel Balmaseda
- Laboratory Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministerio de Salud, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Chieh-Hsi Wu
- Department of Statistics, University of Oxford, Oxford, UK
| | - M Azim Ansari
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rory Bowden
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Shigeo Yagi
- California Department of Public Health, Richmond, CA, USA
| | | | - Trevor Brooks
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medcine, Baltimore, MD, USA
| | - Michael Busch
- Blood Systems Research Institute, San Francisco, CA, USA
| | - José E Muñoz-Medina
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Cesar R González-Bonilla
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Steven Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - David Bonsall
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA; Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
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Chiodini RJ, Dowd SE, Barron JN, Galandiuk S, Davis B, Glassing A. Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn's disease of the terminal ileum. J Med Microbiol 2018; 67:549-559. [PMID: 29458679 DOI: 10.1099/jmm.0.000690] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Crohn's disease is a chronic debilitating intestinal syndrome of unknown aetiology that is thought to result in part from an imbalance (dysbiosis) of the intestinal microbial populations, known as the microbiota. In this study we sought to compare the microbiota at the mucosal and submucosal levels at the resection margin in Crohn's disease to those in other intestinal dysbiotic disease controls to determine the level of bacterial translocation. METHODOLOGY 16S microbiota sequencing was performed on DNA extracted from mucosal and submucosal samples from resected intestinal tissues from Crohn's disease and controls. RESULTS Grossly normal appearing tissue at the resection margin showed early signs, suggesting bacterial translocation, with two bacterial families having penetrated the mucosal surfaces. In contrast, 4 and 13 bacterial families were present within submucosal tissues at the disease centre and disease margin, respectively. Although there was no significant difference in biodiversity, there was increased bacterial richness in the Crohn's disease group as compared to non-IBD controls. CONCLUSION The presence and/or absence of certain bacteria suggested disease-specific ecological or micro-environmental pressures driving or excluding certain organisms in Crohn's disease. The data suggest that several of the dysbiotic conditions previously reported for Crohn's disease are not unique but common to general dysbiosis. The examination of multiple intestinal sites in advanced disease may provide a spectrum of disease from early onset at the resection margin to active disease at the disease margin and late-stage fibrostenotic disease at the centre of the lesion, and a unique etiopathogenic view of Crohn's disease.
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Affiliation(s)
- Rodrick J Chiodini
- Department of Biological and Physical Sciences, Montana State University-Billings, Billings, MT, USA.,St Vincent Healthcare, Sisters of Charity of Leavenworth Health System, Billings, MT, USA
| | - Scot E Dowd
- Molecular Research (Mr DNA), Shallowater, TX, USA
| | - James N Barron
- Department of Biological and Physical Sciences, Montana State University-Billings, Billings, MT, USA
| | - Susan Galandiuk
- Department of Surgery, University of Louisville, Louisville, KY, USA
| | - Brian Davis
- Department of Surgery, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Angela Glassing
- Department of Biological and Physical Sciences, Montana State University-Billings, Billings, MT, USA
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Street TL, Sanderson ND, Atkins BL, Brent AJ, Cole K, Foster D, McNally MA, Oakley S, Peto L, Taylor A, Peto TEA, Crook DW, Eyre DW. Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing. J Clin Microbiol 2017; 55:2334-47. [PMID: 28490492 DOI: 10.1128/JCM.00462-17] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/08/2017] [Indexed: 01/08/2023] Open
Abstract
Culture of multiple periprosthetic tissue samples is the current gold standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through culture of sonication fluid from explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI. We compared metagenomic sequencing with standard aerobic and anaerobic culture in 97 sonication fluid samples from prosthetic joint and other orthopedic device infections. Reads from Illumina MiSeq sequencing were taxonomically classified using Kraken. Using 50 derivation samples, we determined optimal thresholds for the number and proportion of bacterial reads required to identify an infection and confirmed our findings in 47 independent validation samples. Compared to results from sonication fluid culture, the species-level sensitivity of metagenomic sequencing was 61/69 (88%; 95% confidence interval [CI], 77 to 94%; for derivation samples 35/38 [92%; 95% CI, 79 to 98%]; for validation samples, 26/31 [84%; 95% CI, 66 to 95%]), and genus-level sensitivity was 64/69 (93%; 95% CI, 84 to 98%). Species-level specificity, adjusting for plausible fastidious causes of infection, species found in concurrently obtained tissue samples, and prior antibiotics, was 85/97 (88%; 95% CI, 79 to 93%; for derivation samples, 43/50 [86%; 95% CI, 73 to 94%]; for validation samples, 42/47 [89%; 95% CI, 77 to 96%]). High levels of human DNA contamination were seen despite the use of laboratory methods to remove it. Rigorous laboratory good practice was required to minimize bacterial DNA contamination. We demonstrate that metagenomic sequencing can provide accurate diagnostic information in PJI. Our findings, combined with the increasing availability of portable, random-access sequencing technology, offer the potential to translate metagenomic sequencing into a rapid diagnostic tool in PJI.
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172
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Pushpanathan P, Srikanth P, Seshadri KG, Selvarajan S, Pitani RS, Kumar TD, Janarthanan R. Gut Microbiota in Type 2 Diabetes Individuals and Correlation with Monocyte Chemoattractant Protein1 and Interferon Gamma from Patients Attending a Tertiary Care Centre in Chennai, India. Indian J Endocrinol Metab 2016; 20:523-530. [PMID: 27366720 PMCID: PMC4911843 DOI: 10.4103/2230-8210.183474] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) and obesity are associated with changes in gut microbiota and characterized by chronic low-grade inflammation. Monocyte chemoattractant protein-1 (MCP-1) and interferon gamma (IFNγ) are proinflammatory cytokines which play an important role in the development of T2DM. We undertook this study to analyze the gut microbiota of T2DM and nondiabetic subjects and to determine the profile of MCP 1 and IFNγ in the same subjects attending a tertiary care center in Chennai, Tamil Nadu, India. METHODS The study included 30 subjects with clinical details. Stool and blood samples were collected from all the subjects. DNA was extracted from fecal samples and polymerase chain reaction was done using fusion primers. Metagenomic analysis was performed using ion torrent sequencing. The reads obtained were in FASTA format and reported as operational taxonomic units. Human MCP 1 and IFNγ enzyme linked immunosorbent assay (ELISA) were performed for 23 serum samples. RESULTS The study consisted of 30 subjects; 17 were T2DM and 13 were nondiabetics. The gut microbiota among T2DM consisted predominantly of Gram negative bacteria; Escherichia and Prevotella, when compared with the nondiabetic group with predominantly Gram positive organisms suchas Faecalibacterium, Eubacterium, and Bifidobacterium. The mean MCP-1 values in the diabetic group were 232.8 pg/ml and in the nondiabetic group 170.84 pg/ml. IFNγ (mean 385.5 pg/ml) was raised in glycated hemoglobin (HbA1c) group of 6.5-7.5% which was statistically significant. Association of Escherichia with T2DM and association of Bifidobacteria in the nondiabetics were also statistically significant. CONCLUSION Escherichia counts were elevated in T2DM with HbA1c of 6.5-8.5% which was statistically significant suggesting that lipopolysaccharides present in the cell wall of Gram-negative bacteria may be responsible for low-grade inflammation as evidenced by elevated MCP-1 and IFNγ levels in T2DM with the same HbA1c levels.
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Affiliation(s)
- Premalatha Pushpanathan
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India
| | - Padma Srikanth
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India
| | - Krishna G. Seshadri
- Department of Endocrinology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India
| | - Sribal Selvarajan
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India
| | - Ravi Shankar Pitani
- Department of Community Medicine, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India
| | - Thomas David Kumar
- Shrimpex Biotech Services Private Limited, Sholinganallur, Chennai, Tamil Nadu, India
| | - R. Janarthanan
- Shrimpex Biotech Services Private Limited, Sholinganallur, Chennai, Tamil Nadu, India
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Smelov V, Naber K, Bjerklund Johansen TE. Letter to the Editor: Diagnostic Criteria in Urological Diseases do not Always Match with Findings by Extended Culture Techniques and Metagenomic Sequencing of 16S rDNA. Open Microbiol J 2016; 10:23-6. [PMID: 27006726 PMCID: PMC4780506 DOI: 10.2174/1874285801610010023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 11/30/2022] Open
Abstract
Some diseases of the urinary tract are defined by the presence of microorganisms while others are defined by their absence. The underlying idea has always been that urine from healthy subjects is sterile and a negative urine culture has usually been taken as discriminative for an infection to be absent. Several disorders with symptoms that resemble infections are regarded as separate entities based on the exclusion of bacterial growth such as overactive neurogenic bladder and pelvic pain syndromes. During the recent years two paradigmata related to the role of bacteria in urological disease classification have changed completely. Firstly, bacteriuria does not necessarily mean an infection, and secondly, if extended sets of culture media for identification of fastidious and anaerobic bacteria or culture-independent metagenomic sequencing (MGS) is applied, a broad range of even non-culturable bacteria has been detected in the ”sterile” bladder urine in healthy individuals. The aim of this editorial is to initiate a discussion to redefine the criteria for urinary tract infections and non-infectious urological disorders with similar symptoms. Clinical studies, in which extended sets of culture media and MGS are integrated, are needed to clarify the pathogenesis of urological disorders where bacteria may play a role. The pure detection of bacteria in the urine does not by itself prove an infectious etiology of a specific disorder. It is important to avoid that results of new technologies lead to unnecessary antibiotic consumption with unwanted collateral damage and adverse events.
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Affiliation(s)
- Vitaly Smelov
- Screening Group, International Agency for Research on Cancer, World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, France
| | - Kurt Naber
- Technical University of Munich, Karl-Bickleder-Str. 44c, 94315 Straubing, Germany
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Schoster A, Guardabassi L, Staempfli HR, Abrahams M, Jalali M, Weese JS. The longitudinal effect of a multi-strain probiotic on the intestinal bacterial microbiota of neonatal foals. Equine Vet J 2015; 48:689-696. [PMID: 26509834 DOI: 10.1111/evj.12524] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 04/22/2015] [Accepted: 10/14/2015] [Indexed: 12/11/2022]
Abstract
REASONS FOR PERFORMING THE STUDY The microbiota plays a key role in health and disease. Probiotics are a potential way to therapeutically modify the intestinal microbiota and prevent disease. OBJECTIVES The aim of this study was to investigate the effects of probiotics on the bacterial microbiota of foals during and after administration. STUDY DESIGN Randomised placebo controlled field trial. METHODS Thirty-eight healthy neonatal foals enrolled in a previous study were selected. The foals had received a multi-strain probiotic (four Lactobacillus spp. 3-4 × 103 colony-forming units (cfu)/g each, Bifidobacterium animalis spp. lactis, 1 × 103-4 cfu/g) or placebo once daily for 3 weeks. A total of 3 faecal samples were collected from each foal at 2-week intervals and assessed via metagenomic sequencing. The Wilcoxon test was used to compare data between treatment groups. RESULTS There were no changes on the phylum, order or class level between treatment groups at any age (all P>0.05) but some significant changes in relative abundance of families. Probiotic administration did not result in an increased relative abundance of lactobacilli or bifidobacteria at any age (Lactobacillus: P = 0.9, P = 0.1 and P = 0.2, Bifidobacterium: P = 0.3, P = 0.6 and P = 0.1 for Weeks 2, 4 and 6, respectively). Lactobacillus was enriched in the probiotic group at Week 6 on LEfSe analysis (linear discriminant analysis score 0.34, P = 0 .02). There was no effect on alpha diversity (all P>0.2) or community structure when parsimony and unifrac analysis were applied (all P>0.6). CONCLUSIONS There were limited effects of probiotic treatment on the bacterial microbiota of foals. The studied probiotic based on lactobacilli and bifidobacteria has a limited potential for therapeutic modification of the gastrointestinal microbiota.
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Affiliation(s)
- A Schoster
- Vetsuisse Faculty, Equine Department, University of Zurich, Switzerland. .,Faculty of Health and Medical Science, Department of Veterinary Disease Biology, University of Copenhagen, Denmark.
| | - L Guardabassi
- Faculty of Health and Medical Science, Department of Veterinary Disease Biology, University of Copenhagen, Denmark
| | - H R Staempfli
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Canada
| | - M Abrahams
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Canada
| | - M Jalali
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Canada
| | - J S Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Canada
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Wang X, Van Nostrand JD, Deng Y, Lü X, Wang C, Zhou J, Han X. Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China's grasslands. FEMS Microbiol Ecol 2015; 91:fiv133. [PMID: 26519142 DOI: 10.1093/femsec/fiv133] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2015] [Indexed: 11/14/2022] Open
Abstract
Patterns of variation in plant and animal diversity along precipitation gradients have been extensively studied, but much less is known about how and to what extent precipitation affects the biogeographic distribution of microbial diversity in arid areas across large spatial scales. Here we collected soils from 54 sites along a 3700 km transect covering a wide range of grassland ecosystems with distinct aridity gradients. We quantified the bacterial community diversity and the effects of climate, edaphic parameter and geographic distance on the bacterial community structure using high-throughput 16S rRNA gene sequencing. Of the 35 phyla detected, 6 were dominant: Actinobacteria, Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Bacteroidetes and Planctomycetes. Aridity was a major factor influencing bacterial diversity, community composition and taxon abundance. Although the pattern of bacterial species richness is markedly different from that of plant species richness, most soil bacteria were endemic to particular bioregions like macro-organisms. Community similarity significantly declined with environmental distance and geographic distance (r = -0.579 and -0.773, respectively). Geographic distance (historical contingencies) contributed more to bacterial community variation (36.02%) than combined environmental factors (24.06%). Overall, our results showed that geographic distance and climatic factors concurrently govern bacterial biogeographic patterns in arid and semi-arid grassland.
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Affiliation(s)
- Xiaobo Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, PR China University of Chinese Academy of Sciences, Beijing 100049, PR China Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
| | - Ye Deng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Xiaotao Lü
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, PR China
| | - Chao Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, PR China
| | - Jizhong Zhou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Xingguo Han
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, PR China
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Guo J, Peng Y, Ni BJ, Han X, Fan L, Yuan Z. Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing. Microb Cell Fact 2015; 14:33. [PMID: 25880314 PMCID: PMC4381419 DOI: 10.1186/s12934-015-0218-4] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [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: 12/12/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anaerobic digestion has been widely applied to treat the waste activated sludge from biological wastewater treatment and produce methane for biofuel, which has been one of the most efficient solutions to both energy crisis and environmental pollution challenges. Anaerobic digestion sludge contains highly complex microbial communities, which play crucial roles in sludge treatment. However, traditional approaches based on 16S rRNA amplification or fluorescent in situ hybridization cannot completely reveal the whole microbial community structure due to the extremely high complexity of the involved communities. In this sense, the next-generation high-throughput sequencing provides a powerful tool for dissecting microbial community structure and methane-producing pathways in anaerobic digestion. RESULTS In this work, the metagenomic sequencing was used to characterize microbial community structure of the anaerobic digestion sludge from a full-scale municipal wastewater treatment plant. Over 3.0 gigabases of metagenomic sequence data were generated with the Illumina HiSeq 2000 platform. Taxonomic analysis by MG-RAST server indicated that overall bacteria were dominant (~93%) whereas a considerable abundance of archaea (~6%) were also detected in the anaerobic digestion sludge. The most abundant bacterial populations were found to be Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Key microorganisms and related pathways involved in methanogenesis were further revealed. The dominant proliferation of Methanosaeta and Methanosarcina, together with the functional affiliation of enzymes-encoding genes (acetate kinase (AckA), phosphate acetyltransferase (PTA), and acetyl-CoA synthetase (ACSS)), suggested that the acetoclastic methanogenesis is the dominant methanogenesis pathway in the full-scale anaerobic digester. CONCLUSIONS In short, the metagenomic sequencing study of this work successfully dissected the detail microbial community structure and the dominated methane-producing pathways of a full-scale anaerobic digester. The knowledge garnered would facilitate to develop more efficient full-scale anaerobic digestion systems to achieve high-rate waste sludge treatment and methane production.
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Affiliation(s)
- Jianhua Guo
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing, 100124, Peoples' Republic of China.
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Yongzhen Peng
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing, 100124, Peoples' Republic of China.
| | - Bing-Jie Ni
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Xiaoyu Han
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing, 100124, Peoples' Republic of China.
- Beijing Drainage Group Co., Ltd, Beijing, 100022, Peoples' Republic of China.
| | - Lu Fan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
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Yolken RH, Jones-Brando L, Dunigan DD, Kannan G, Dickerson F, Severance E, Sabunciyan S, Talbot CC Jr, Prandovszky E, Gurnon JR, Agarkova IV, Leister F, Gressitt KL, Chen O, Deuber B, Ma F, Pletnikov MV, Van Etten JL. Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice. Proc Natl Acad Sci U S A 2014; 111:16106-11. [PMID: 25349393 DOI: 10.1073/pnas.1418895111] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chloroviruses (family Phycodnaviridae) are large DNA viruses known to infect certain eukaryotic green algae and have not been previously shown to infect humans or to be part of the human virome. We unexpectedly found sequences homologous to the chlorovirus Acanthocystis turfacea chlorella virus 1 (ATCV-1) in a metagenomic analysis of DNA extracted from human oropharyngeal samples. These samples were obtained by throat swabs of adults without a psychiatric disorder or serious physical illness who were participating in a study that included measures of cognitive functioning. The presence of ATCV-1 DNA was confirmed by quantitative PCR with ATCV-1 DNA being documented in oropharyngeal samples obtained from 40 (43.5%) of 92 individuals. The presence of ATCV-1 DNA was not associated with demographic variables but was associated with a modest but statistically significant decrease in the performance on cognitive assessments of visual processing and visual motor speed. We further explored the effects of ATCV-1 in a mouse model. The inoculation of ATCV-1 into the intestinal tract of 9-11-wk-old mice resulted in a subsequent decrease in performance in several cognitive domains, including ones involving recognition memory and sensory-motor gating. ATCV-1 exposure in mice also resulted in the altered expression of genes within the hippocampus. These genes comprised pathways related to synaptic plasticity, learning, memory formation, and the immune response to viral exposure.
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Abstract
Increasing evidence has accumulated to support that the human gut is a reservoir for antibiotic resistance genes. We previously identified more than 1000 genes displaying high similarity with known antibiotic resistance genes in the human gut gene set generated from the Chinese, Danish, and Spanish populations. Here, first, we add our new understanding of antibiotic resistance genes in the US and the Japanese populations; next, we describe the structure of a vancomycin-resistant operon in a Danish sample; and finally, we provide discussions on the correlation of the abundance of resistance genes in human gut with the antibiotic consumption in human medicine and in animal husbandry. These results, combined with those we published previously, provide comprehensive insights into the antibiotic resistance genes in the human gut microbiota at a population level.
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Affiliation(s)
- Yongfei Hu
- CAS Key Laboratory of Pathogenic Microbiology & Immunology; Institute of Microbiology; Chinese Academy of Sciences; Beijing, China,Beijing Key Laboratory of Microbial Drug Resistance and Resistome; Beijing, China
| | - Xi Yang
- CAS Key Laboratory of Pathogenic Microbiology & Immunology; Institute of Microbiology; Chinese Academy of Sciences; Beijing, China,Beijing Key Laboratory of Microbial Drug Resistance and Resistome; Beijing, China
| | - Na Lu
- CAS Key Laboratory of Pathogenic Microbiology & Immunology; Institute of Microbiology; Chinese Academy of Sciences; Beijing, China,Beijing Key Laboratory of Microbial Drug Resistance and Resistome; Beijing, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology & Immunology; Institute of Microbiology; Chinese Academy of Sciences; Beijing, China,Beijing Key Laboratory of Microbial Drug Resistance and Resistome; Beijing, China,Correspondence to: Baoli Zhu,
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