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Wang K, Zhang Z, Mo ZS, Yang XH, Lin BL, Peng L, Xu Y, Lei CY, Zhuang XD, Lu L, Yang RF, Chen T, Gao ZL. Gut microbiota as prognosis markers for patients with HBV-related acute-on-chronic liver failure. Gut Microbes 2021; 13:1-15. [PMID: 34006193 PMCID: PMC8143260 DOI: 10.1080/19490976.2021.1921925] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The gut microbiota in the hepatitis B virus related acute-on-chronic liver failure (HBV-ACLF) is poorly defined. We aim to uncover the characteristics of the gut microbiota in HBV-ACLF and in other HBV associated pathologies. We analyzed the gut microbiome in patients with HBV-ACLF or other HBV associated pathologies and healthy individuals by 16S rRNA sequencing and metagenomic sequencing of fecal samples. 212 patients with HBV-ACLF, 252 with chronic hepatitis B (CHB), 162 with HBV-associated cirrhosis (HBV-LC) and 877 healthy individuals were recruited for the study. CHB and HBV-LC patients are grouped as HBV-Other. We discovered striking differences in the microbiome diversity between the HBV-ACLF, HBV-Other and healthy groups using 16S rRNA sequencing. The ratio of cocci to bacilli was significantly elevated in the HBV-ACLF group compared with healthy group. Further analysis within the HBV-ACLF group identified 52 genera showing distinct richness within the group where Enterococcus was enriched in the progression group whilst Faecalibacterium was enriched in the regression group. Metagenomic sequencing validated these findings and further uncovered an enrichment of Lactobacillus casei paracasei in progression group, while Alistipes senegalensis, Faecalibacterium prausnitzii and Parabacteroides merdae dominated the regression group. Importantly, our analysis revealed that there was a rapid increase of Enterococcus faecium during the progression of HBV-ACLF. The gut microbiota displayed distinct composition at different phases of HBV-ACLF. High abundance of Enterococcus is associated with progression while that of Faecalibacterium is associated with regression of HBV-ACLF. Therefore, the microbiota features hold promising potential as prognostic markers for HBV-ACLF.
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Affiliation(s)
- Ke Wang
- Department of Infectious Diseases and Guangdong Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Zhao Zhang
- Research and Development Department, Guangdong Longsee Biomedical Corporation, Guangzhou, Guangdong, China
| | - Zhi-Shuo Mo
- Department of Infectious Diseases and Guangdong Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Xiao-Hua Yang
- Department of Infectious Diseases and Guangdong Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Bing-Liang Lin
- Department of Infectious Diseases and Guangdong Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Liang Peng
- Department of Infectious Diseases and Guangdong Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Yang Xu
- Research and Development Department, Guangdong Longsee Biomedical Corporation, Guangzhou, Guangdong, China
| | - Chun-Yan Lei
- Research and Development Department, Guangdong Longsee Biomedical Corporation, Guangzhou, Guangdong, China
| | - Xiao-Dong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ling Lu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Rui-Fu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China,Rui-Fu Yang State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tao Chen
- Research and Development Department, Guangdong Longsee Biomedical Corporation, Guangzhou, Guangdong, China,Tao Chen Research and Development Department, Guangdong Longsee Biomedical Corporation, Guangzhou, Guangdong, China
| | - Zhi-Liang Gao
- Department of Infectious Diseases and Guangdong Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China,CONTACT Zhi-Liang Gao Department of Infectious Diseases and Guangdong Key Laboratory of Liver Disease Research, Third Affiliated Hospital of Sun Yat-sen University, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
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102
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Arunasri K, Sai Prashanthi G, Tyagi M, Pappuru RR, Shivaji S. Intraocular Viral Communities Associated With Post-fever Retinitis. Front Med (Lausanne) 2021; 8:724195. [PMID: 34869420 PMCID: PMC8639604 DOI: 10.3389/fmed.2021.724195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/12/2021] [Accepted: 09/27/2021] [Indexed: 01/14/2023] Open
Abstract
The virome of ocular fluids is naive. The results of this study highlight the virome in the vitreous fluid of the eye of individuals without any ocular infection and compare it with the virome of the vitreous fluid of individuals with retinitis. A total of 1,016,037 viral reads were generated from 25 vitreous fluid samples comprising control and post-fever retinitis (PFR) samples. The top 10 viral families in the vitreous fluids comprised of Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae, Poxviridae, Iridoviridae, Podoviridae, Retroviridae, Baculoviridae, and Flaviviridae. Principal coordinate analysis and heat map analysis clearly discriminated the virome of the vitreous fluid of the controls from that of the PFR virome. The abundance of 10 viral genera increased significantly in the vitreous fluid virome of the post-fever retinitis group compared with the control group. Genus Lymphocryptovirus, comprising the human pathogen Epstein-Barr virus (EBV) that is also implicated in ocular infections was significantly abundant in eight out of the nine vitreous fluid viromes of post-fever retinitis group samples compared with the control viromes. Human viruses, such as Hepacivirus, Circovirus, and Kobuvirus, were also significantly increased in abundance in the vitreous fluid viromes of post-fever retinitis group samples compared with the control viromes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analysis and the network analysis depicted an increase in the immune response by the host in the post-fever retinitis group compared with the control group. All together, the results of the study indicate changes in the virome in the vitreous fluid of patients with the post-fever retinitis group compared to the control group.
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Affiliation(s)
- Kotakonda Arunasri
- Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, India
| | | | - Mudit Tyagi
- Smt. Kanuri Santhamma Center for Vitreo Retinal Diseases, L. V. Prasad Eye Institute, Hyderabad, India
| | - Rajeev R. Pappuru
- Smt. Kanuri Santhamma Center for Vitreo Retinal Diseases, L. V. Prasad Eye Institute, Hyderabad, India
| | - Sisinthy Shivaji
- Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, India
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103
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Wang H, Ren D, Li H, Wang S. Periprosthetic Joint Infection Caused by Mycoplasma hominis, Diagnosed Using Metagenomic Sequencing. Int J Gen Med 2021; 14:7003-7006. [PMID: 34707391 PMCID: PMC8544117 DOI: 10.2147/ijgm.s330924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/28/2021] [Indexed: 12/28/2022] Open
Abstract
To our knowledge, the periprosthetic joint infection (PJI) caused by Mycoplasma hominis is a rare postoperative complication after total knee arthroplasty (TKA). Just a few cases associated with Mycoplasma hominis infection after TKA were reported all over the world currently. In view of the difficulty involved in isolating this microorganism, Mycoplasma hominis infection may be under-recognized and should be considered in culture-negative cases where the microbial etiology is not easily identified. Metagenomic sequencing is a new tool to identify pathogens undetected by conventional methods. In this report, we present a case where metagenomic sequencing was used to identify Mycoplasma hominis as a novel PJI pathogen after TKA in our hospital.
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Affiliation(s)
- Haiying Wang
- Department of Orthopaedic Surgery, Baoding No.1 Central Hospital, Baoding, 071000, People's Republic of China
| | - Dongliang Ren
- Department of Orthopaedic Surgery, Baoding No.1 Central Hospital, Baoding, 071000, People's Republic of China
| | - Hui Li
- Department of Orthopaedic Surgery, Baoding No.1 Central Hospital, Baoding, 071000, People's Republic of China
| | - Shunyi Wang
- Department of Orthopaedic Surgery, Baoding No.1 Central Hospital, Baoding, 071000, People's Republic of China
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104
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Qin H, Peng J, Liu L, Wu J, Pan L, Huang X, Huang M, Qiu H, Du B. A Retrospective Paired Comparison Between Untargeted Next Generation Sequencing and Conventional Microbiology Tests With Wisely Chosen Metagenomic Sequencing Positive Criteria. Front Med (Lausanne) 2021; 8:686247. [PMID: 34692715 PMCID: PMC8526841 DOI: 10.3389/fmed.2021.686247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/25/2021] [Indexed: 11/29/2022] Open
Abstract
Objectives: To evaluate the performance of metagenomic next generation sequencing (mNGS) using adequate criteria for the detection of pathogens in lower respiratory tract (LRT) samples with a paired comparison to conventional microbiology tests (CMT). Methods: One hundred sixty-seven patients were reviewed from four different intensive care units (ICUs) in mainland China during 2018 with both mNGS and CMT results of LRT samples available. The reads per million ratio (RPMsample/RPMnon−template−control ratio) and standardized strictly mapped reads number (SDSMRN) were the two criteria chosen for identifying positive pathogens reported from mNGS. A McNemar test was used for a paired comparison analysis between mNGS and CMT. Results: One hundred forty-nine cases were counted into the final analysis. The RPMsample/RPMNTC ratio criterion performed better with a higher accuracy for bacteria, fungi, and virus than SDSMRN criterion [bacteria (RPMsample/RPMNTC ratio vs. SDSMRN), 65.1 vs. 55.7%; fungi, 75.8 vs. 71.1%; DNA virus, 86.3 vs. 74.5%; RNA virus, 90.9 vs. 81.8%]. The mNGS was also superior in bacteria detection only if an SDSMRN ≥3 was used as a positive criterion with a paired comparison to culture [SDSMRN positive, 92/149 (61.7%); culture positive, 54/149 (36.2%); p < 0.001]; however, it was outperformed with significantly more fungi and DNA virus identification when choosing both criteria for positive outliers [fungi (RPMsample/RPMNTC ratio vs. SDSMRN vs. culture), 23.5 vs. 29.5 vs. 8.7%, p < 0.001; DNA virus (RPMsample/RPMNTC ratio vs. SDSMRN vs. PCR), 14.1 vs. 20.8 vs. 11.8%, p < 0.05]. Conclusions: Metagenomic next generation sequencing may contribute to revealing the LRT infection etiology in hospitalized groups of potential fungal infections and in situations with less access to the multiplex PCR of LRT samples from the laboratory by choosing a wise criterion like the RPMsample/RPMNTC ratio.
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Affiliation(s)
- Hanyu Qin
- State Key Laboratory of Complex, Severe and Rare Disease, Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jinmin Peng
- State Key Laboratory of Complex, Severe and Rare Disease, Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ling Liu
- Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Jing Wu
- Department of Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingai Pan
- Department of Critical Care Medicine, Sichuan Provincial Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Sichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Xiaobo Huang
- Department of Critical Care Medicine, Sichuan Provincial Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Sichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Man Huang
- Department of Intensive Care Unit, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haibo Qiu
- Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Bin Du
- State Key Laboratory of Complex, Severe and Rare Disease, Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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105
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Qiu S, Zeng G, Li P, Li X, Liu H, Du X, Liu H, Zhang H, Xiang X, Wang H, Chen X, Yang G, Tian S, Wang L, Yang M, Yang C, Gao L, Hu S, Song H, Zhan Z. Pneumonia Patients Caused by Co-infection With SARS-CoV-2 and Human Adenovirus in China. Front Med (Lausanne) 2021; 8:735779. [PMID: 34650998 PMCID: PMC8505694 DOI: 10.3389/fmed.2021.735779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/03/2021] [Accepted: 08/30/2021] [Indexed: 01/08/2023] Open
Abstract
Objectives: To data, no patients with obvious epidemiological relationship co-infected with SARS-CoV-2 and other pathogens have been reported. Here, we investigated 10 patients caused by co-infection with SARS-CoV-2 and human adenovirus (HAdV), resulting in third-generation transmission. Materials and Methods: From Jan 15, 2020, we enrolled 10 patients with pneumonia in Hunan Province, China. Epidemiological, clinical, and laboratory investigation results from these patients were analyzed. An epidemiological investigation was performed to assess whether patient infections were linked using conventional methods and metagenomic sequencing. Results: The presence of co-infection with SARS-CoV-2 and HAdV was determined via RT-PCR and metagenomic sequencing. Phylogenetic analysis revealed that SARS-CoV-2 and HAdV genomes clustered together, with similar genetic relationships. The first patient likely became co-infected during meetings or travel in Wuhan. The patient transmitted the virus via dinners and meetings, which resulted in four second-generation cases. Then, a second-generation case transmitted the virus to her family members or relatives via presymptomatic transmission. Conclusions: This study described an example of co-infection with SARS-CoV-2 and HAdV in pneumonia patients, which caused third-generation cases and inter-regional transmission via meetings, household interactions, and dinner parties. We also observed the persistent and presymptomatic transmission of co-infection, which has the potential to make the continued control of the COVID-19 pandemic challenging. Continuous surveillance is needed to monitor the prevalence, infectivity, transmissibility, and pathogenicity of SARS-CoV-2 co-infection with other pathogens to evaluate its real risk.
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Affiliation(s)
- Shaofu Qiu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ge Zeng
- Hunan Provincial Center for Disease Control and Prevention, Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Changsha, China
| | - Peihan Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xiaohui Li
- Wangcheng Center for Disease Control and Prevention, Changsha, China
| | - Hongbo Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xinying Du
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbo Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Heng Zhang
- Changsha Center for Disease Control and Prevention, Changsha, China
| | - Xingyu Xiang
- Hunan Provincial Center for Disease Control and Prevention, Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Changsha, China
| | - Hui Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xiangbing Chen
- Wangcheng Center for Disease Control and Prevention, Changsha, China
| | - Guangyao Yang
- Wangcheng Center for Disease Control and Prevention, Changsha, China
| | - Sai Tian
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ligui Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Mingjuan Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chaojie Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Lidong Gao
- Hunan Provincial Center for Disease Control and Prevention, Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Changsha, China
| | - Shixiong Hu
- Hunan Provincial Center for Disease Control and Prevention, Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Changsha, China
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Zhifei Zhan
- Hunan Provincial Center for Disease Control and Prevention, Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Changsha, China
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106
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Song W, Sun LY, Zhu ZJ. Effects of Previous Kasai Surgery on Gut Microbiota and Bile Acid in Biliary Atresia With End-Stage Liver Disease. Front Med (Lausanne) 2021; 8:704328. [PMID: 34646837 PMCID: PMC8502819 DOI: 10.3389/fmed.2021.704328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/02/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022] Open
Abstract
Background and Aims: Biliary atresia (BA) is the most common cholestatic liver disease in neonates. Although the Kasai procedure can improve temporary biliary drainage in some cases, complications and liver fibrosis still develop. Liver transplantation is the ultimate treatment. The current study aimed to investigate the effect of previous Kasai surgery on gut microbiota and bile acid in BA with end-stage liver disease. Methods: Patients with BA with end-stage liver disease were divided into two groups according to whether they had previously undergone Kasai surgery (non-Kasai: n = 8, post-Kasai: n = 8). Metagenomic sequencing and ultraperformance liquid chromatography/tandem mass spectrometry were performed to identify the gut microbiota and bile acid. Results: Previous Kasai surgery had some effects on gut microbiota and bile acid in BA with end-stage liver disease. In the gut microbiome, the differential species were mainly distributed at the species level. Veillonella atypica had a significant increase in the non-Kasai group (P < 0.05). Bacteroides spp., Prevotella spp., Barnesiella spp., Parabacteroides spp., Heliobacterium spp., Erysipelatoclostridium spp. and Diaporthe spp. were increased in the post-Kasai group (P < 0.05). Concerning functional profiles, methionine biosynthesis was enriched in the non-Kasai group, while pyridoxal biosynthesis and riboflavin biosynthesis were enriched in the post-Kasai group (linear discriminant analysis > 2, P < 0.05). In stools, 17 bile acids were distinctly elevated in the post-Kasai group, such as cholic acid, chenodeoxycholic acid, β-muricholic acid and tauro α-muricholate (P < 0.05). Spearman correlation test showed that V. atypica had an enormously positive correlation with liver enzymes. Faecalibacterium prausnitzii and Escherichia coli were associated with derivatives of the alternative pathway of bile acid metabolism. Conclusion: Previous Kasai surgery can improve the gut microbiota and bile acid in patients with BA with end-stage liver disease. This improvement contributes to maintaining the intestinal barrier.
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Affiliation(s)
- Wei Song
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Li-Ying Sun
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China.,Department of Intensive Care Unit, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhi-Jun Zhu
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
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107
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Song W, Sun LY, Zhu ZJ, Wei L, Qu W, Zeng ZG, Liu Y, Zhang HM, Guo W. Association of Gut Microbiota and Metabolites With Disease Progression in Children With Biliary Atresia. Front Immunol 2021; 12:698900. [PMID: 34630385 PMCID: PMC8495239 DOI: 10.3389/fimmu.2021.698900] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 04/22/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
Background and Aims Biliary atresia is the most common cause of liver disease and liver transplantation in children. The accumulation of bile acids in hepatocytes and the stimulation of the intestinal microbiome can aggravate the disease progression. This study investigated changes in the composition of the gut microbiota and its metabolites in biliary atresia and the possible effects of these changes on disease progression. Methods Stool samples of biliary atresia at different disease stages and matched control individuals were collected (early stage: 16 patients, 16 controls; later stage: 16 patients, 10 controls). Metagenomic sequencing was performed to evaluate the gut microbiota structure. Untargeted metabolomics was performed to detect and analyze the metabolites and bile acid composition. Results A disturbed gut microbiota structure occurred in the early and later stages of biliary atresia. Klebsiella, Streptococcus, Veillonella, and Enterococcus have always been dominant. The abundance of V. atypica displayed significant changes between the early and later stages of biliary atresia. Combined with clinical indicators, Spearman’s analysis showed that Klebsiella and Veillonella atypica strongly correlated with liver enzymes. Enterococcus faecium had an enormously positive relationship with lithocholic acid derivatives. Metabolites involved in tryptophan metabolism were changed in the patients with biliary atresia, which had a significant association with stool V. atypica and blood total bilirubin (p < 0.05). Conclusions The liver damage of biliary atresia was directly or indirectly exacerbated by the interaction of enriched Klebsiella (K. pneumoniae), Veillonella (V. atypica), and Enterococcus (E. faecium) with dysmetabolism of tryptophan and bile acid.
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Affiliation(s)
- Wei Song
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Li-Ying Sun
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China.,Department of Intensive Care Unit, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhi-Jun Zhu
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Lin Wei
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Wei Qu
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Zhi-Gui Zeng
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Ying Liu
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Hai-Ming Zhang
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Wei Guo
- Hangkong Hospital, China Capital University, Beijing, China
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108
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Fida M, Wolf MJ, Hamdi A, Vijayvargiya P, Esquer Garrigos Z, Khalil S, Greenwood-Quaintance KE, Thoendel MJ, Patel R. Detection of Pathogenic Bacteria From Septic Patients Using 16S Ribosomal RNA Gene-Targeted Metagenomic Sequencing. Clin Infect Dis 2021; 73:1165-1172. [PMID: 33893492 PMCID: PMC8492209 DOI: 10.1093/cid/ciab349] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 12/04/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Conventional blood cultures were compared to plasma cell-free DNA-based 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR)/next-generation sequencing (NGS) for detection and identification of potential pathogens in patients with sepsis. METHODS Plasma was prospectively collected from 60 adult patients with sepsis presenting to the Mayo Clinic (Minnesota) Emergency Department from March through August 2019. Results of routine clinical blood cultures were compared to those of 16S rRNA gene NGS. RESULTS Nineteen (32%) subjects had positive blood cultures, of which 13 yielded gram-negative bacilli, 5 gram-positive cocci, and 1 both gram-negative bacilli and gram-positive cocci. 16S rRNA gene NGS findings were concordant in 11. For the remaining 8, 16S rRNA gene NGS results yielded discordant detections (n = 5) or were negative (n = 3). Interestingly, Clostridium species were additionally detected by 16S rRNA gene NGS in 3 of the 6 subjects with gastrointestinal sources of gram-negative bacteremia and none of the 3 subjects with urinary sources of gram-negative bacteremia. In the 41 remaining subjects, 16S rRNA gene NGS detected at least 1 potentially pathogenic organism in 17. In 15, the detected microorganism clinically correlated with the patient's syndrome. In 17 subjects with a clinically defined infectious syndrome, neither test was positive; in the remaining 7 subjects, a noninfectious cause of clinical presentation was identified. CONCLUSIONS 16S rRNA gene NGS may be useful for detecting bacteria in plasma of septic patients. In some cases of gram-negative sepsis, it may be possible to pinpoint a gastrointestinal or urinary source of sepsis based on the profile of bacteria detected in plasma.
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Affiliation(s)
- Madiha Fida
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J Wolf
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ahmed Hamdi
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Prakhar Vijayvargiya
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississipi, USA
| | - Zerelda Esquer Garrigos
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississipi, USA
| | - Sarwat Khalil
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Matthew J Thoendel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
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109
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Ho M, Moon D, Pires-Alves M, Thornton PD, McFarlin BL, Wilson BA. Recovery of microbial community profile information hidden in chimeric sequence reads. Comput Struct Biotechnol J 2021; 19:5126-5139. [PMID: 34589188 PMCID: PMC8453192 DOI: 10.1016/j.csbj.2021.08.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022] Open
Abstract
Sample-dependent inconsistencies in PCR-based and metagenomic sequencing analyses. Caveats associated with contig-based assembly programs for microbiome studies. More sample diversity/complexity yields more chimeric reads from PCR amplification. BlastBin includes consideration of chimeric reads for assigning and counting taxa. BlastBin enables recovery of information lost due to chimera formation. BlastBin 16S rRNA profiles more closely resemble metagenomic read-based profiles.
The next frontier in the field of microbiome studies is identification of all microbes present in the microbiome and accurate determination of their abundance such that microbiome profiles can serve as reliable assessments of health or disease status. PCR-based 16S rRNA gene sequencing and metagenome shotgun sequencing technologies are the prevailing approaches used in microbiome analyses. Each poses a number of technical challenges associated with PCR amplification, sample availability, and cost of processing and analysis. In general, results from these two approaches rarely agree completely with each other. Here, we compare these methods utilizing a set of vaginal swab and lavage specimens from a cohort of 42 pregnant women collected for a pilot study exploring the effect of the vaginal microbiome on preterm birth. We generated the microbial community profiles from the sequencing reads of the V3V4 and V4V5 regions of the 16S rRNA gene in the vaginal swab and lavage samples. For a subset of the vaginal samples from 12 subjects, we also performed metagenomic shotgun sequencing analysis and compared the results obtained from the PCR-based sequencing methods. Our findings suggest that sample composition and complexity, particularly at the species level, are major factors that must be considered when analyzing and interpreting microbiome data. Our approach to sequence analysis includes consideration of chimeric reads, by using our chimera-counting BlastBin program, and enables recovery of microbial content information generated during PCR-based sequencing methods, such that the microbial profiles more closely resemble those obtained from metagenomic read-based approaches.
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Affiliation(s)
- Mengfei Ho
- Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, United States
| | - Damee Moon
- Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, United States
| | - Melissa Pires-Alves
- Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, United States
| | - Patrick D Thornton
- Department of Human Development Nursing Science, College of Nursing, University of Illinois at Chicago, United States
| | - Barbara L McFarlin
- Department of Human Development Nursing Science, College of Nursing, University of Illinois at Chicago, United States
| | - Brenda A Wilson
- Department of Microbiology, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, United States
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Hu D, Yang J, Qi Y, Li B, Li K, Mok KM. Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment. Front Vet Sci 2021; 8:708512. [PMID: 34490397 PMCID: PMC8416479 DOI: 10.3389/fvets.2021.708512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/07/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022] Open
Abstract
Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to determine the corresponding changes of their functional attributes based on metagenomic sequencing. Results showed that in archaea, the methanogen of Euryarchaeota was the dominant phylum. Under this phylum, anthelmintic treatment increased the Methanobrevibacter genus and decreased the Methanocorpusculum genus and two other dominant archaea species, Methanocorpusculum labreanum and Methanocorpusculum bavaricum. In bacteria, Firmicutes and Bacteroidetes were the dominant phyla. Anthelmintic treatment increased the genera of Clostridium and Eubacterium and decreased those of Bacteroides and Prevotella and dominant bacteria species. These altered genera were associated with immunity and digestion. In eukaryota, anthelmintic treatment also changed the genera related to digestion and substantially decreased the relative abundances of identified species. In virus, anthelmintic treatment increased the genus of unclassified_d__Viruses and decreased those of unclassified_f__Siphoviridae and unclassified_f__Myoviridae. Most of the identified viral species were classified into phage, which were more sensitive to anthelmintic treatment than other viruses. Furthermore, anthelmintic treatment was found to increase the number of pathogens related to some clinical diseases in horses. The COG and KEGG function analysis showed that the intestinal microbiota of Przewalski's horse mainly participated in the carbohydrate and amino acid metabolism. The anthelmintic treatment did not change their overall function; however, it displaced the population of the functional microbes involved in each function or pathway. These results provide a complete view on the changes caused by anthelmintic treatment in the intestinal microbiota of the Przewalski's horses.
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Affiliation(s)
- Dini Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jianming Yang
- Xinjiang Research Centre for Breeding Przewalski's Horse, Urumqi, China
| | - Yingjie Qi
- Xinjiang Kalamaili Ungulate Nature Reserve Management Center, Changji, China
| | - Boling Li
- China National Environment Monitoring Centre, Beijing, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Kai Meng Mok
- Department of Civil and Environmental Engineering, University of Macau, Macao, China
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111
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Nelsen A, Lin CM, Hause BM. Porcine Parvovirus 2 Is Predominantly Associated With Macrophages in Porcine Respiratory Disease Complex. Front Vet Sci 2021; 8:726884. [PMID: 34485445 PMCID: PMC8414833 DOI: 10.3389/fvets.2021.726884] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 06/17/2021] [Accepted: 07/05/2021] [Indexed: 11/27/2022] Open
Abstract
Porcine respiratory disease complex (PRDC) is a significant source of morbidity and mortality, manifested by pneumonia of multiple etiologies, where a variety of pathogens and environment and management practices play a role in the disease. Porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus (IAV), and porcine circovirus 2 (PCV2) are well-established pathogens in PRDC. Porcine parvovirus 2 (PPV2) has been identified in both healthy and clinically diseased pigs at a high prevalence worldwide. Despite widespread circulation, the significance of PPV2 infection in PRDC and its association with other co-infections are unclear. Here, PPV2 was detected in the lung tissue in 39 of 100 (39%) PRDC-affected pigs by quantitative polymerase chain reaction (qPCR). Using in situ hybridization (ISH) in conjunction with tissue microarrays (TMA), PPV2 infection was localized in alveolar macrophages and other cells in the lungs with interstitial pneumonia in 28 of 99 (28.2%) samples. Viral load tended to correlate with the number of macrophages in the lungs. Assessment of the frequency, viral titers, and tissue distributions showed no association between infection of PPV2 and other major viral respiratory pathogens. In one-third of the PPV2-positive samples by qPCR, no other known viruses were identified by metagenomic sequencing. The genome sequences of PPV2 were 99.7% identical to the reference genomes. Although intensive intranuclear and intracytoplasmic signals of PPV2 were mainly detected in alveolar macrophages by ISH, no obvious virus replication was noted in in vitro cell culture. Together, these results suggest that PPV2 is associated, but may not be the sole causative agent, with PRDC, warranting the control and prevention of this underdiagnosed virus.
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Affiliation(s)
- April Nelsen
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States
| | - Chun-Ming Lin
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States.,Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD, United States
| | - Ben M Hause
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States.,Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD, United States
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Piantadosi A, Mukerji SS, Ye S, Leone MJ, Freimark LM, Park D, Adams G, Lemieux J, Kanjilal S, Solomon IH, Ahmed AA, Goldstein R, Ganesh V, Ostrem B, Cummins KC, Thon JM, Kinsella CM, Rosenberg E, Frosch MP, Goldberg MB, Cho TA, Sabeti P. Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis. mBio 2021; 12:e0114321. [PMID: 34465023 PMCID: PMC8406231 DOI: 10.1128/mbio.01143-21] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/02/2021] [Indexed: 01/21/2023] Open
Abstract
Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections.
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Affiliation(s)
- Anne Piantadosi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Shibani S. Mukerji
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Simon Ye
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard-MIT Program of Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - Michael J. Leone
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lisa M. Freimark
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daniel Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jacob Lemieux
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Sanjat Kanjilal
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Isaac H. Solomon
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Asim A. Ahmed
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Children’s Hospital, Boston, Massachusetts, USA
| | - Robert Goldstein
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Vijay Ganesh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Bridget Ostrem
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Kaelyn C. Cummins
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jesse M. Thon
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Cormac M. Kinsella
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Matthew P. Frosch
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marcia B. Goldberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Tracey A. Cho
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- University of Iowa, Department of Neurology, Iowa City, Iowa, USA
| | - Pardis Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Lu L, Ashworth J, Nguyen D, Li K, Smith DB, Woolhouse M. No Exchange of Picornaviruses in Vietnam between Humans and Animals in a High-Risk Cohort with Close Contact despite High Prevalence and Diversity. Viruses 2021; 13:v13091709. [PMID: 34578290 PMCID: PMC8473303 DOI: 10.3390/v13091709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 02/03/2023] Open
Abstract
Hospital-based and community-based 'high-risk cohort' studies investigating humans at risk of zoonotic infection due to occupational or residential exposure to animals were conducted in Vietnam, with diverse viruses identified from faecal samples collected from humans, domestic and wild animals. In this study, we focus on the positive-sense RNA virus family Picornaviridae, investigating the prevalence, diversity, and potential for cross-species transmission. Through metagenomic sequencing, we found picornavirus contigs in 23% of samples, belonging to 15 picornavirus genera. Prevalence was highest in bats (67%) while diversity was highest in rats (nine genera). In addition, 22% of the contigs were derived from novel viruses: Twelve phylogenetically distinct clusters were observed in rats of which seven belong to novel species or types in the genera Hunnivirus, Parechovirus, Cardiovirus, Mosavirus and Mupivirus; four distinct clusters were found in bats, belonging to one novel parechovirus species and one related to an unclassified picornavirus. There was no evidence for zoonotic transmission in our data. Our study provides an improved knowledge of the diversity and prevalence of picornaviruses, including a variety of novel picornaviruses in rats and bats. We highlight the importance of monitoring the human-animal interface for possible spill-over events.
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Affiliation(s)
- Lu Lu
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
- Correspondence:
| | - Jordan Ashworth
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
| | - Dung Nguyen
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (D.N.); (D.B.S.)
| | - Kejin Li
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (D.N.); (D.B.S.)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
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Hong J, Bo T, Xi L, Xu X, He N, Zhan Y, Li W, Liang P, Chen Y, Shi J, Li D, Yan F, Gu W, Wang W, Liu R, Wang J, Wang Z, Ning G. Reversal of Functional Brain Activity Related to Gut Microbiome and Hormones After VSG Surgery in Patients With Obesity. J Clin Endocrinol Metab 2021; 106:e3619-e3633. [PMID: 33950216 PMCID: PMC8372652 DOI: 10.1210/clinem/dgab297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Indexed: 12/19/2022]
Abstract
CONTEXT Vertical sleeve gastrectomy (VSG) is becoming a prioritized surgical intervention for obese individuals; however, the brain circuits that mediate its effective control of food intake and predict surgical outcome remain largely unclear. OBJECTIVE We investigated VSG-correlated alterations of the gut-brain axis. METHODS In this observational cohort study, 80 patients with obesity were screened. A total of 36 patients together with 26 normal-weight subjects were enrolled and evaluated using the 21-item Three-Factor Eating Questionnaire (TFEQ), MRI scanning, plasma intestinal hormone analysis, and fecal sample sequencing. Thirty-two patients underwent VSG treatment and 19 subjects completed an average of 4-month follow-up evaluation. Data-driven regional homogeneity (ReHo) coupled with seed-based connectivity analysis were used to quantify VSG-related brain activity. Longitudinal alterations of body weight, eating behavior, brain activity, gastrointestinal hormones, and gut microbiota were detected and subjected to repeated measures correlation analysis. RESULTS VSG induced significant functional changes in the right putamen (PUT.R) and left supplementary motor area, both of which correlated with weight loss and TFEQ scores. Moreover, postprandial levels of active glucagon-like peptide-1 (aGLP-1) and Ghrelin were associated with ReHo of PUT.R; meanwhile, relative abundance of Clostridia increased by VSG was associated with improvements in aGLP-1 secretion, PUT.R activity, and weight loss. Importantly, VSG normalized excessive functional connectivities with PUT.R, among which baseline connectivity between PUT.R and right orbitofrontal cortex was related to postoperative weight loss. CONCLUSION VSG causes correlated alterations of gut-brain axis, including Clostridia, postprandial aGLP-1, PUT.R activity, and eating habits. Preoperative connectivity of PUT.R may represent a potential predictive marker of surgical outcome in patients with obesity.
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Affiliation(s)
- Jie Hong
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | - Tingting Bo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liuqing Xi
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | | | - Naying He
- Department of Radiology, Ruijin Hospital, SJTUSM, Shanghai 200025, China
| | - Yafeng Zhan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanyu Li
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | - Peiwen Liang
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | - Yufei Chen
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | - Juan Shi
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | - Danjie Li
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | - Fuhua Yan
- Department of Radiology, Ruijin Hospital, SJTUSM, Shanghai 200025, China
| | - Weiqiong Gu
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | - Weiqing Wang
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | - Ruixin Liu
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | - Jiqiu Wang
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
| | - Zheng Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Guang Ning
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of Chinese Health Commission, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China
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115
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Bhatta TR, Chamings A, Alexandersen S. Exploring the Cause of Diarrhoea and Poor Growth in 8-11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing. Viruses 2021; 13:1608. [PMID: 34452472 DOI: 10.3390/v13081608] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/22/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022] Open
Abstract
Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.
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Teng Z, Shi Y, Peng Y, Zhang H, Luo X, Lun X, Xia L, You Y, Li Z, Zhang W, Zhang Y, Dong S, Guo W, Kan B, Pang B, Xu J, Qin A. Severe Case of Rickettsiosis Identified by Metagenomic Sequencing, China. Emerg Infect Dis 2021; 27:1530-1532. [PMID: 33900186 PMCID: PMC8084477 DOI: 10.3201/eid2705.203265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A case of Rickettsia sibirica subspecies sibirica BJ-90 infection in China was identified by metagenomic analysis of an eschar biopsy specimen and confirmed by nested PCR. Seroprevalence of spotted fever group Rickettsia was ≈17.4% among the local population. This report highlights the threat of rickettsioses to public health in the Qinghai–Tibet Plateau.
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117
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Guo L, Zhang D, Fu S, Zhang J, Zhang X, He J, Peng C, Zhang Y, Qiu Y, Ye C, Liu Y, Wu Z, Hu CAA. Metagenomic Sequencing Analysis of the Effects of Colistin Sulfate on the Pig Gut Microbiome. Front Vet Sci 2021; 8:663820. [PMID: 34277753 PMCID: PMC8282896 DOI: 10.3389/fvets.2021.663820] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 02/03/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
The gut microbiome plays important roles in maintaining host health, and inappropriate use of antibiotics can cause imbalance, which may contribute to serious disease. However, despite its promise, using metagenomic sequencing to explore the effects of colistin on gut microbiome composition in pig has not been reported. Herein, we evaluated the roles of colistin in gut microbiome modulation in pigs. Metagenomic analysis demonstrated that overall microbial diversity was higher in the colistin group compared with the control group. Antibiotic Resistance Genes Database analysis demonstrated that following colistin treatment, expression levels of tsnr, ant6ia, tetq, oleb, norm, ant3ia, and mexh were significantly upregulated, indicating that colistin may induce transformation of antibiotic resistance genes. Colistin also affected the microbiome distribution patterns at both genus and phylum levels. In addition, at the species level, colistin significantly reduced the abundance of Prevotella copri, Phascolarctobacterium succinatutens, and Prevotella stercorea and enhanced the abundance of Treponema succinifaciens and Acidaminococcus fermentans compared to the control group. Gene Ontology analysis demonstrated that following treatment with colistin, metabolic process, cellular process, and single-organism process were the dominant affected terms. Kyoto Encyclopedia of Genes and Genomes analysis showed that oxidative phosphorylation, protein processing in endoplasmic reticulum, various types of N-glycan biosynthesis, protein processing in endoplasmic reticulum, pathogenic Escherichia coli infection, and mitogen-activated protein kinase signaling pathway–yeast were the dominant signaling pathways in the colistin group. Overall, our results suggested that colistin affects microbial diversity and may modulate gut microbiome composition in pig, potentially providing novel strategy or antibiotic rationalization pertinent to human and animal health.
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Affiliation(s)
- Ling Guo
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Dan Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Shulin Fu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Jiacheng Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Xiaofang Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Jing He
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Chun Peng
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Yunfei Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Yinsheng Qiu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Chun Ye
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Yu Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Zhongyuan Wu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Chien-An Andy Hu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, United States
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Xie G, Zheng H, Qiu Z, Lin Z, Peng Q, Dula Bealu G, Elsheery NI, Lu Y, Shen C, Fu J, Yang H, Han J, Lu J, Liu G. Study on relationship between bacterial diversity and quality of Huangjiu (Chinese Rice Wine) fermentation. Food Sci Nutr 2021; 9:3885-3892. [PMID: 34262745 PMCID: PMC8269602 DOI: 10.1002/fsn3.2369] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 10/06/2020] [Revised: 04/27/2021] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
Huangjiu (Chinese rice wine) is brewed in an open environment, where bacteria play an important role during the fermentation process. In this study, bacterial community structure and composition changes in the fermented mash liquid of mechanized Huangjiu, well-fermented manual Huangjiu (wines of good qualities), and poorly fermented manual Huangjiu (wines of poor qualities: spoilage, high acidity, low alcohol content) in different fermentation stages from Guyuelongshan Shaoxing Huangjiu company were analyzed via metagenomic sequencing. And bacterial metabolic difference was analyzed via gene prediction of metabolic pathway enzymes. The results showed that the bacterial diversity degree was abundant, and the number of bacterial species in every sample was approximately 200-400. Lactic acid bacteria (LAB) dominated the bacterial community of Huangjiu fermentation, and lactobacillus was predominant species in well-fermented Huangjiu while Lactobacillus brevis had an absolute dominance in spoilage Huangjiu. Further, gene prediction revealed that transformation of malate to pyruvate and lactate anabolism was more active in mash liquid of well-fermented manual Huangjiu, while acetate accumulation was stronger in mash liquid of poorly fermented manual Huangjiu, which explained acidity excess reason in poorly fermented Huangjiu at gene level.
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Affiliation(s)
- Guangfa Xie
- College of Biology and Environmental EngineeringCollege of Shaoxing CRWZhejiang Shuren UniversityHangzhouChina
| | - Huajun Zheng
- School of Life ScienceNational Engineering Research Center for Chinese CRW (Branch Center)Shaoxing UniversityShaoxingChina
| | - Zheling Qiu
- Shaoxing Jianhu Brewing Co., LtdShaoxingChina
| | - Zichen Lin
- School of Life ScienceNational Engineering Research Center for Chinese CRW (Branch Center)Shaoxing UniversityShaoxingChina
| | - Qi Peng
- School of Life ScienceNational Engineering Research Center for Chinese CRW (Branch Center)Shaoxing UniversityShaoxingChina
- California Institute of Food and Agricultural ResearchUniversity of CaliforniaDavisCAUSA
| | - Girma Dula Bealu
- School of Life ScienceNational Engineering Research Center for Chinese CRW (Branch Center)Shaoxing UniversityShaoxingChina
| | | | - Yin Lu
- College of Biology and Environmental EngineeringCollege of Shaoxing CRWZhejiang Shuren UniversityHangzhouChina
| | - Chi Shen
- School of Life ScienceNational Engineering Research Center for Chinese CRW (Branch Center)Shaoxing UniversityShaoxingChina
| | - Jianwei Fu
- School of Life ScienceNational Engineering Research Center for Chinese CRW (Branch Center)Shaoxing UniversityShaoxingChina
| | - Huanyi Yang
- School of Life ScienceNational Engineering Research Center for Chinese CRW (Branch Center)Shaoxing UniversityShaoxingChina
| | | | - Jian Lu
- School of BiotechnologyNational Engineering Laboratory for Cereal Fermentation TechnologyJiangnan UniversityWuxiChina
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Song W, Sun LY, Zhu ZJ, Wei L, Qu W, Zeng ZG, Yang YS. Characteristics of Gut Microbiota in Children With Biliary Atresia After Liver Transplantation. Front Physiol 2021; 12:704313. [PMID: 34262484 PMCID: PMC8273867 DOI: 10.3389/fphys.2021.704313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/02/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
Background and Aims Biliary atresia (BA) is an idiopathic neonatal cholestasis and is the most common indication in pediatric liver transplantation (LT). Previous studies have suggested that the gut microbiota (GM) in BA is disordered. However, the effect of LT on gut dysbiosis in patients with BA has not yet been elucidated. Methods Patients with BA (n = 16) and healthy controls (n = 10) were recruited. In the early life of children with BA, Kasai surgery is a typical procedure for restoring bile flow. According to whether BA patients had previously undergone Kasai surgery, we divided the post-LT patients into the with-Kasai group (n = 8) and non-Kasai group (n = 8). Fecal samples were collected in both the BA and the control group; among BA patients, samples were obtained again 6 months after LT. A total of 40 fecal samples were collected, of which 16 were pre-LT, 14 were post-LT (8 were with-Kasai, 6 were non-Kasai), and 10 were from the control group. Metagenomic sequencing was performed to evaluate the GM. Results The Kruskal-Wallis test showed a statistically significant difference in the number of genes between the pre-LT and the control group, the pre-LT and the post-LT group (P < 0.05), but no statistical difference between the post-LT and the control group. Principal coordinate analysis also showed that the microbiome structure was similar between the post-LT and control group (P > 0.05). Analysis of the GM composition showed a significant decrease in Serratia, Enterobacter, Morganella, Skunalikevirus, and Phifllikevirus while short chain fatty acid (SCFA)-producing bacteria such as Roseburia, Blautia, Clostridium, Akkermansia, and Ruminococcus were increased after LT (linear discriminant analysis > 2, P < 0.05). However, they still did not reach the normal control level. Concerning functional profiles, lipopolysaccharide metabolism, multidrug resistance, polyamine biosynthesis, GABA biosynthesis, and EHEC/EPEC pathogenicity signature were more enriched in the post-LT group compared with the control group. Prior Kasai surgery had a specific influence on the postoperative GM. Conclusion LT partly improved the GM in patients with BA, which provided new insight into understanding the role of LT in BA.
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Affiliation(s)
- Wei Song
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Li-Ying Sun
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China.,Department of Intensive Care Unit, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhi-Jun Zhu
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Lin Wei
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Wei Qu
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Zhi-Gui Zeng
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing, China
| | - Yun-Sheng Yang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
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Young RB, Marcelino VR, Chonwerawong M, Gulliver EL, Forster SC. Key Technologies for Progressing Discovery of Microbiome-Based Medicines. Front Microbiol 2021; 12:685935. [PMID: 34239510 PMCID: PMC8258393 DOI: 10.3389/fmicb.2021.685935] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 03/26/2021] [Accepted: 05/25/2021] [Indexed: 12/22/2022] Open
Abstract
A growing number of experimental and computational approaches are illuminating the “microbial dark matter” and uncovering the integral role of commensal microbes in human health. Through this work, it is now clear that the human microbiome presents great potential as a therapeutic target for a plethora of diseases, including inflammatory bowel disease, diabetes and obesity. The development of more efficacious and targeted treatments relies on identification of causal links between the microbiome and disease; with future progress dependent on effective links between state-of-the-art sequencing approaches, computational analyses and experimental assays. We argue determining causation is essential, which can be attained by generating hypotheses using multi-omic functional analyses and validating these hypotheses in complex, biologically relevant experimental models. In this review we discuss existing analysis and validation methods, and propose best-practice approaches required to enable the next phase of microbiome research.
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Affiliation(s)
- Remy B Young
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Emily L Gulliver
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
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Ge M, Gan M, Yan K, Xiao F, Yang L, Wu B, Xiao M, Ba Y, Zhang R, Wang J, Cheng G, Wang L, Cao Y, Zhou W, Hu L. Combining Metagenomic Sequencing With Whole Exome Sequencing to Optimize Clinical Strategies in Neonates With a Suspected Central Nervous System Infection. Front Cell Infect Microbiol 2021; 11:671109. [PMID: 34222042 PMCID: PMC8253254 DOI: 10.3389/fcimb.2021.671109] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 02/23/2021] [Accepted: 05/27/2021] [Indexed: 12/02/2022] Open
Abstract
Objectives Central nervous system (CNS) infection has a high incidence and mortality in neonates, but conventional tests are time-consuming and have a low sensitivity. Some rare genetic diseases may have some similar clinical manifestations as CNS infection. Therefore, we aimed to evaluate the performance of metagenomic next-generation sequencing (mNGS) in diagnosing neonatal CNS infection and to explore the etiology of neonatal suspected CNS infection by combining mNGS with whole exome sequencing (WES). Methods We prospectively enrolled neonates with a suspected CNS infection who were admitted to the neonatal intensive care unit(NICU) from September 1, 2019, to May 31, 2020. Cerebrospinal fluid (CSF) samples collected from all patients were tested by using conventional methods and mNGS. For patients with a confirmed CNS infection and patients with an unclear clinical diagnosis, WES was performed on blood samples. Results Eighty-eight neonatal patients were enrolled, and 101 CSF samples were collected. Fourty-three blood samples were collected for WES. mNGS showed a sample diagnostic yield of 19.8% (20/101) compared to 4.95% (5/101) for the conventional methods. In the empirical treatment group, the detection rate of mNGS was significantly higher than that of conventional methods [27% vs. 6.3%, p=0.002]. Among the 88 patients, 15 patients were etiologically diagnosed by mNGS alone, five patients were etiologically identified by WES alone, and one patient was diagnosed by both mNGS and WES. Twelve of 13 diagnoses based solely on mNGS had a likely clinical effect. Six patients diagnosed by WES also experienced clinical effect. Conclusions For patients with a suspected CNS infections, mNGS combined with WES might significantly improve the diagnostic rate of the etiology and effectively guide clinical strategies.
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Affiliation(s)
- Mengmeng Ge
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Mingyu Gan
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Kai Yan
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Feifan Xiao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Lin Yang
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Shanghai, China
| | - Mili Xiao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Yin Ba
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Rong Zhang
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Jin Wang
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Guoqiang Cheng
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Laishuan Wang
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Yun Cao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Wenhao Zhou
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China.,Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
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Crawford E, Kamm J, Miller S, Li LM, Caldera S, Lyden A, Yokoe D, Nichols A, Tran NK, Barnard SE, Conner PM, Nambiar A, Zinter MS, Moayeri M, Serpa PH, Prince BC, Quan J, Sit R, Tan M, Phelps M, Derisi JL, Tato CM, Langelier C. Investigating Transfusion-related Sepsis Using Culture-Independent Metagenomic Sequencing. Clin Infect Dis 2021; 71:1179-1185. [PMID: 31563940 PMCID: PMC7442849 DOI: 10.1093/cid/ciz960] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 06/25/2019] [Accepted: 09/25/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Transfusion-related sepsis remains an important hospital infection control challenge. Investigation of septic transfusion events is often restricted by the limitations of bacterial culture in terms of time requirements and low yield in the setting of prior antibiotic administration. METHODS In 3 gram-negative septic transfusion cases, we performed metagenomic next-generation sequencing (mNGS) of direct clinical blood specimens in addition to standard culture-based approaches utilized for infection control investigations. Pathogen detection leveraged IDSeq, a new open-access microbial bioinformatics portal. Phylogenetic analysis was performed to assess microbial genetic relatedness and understand transmission events. RESULTS mNGS of direct clinical blood specimens afforded precision detection of pathogens responsible for each case of transfusion-related sepsis and enabled discovery of a novel Acinetobacter species in a platelet product that had become contaminated despite photochemical pathogen reduction. In each case, longitudinal assessment of pathogen burden elucidated the temporal sequence of events associated with each transfusion-transmitted infection. We found that informative data could be obtained from culture-independent mNGS of residual platelet products and leftover blood specimens that were either unsuitable or unavailable for culture or that failed to grow due to prior antibiotic administration. We additionally developed methods to enhance accuracy for detecting transfusion-associated pathogens that share taxonomic similarity to contaminants commonly found in mNGS library preparations. CONCLUSIONS Culture-independent mNGS of blood products afforded rapid and precise assessment of pathogen identity, abundance, and genetic relatedness. Together, these challenging cases demonstrated the potential for metagenomics to advance existing methods for investigating transfusion-transmitted infections.
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Affiliation(s)
- Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Microbiology and Immunology, University of California-San Francisco, San Francisco, California, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Lucy M Li
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Saharai Caldera
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Deborah Yokoe
- Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA.,Department of Hospital Epidemiology and Infection Prevention, University of California-San Francisco, San Francisco, California, USA
| | - Amy Nichols
- Department of Hospital Epidemiology and Infection Prevention, University of California-San Francisco, San Francisco, California, USA
| | - Nam K Tran
- Department of Pathology and Laboratory Medicine, University of California-Davis, Davis, California, USA
| | - Sarah E Barnard
- Department of Pathology and Laboratory Medicine, University of California-Davis, Davis, California, USA
| | - Peter M Conner
- Department of Pathology and Laboratory Medicine, University of California-Davis, Davis, California, USA
| | - Ashok Nambiar
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Matt S Zinter
- Division of Pulmonary and Critical Care Medicine, Department of Pediatrics, University of California-San Francisco, San Francisco, California, USA
| | - Morvarid Moayeri
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Paula Hayakawa Serpa
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Brian C Prince
- Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Jenai Quan
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rene Sit
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Michelle Tan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Joseph L Derisi
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California, USA
| | | | - Charles Langelier
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Division of Infectious Diseases, Department of Medicine, University of California-San Francisco, San Francisco, California, USA
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Zhang Y, Chen H, Wang J, Wang S, Wu J, Zhou Y, Wang X, Luo F, Tu X, Chen Q, Huang Y, Ju W, Peng X, Rao J, Wang L, Jiang N, Ai J, Zhang W. Emergence and Autochthonous Transmission of Dengue Virus Type I in a Low-Epidemic Region in Southeast China. Front Cell Infect Microbiol 2021; 11:638785. [PMID: 33842388 PMCID: PMC8024628 DOI: 10.3389/fcimb.2021.638785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
Background Dengue fever is a mosquito-borne febrile illness. Southeast Asia experienced severe dengue outbreaks in 2019, and over 1000 cases had been reported in Jiangxi, a previously known low-epidemic region in China. However, the emergence of a dengue virus epidemic in a non-epidemic region remains unclear. Methods We enrolled 154 dengue fever patients from four hospitals in Jiangxi, from April 2019 to September 2019. Real-time PCR, NS1 antigen rapid test, and IgM, IgG tests were performed, and 14 samples were outsourced to be sequenced metagenomically. Results Among the 154 cases, 42 were identified as imported and most of them returned from Cambodia. A total of 113 blood samples were obtained and 106 were identified as DENV-1, two as DENV-2, and five were negative through RT-PCR. All DENV-1 strains sequenced in this study were all classified to one cluster and owned a high similarity with a Cambodia strain isolated in 2019. The evolutionary relationships of amino acid were consistent with that of nucleotide genome result. The sequence-based findings of Jiangxi strains were consistent with epidemiological investigation. Conclusion Epidemiological analysis demonstrated that the emergence of dengue cases led to autochthonous transmission in several cities in Jiangxi, a low-epidemic region before. This study emphasized future prevention and control of dengue fever in both epidemic and non-epidemic regions.
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Affiliation(s)
- Yi Zhang
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Hongyi Chen
- Department of Infectious Disease, Nanchang Ninth Hospital, Nanchang, China
| | - Jingen Wang
- Department of Infectious Disease, Zhangshu People's Hospital, Yichun, China
| | - Shumei Wang
- Department of Infectious Disease, Nanchang Ninth Hospital, Nanchang, China
| | - Jing Wu
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yang Zhou
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinyu Wang
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Feibing Luo
- Department of Infectious Disease, Fengcheng People's Hospital, Yichun, China
| | - Xianglin Tu
- Department of Infectious Disease, Nanchang Ninth Hospital, Nanchang, China
| | - Qiubo Chen
- Department of Infectious Disease, Zhangshu People's Hospital, Yichun, China
| | - Yanxia Huang
- Department of Infectious Disease, Nanchang Ninth Hospital, Nanchang, China
| | - Weihua Ju
- Department of Infectious Disease, Nanchang Ninth Hospital, Nanchang, China
| | - Xuping Peng
- Department of Infectious Disease, Nanchang Ninth Hospital, Nanchang, China
| | - Jianfeng Rao
- Department of Infectious Disease, Nanchang Ninth Hospital, Nanchang, China
| | - Li Wang
- Department of Infectious Disease, Nanchang Ninth Hospital, Nanchang, China
| | - Ning Jiang
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Jingwen Ai
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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Li B, Chen Z, Zhang F, Liu Y, Yan T. Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics. FEMS Microbiol Ecol 2021; 96:5894923. [PMID: 32816017 DOI: 10.1093/femsec/fiaa172] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 05/08/2019] [Accepted: 08/18/2020] [Indexed: 11/14/2022] Open
Abstract
Widespread occurrence of antibiotic resistance genes (ARGs) has become an important clinical issue. Studying ARGs in pristine soil environments can help to better understand the intrinsic soil resistome. In this study, 10 soil samples were collected from a high elevation and relatively pristine Tibetan area, and metagenomic sequencing and bioinformatic analyses were conducted to investigate the microbial diversity, the abundance and diversity of ARGs and the mobility potential of ARGs as indicated by different mobile genetic elements (MGEs). A total of 48 ARG types with a relative abundance of 0.05-0.28 copies of ARG/copy of 16S rRNA genes were detected in Tibetan soil samples. The observed ARGs were mainly associated with antibiotics that included glycopeptide and rifamycin; the most abundant ARGs were vanRO and vanSO. Low abundance of MGEs and potentially plasmid-related ARGs indicated a low horizontal gene transfer risk of ARGs in the pristine soil. Pearson correlation and redundancy analyses showed that temperature and total organic carbon were the major environmental factors controlling both microbial diversity and ARG abundance and diversity.
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Affiliation(s)
- Bo Li
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Zeng Chen
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fan Zhang
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tao Yan
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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125
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Jiang H, Fang S, Yang H, Chen C. Identification of the relationship between the gut microbiome and feed efficiency in a commercial pig cohort. J Anim Sci 2021; 99:6133345. [PMID: 33570553 DOI: 10.1093/jas/skab045] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/05/2021] [Indexed: 12/11/2022] Open
Abstract
Feed efficiency (FE) is an economically important trait in pig production. Gut microbiota plays an important role in energy harvest, nutrient metabolism, and fermentation of dietary indigestible components. Whether and which gut microbes affect FE in pigs are largely unknown. Here, a total of 208 healthy Duroc pigs were used as experimental materials. Feces and serum samples were collected at the age of 140 d. We first performed 16S rRNA gene and metagenomic sequencing analysis to investigate the relationship between the gut microbiome and porcine residual feed intake (RFI). 16S rRNA gene sequencing analysis detected 21 operational taxonomic units showing the tendency to correlation with the RFI (P < 0.01). Metagenomic sequencing further identified that the members of Clostridiales, e.g., Ruminococcus flavefaoiens, Lachnospiraceae bacterium 28-4, and Lachnospiraceae phytofermentans, were enriched in pigs with low RFI (high-FE), while 11 bacterial species including 5 Prevotella spp., especially, the Prevotella copri, had higher abundance in pigs with high RFI. Functional capacity analysis suggested that the gut microbiome of low RFI pigs had a high abundance of the pathways related to amino acid metabolism and biosynthesis, but a low abundance of the pathways associated with monosaccharide metabolism and lipopolysaccharide biosynthesis. Serum metabolome and fecal short-chain fatty acids were determined by UPLC-QTOF/MS and gas chromatography, respectively. Propionic acid in feces and the serum metabolites related to amino acid metabolism were negatively correlated with the RFI. The results from this study may provide potential gut microbial biomarkers that could be used for improving FE in pig production industry.
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Affiliation(s)
- Hui Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, PR China
| | - Shaoming Fang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, PR China
| | - Hui Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, PR China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, PR China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, PR China
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126
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Chu W, Han Q, Xu J, Wang J, Sun Y, Li W, Chen ZJ, Du Y. Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome. Fertil Steril 2021; 113:1286-1298.e4. [PMID: 32482258 DOI: 10.1016/j.fertnstert.2020.01.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [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: 09/27/2019] [Revised: 12/25/2019] [Accepted: 01/21/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To identify different microbial species in women with polycystic ovary syndrome (PCOS) and reveal a possible relationship between gut dysbiosis and pathological changes. DESIGN Cross-sectional study. SETTING Academic institution. PATIENT(S) Reproductive-aged women with PCOS (n = 14) and controls (n = 14) from the Centre for Reproductive Medicine. INTERVENTION(S) Shotgun metagenomic sequencing on fecal samples from patients, and clinical parameters (including body mass index, endocrine hormone levels, and glycemia level) gathered for correlation analysis. MAIN OUTCOME MEASURE(S) Identification of different gut microbial strains and relativity between microbiota and clinical parameters. RESULT(S) We found several microbial strains were statistically significantly more abundant in the PCOS group, including Parabacteroides merdae, Bacteroides fragilis, and strains of Escherichia and Shigella, whereas Faecalibacterium prausnitzii was enriched in the control group. Metagenomic species (MGS) analysis revealed that the microbes of the PCOS group were negatively correlated with those of the control group. Of note, we observed a positive correlation between MGS relevant to PCOS and endocrine disorders, including body mass index and elevated levels of serum testosterone, luteinizing hormone, and antimüllerian hormone. Functional alterations, reflected by Kyoto Encyclopedia of Genes and Genomes orthologues, could imply potential mechanisms of microbial involvement in the developmental progress of PCOS. CONCLUSION(S) Our findings suggest an intimate association and potential mechanisms linking microbial dysbiosis and the pathophysiologic changes of PCOS. We address the importance of monitoring and modulating microbial composition and functional shifts in future clinical practice.
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Affiliation(s)
- Weiwei Chu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Qixin Han
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Jieying Xu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Juan Wang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Yun Sun
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Weiping Li
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory for Reproductive Endocrinology of Ministry of Education, Center for Reproductive Medicine, Shandong University, Jinan, People's Republic of China
| | - Yanzhi Du
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China.
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127
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Liu F, Kou D, Chen Y, Xue K, Ernakovich JG, Chen L, Yang G, Yang Y. Altered microbial structure and function after thermokarst formation. Glob Chang Biol 2021; 27:823-835. [PMID: 33155741 DOI: 10.1111/gcb.15438] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/05/2020] [Indexed: 05/27/2023]
Abstract
Permafrost thaw could induce substantial carbon (C) emissions to the atmosphere, and thus trigger a positive feedback to climate warming. As the engine of biogeochemical cycling, soil microorganisms exert a critical role in mediating the direction and strength of permafrost C-climate feedback. However, our understanding about the impacts of thermokarst (abrupt permafrost thaw) on microbial structure and function remains limited. Here we employed metagenomic sequencing to analyze changes in topsoil (0-15 cm) microbial communities and functional genes along a permafrost thaw sequence (1, 10, and 16 years since permafrost collapse) on the Tibetan Plateau. By combining laboratory incubation and a two-pool model, we then explored changes in soil labile and stable C decomposition along the thaw sequence. Our results showed that topsoil microbial α-diversity decreased, while the community structure and functional gene abundance did not exhibit any significant change at the early stage of collapse (1 year since collapse) relative to non-collapsed control. However, as the time since the collapse increased, both the topsoil microbial community structure and functional genes differed from the control. Abundances of functional genes involved in labile C degradation decreased while those for stable C degradation increased at the late stage of collapse (16 years since collapse), largely driven by changes in substrate properties along the thaw sequence. Accordingly, faster stable C decomposition occurred at the late stage of collapse compared to the control, which was associated with the increase in relative abundance of functional genes for stable C degradation. These results suggest that upland thermokarst alters microbial structure and function, particularly enhances soil stable C decomposition by modulating microbial functional genes, which could reinforce a warmer climate over the decadal timescale.
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Affiliation(s)
- Futing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Dan Kou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yongliang Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jessica G Ernakovich
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Leiyi Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Guibiao Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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128
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Zhang HN, Cui N, Shen HM. [Metagenomic Analysis Provides Insights into Bacterial Communities, Antibiotic Resistomes, and Public Health Risks in the Dongping Lake Reservoir]. Huan Jing Ke Xue 2021; 42:211-220. [PMID: 33372473 DOI: 10.13227/j.hjkx.202005305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Owing to the long residence times of water, water reservoirs readily contribute to the accumulation of antibiotic resistant gene (ARG). It is of great public health significance to explore bacterial communities, antibiotic resistomes, and the potential public health risks of water reservoirs. In this study, metagenomic sequencing was used to analyze and compare the bacterial communities, ARG profiles, ARG-horizontal transfer, and ARG-carrying pathogens in the water and sediments of the Dongping Lake Reservoir in the dry and the wet seasons. Compared with that of the sediments, the results showed that both the bacterial communities and ARG profiles in the water were significantly influenced by the seasons, and the total ARG abundance in the dry season was significantly higher than that in the wet season. The total ARG abundance in the sediments was higher than that in water, but the horizontal transfer potential of ARG in the water was higher than that in the sediment. A total of 377 ARG subtypes belonging to 20 ARG types were found in this study. Bacitracin and vancomycin resistance genes were the main ARG types in the water and sediments, respectively, and Proteobacteria and Actinobacteria were the major ARG-carrying bacteria in the water and sediments, respectively. In addition, 30 clinical pathogens carrying ARGs were identified, including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella enterica, and Acinetobacter bohemicus. More importantly, two Escherichia coli concurrently carried virulence factor and ARG. In summary, this study revealed that a variety of ARG types existed in the Dongping Lake Reservoir, which has posed potential public health risks by contributing to the horizontal transfer of ARG and the accumulation of clinical pathogens. Therefore, it is necessary to regularly monitor the bacterial community and ARG profile in various water bodies.
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Affiliation(s)
- Hong-Na Zhang
- College of Biological Science and Engineering, Hebei University of Economics and Business, Shijiazhuang 050061, China
| | - Na Cui
- College of Biological Science and Engineering, Hebei University of Economics and Business, Shijiazhuang 050061, China
| | - Hong-Miao Shen
- College of Biological Science and Engineering, Hebei University of Economics and Business, Shijiazhuang 050061, China
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129
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Yan Q, Wang Y, Chen X, Jin H, Wang G, Guan K, Zhang Y, Zhang P, Ayaz T, Liang Y, Wang J, Cui G, Sun Y, Xiao M, Kang J, Zhang W, Zhang A, Li P, Liu X, Ulllah H, Ma Y, Li S, Ma T. Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis. Virus Evol 2021; 7:veab022. [PMID: 33959381 PMCID: PMC8087960 DOI: 10.1093/ve/veab022] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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] [Indexed: 12/15/2022] Open
Abstract
Trillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remains unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, for example ethnic origin, on the gut virome is rarely investigated. Here, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing twenty-four healthy adults and six children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals' gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were not only inherited from that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between viruses and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (P < 0.001), and they both correlated the holistic bacterial composition and vice versa. This study provides an overview of the gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.
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Affiliation(s)
- Qiulong Yan
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yu Wang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- Institute of Translational Medicine, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing 210029, China
| | - Xiuli Chen
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Hao Jin
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Saihan District, Hohhot 010018, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Kuiqing Guan
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Yue Zhang
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Pan Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200032, China
| | - Taj Ayaz
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yanshan Liang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Junyi Wang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Guangyi Cui
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Yuanyuan Sun
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Manchun Xiao
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Jian Kang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Wei Zhang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Aiqin Zhang
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Peng Li
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Xueyang Liu
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Hayan Ulllah
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yufang Ma
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Shenghui Li
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Tonghui Ma
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
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130
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Kubacki J, Fraefel C, Bachofen C. Implementation of next-generation sequencing for virus identification in veterinary diagnostic laboratories. J Vet Diagn Invest 2020; 33:235-247. [PMID: 33357110 DOI: 10.1177/1040638720982630] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The value of next-generation sequencing (NGS)-based applications for testing purposes in human medicine is widely recognized. Although NGS-based metagenomic screening may be of interest in veterinary medicine, in particular for intensively farmed livestock species such as pigs, there is a lack of protocols tailored to veterinary requirements, likely because of the high diversity of species and samples. Therefore, we developed an NGS-based protocol for use in veterinary virology and present here different applications in porcine medicine. To develop the protocol, each step of sample preparation was optimized using porcine samples spiked with various RNA and DNA viruses. The resulting protocol was tested with clinical samples previously confirmed to be positive for specific viruses by a diagnostic laboratory. Additionally, we validated the protocol in an NGS viral metagenomics ring trial and tested the protocol on viral multiplex reference material (NIBSC, U.K.). We applied our ViroScreen protocol successfully for 1) virus identification, 2) virus characterization, and 3) herd screening. We identified torque teno sus virus and atypical porcine pestivirus in a neurologic case, determined the full-length genome sequence of swine influenza A virus in field samples, and screened pigs using pen floor fecal samples and chewing rope liquid.
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Affiliation(s)
- Jakub Kubacki
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Claudia Bachofen
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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131
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Takizawa S, Asano R, Fukuda Y, Feng M, Baba Y, Abe K, Tada C, Nakai Y. Change of Endoglucanase Activity and Rumen Microbial Community During Biodegradation of Cellulose Using Rumen Microbiota. Front Microbiol 2020; 11:603818. [PMID: 33391225 PMCID: PMC7775302 DOI: 10.3389/fmicb.2020.603818] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/26/2020] [Indexed: 12/20/2022] Open
Abstract
Treatment with rumen microorganisms improves the methane fermentation of undegradable lignocellulosic biomass; however, the role of endoglucanase in lignocellulose digestion remains unclear. This study was conducted to investigate endoglucanases contributing to cellulose degradation during treatment with rumen microorganisms, using carboxymethyl cellulose (CMC) as a substrate. The rate of CMC degradation increased for the first 24 h of treatment. Zymogram analysis revealed that endoglucanases of 52 and 53 kDa exhibited high enzyme activity for the first 12 h, whereas endoglucanases of 42, 50, and 101 kDa exhibited high enzyme activities from 12 to 24 h. This indicates that the activities of these five endoglucanases shifted and contributed to efficient CMC degradation. Metagenomic analysis revealed that the relative abundances of Selenomonas, Eudiplodinium, and Metadinium decreased after 12 h, which was positively correlated with the 52- and 53-kDa endoglucanases. Additionally, the relative abundances of Porphyromonas, Didinium, unclassified Bacteroidetes, Clostridiales family XI, Lachnospiraceae and Sphingobacteriaceae increased for the first 24 h, which was positively correlated with endoglucanases of 42, 50, and 101 kDa. This study suggests that uncharacterized and non-dominant microorganisms produce and/or contribute to activity of 40, 50, 52, 53, and 101 kDa endoglucanases, enhancing CMC degradation during treatment with rumen microorganisms.
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Affiliation(s)
- Shuhei Takizawa
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan.,Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Ryoki Asano
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Tainai, Japan
| | - Yasuhiro Fukuda
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Mengjia Feng
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Yasunori Baba
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Kenichi Abe
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Tainai, Japan
| | - Chika Tada
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Yutaka Nakai
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Tainai, Japan
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132
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Babiker A, Bradley HL, Stittleburg VD, Ingersoll JM, Key A, Kraft CS, Waggoner JJ, Piantadosi A. Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19. J Clin Microbiol 2020; 59:e02142-20. [PMID: 33067271 DOI: 10.1128/JCM.02142-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 10/13/2020] [Indexed: 12/31/2022] Open
Abstract
Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A [n = 3], human metapneumovirus [n = 2], and human coronavirus OC43 [n = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold (CT ) values correlated with greater SARS-CoV-2 read recovery by mNGS (R 2, 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.
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133
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Damhorst GL, Adelman MW, Woodworth MH, Kraft CS. Current Capabilities of Gut Microbiome-Based Diagnostics and the Promise of Clinical Application. J Infect Dis 2020; 223:S270-S275. [PMID: 33330938 DOI: 10.1093/infdis/jiaa689] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There is increasing evidence for the importance of the gut microbiome in human health and disease. Traditional and modern technologies - from cell culture to next generation sequencing - have facilitated these advances in knowledge. Each of the tools employed in measuring the microbiome exhibits unique capabilities that may be leveraged for clinical diagnostics. However, much still needs to be done to standardize the language and metrics by which a microbiome is characterized. Here we review the capabilities of gut microbiome-based diagnostics, review selected examples, and discuss the outlook towards clinical application.
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Affiliation(s)
- Gregory L Damhorst
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA
| | - Max W Adelman
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA
| | - Michael H Woodworth
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA.,Department of Pathology and Laboratory Medicine; Department of Medicine; Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
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134
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Hazan S, Spradling-Reeves KD, Papoutsis A, Walker SJ. Shotgun Metagenomic Sequencing Identifies Dysbiosis in Triplet Sibling with Gastrointestinal Symptoms and ASD. Children (Basel) 2020; 7:children7120255. [PMID: 33255785 PMCID: PMC7759978 DOI: 10.3390/children7120255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 12/23/2022]
Abstract
The gut microbiome profile of a child with autism spectrum disorder (ASD) and co-occurring gastrointestinal (GI) symptoms was compared to that of her healthy triplet siblings to determine if she exhibited intestinal dysbiosis. Shotgun metagenomic sequencing was performed in individual fecal samples, and relative microbial abundance and diversity was determined. Microbial diversity was lower in sibling #3, coupled with a higher Bacteroidetes/Firmicutes ratio, a lower relative abundance of Actinobacteria, and an increased relative abundance of Proteobacteria. Our findings are suggestive of gut dysbiosis in a child with ASD and co-occurring GI symptoms, compared to her two healthy triplet siblings.
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Affiliation(s)
- Sabine Hazan
- Progenabiome™ Ventura Clinical Trials, 1835 Knoll Dr, Ventura, CA 93003, USA; (S.H.); (A.P.)
| | - Kimberly D. Spradling-Reeves
- Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Blvd, Winston Salem, NC 27157, USA;
| | - Andreas Papoutsis
- Progenabiome™ Ventura Clinical Trials, 1835 Knoll Dr, Ventura, CA 93003, USA; (S.H.); (A.P.)
| | - Stephen J. Walker
- Wake Forest Institute for Regenerative Medicine, 391 Technology Way, Winston Salem, NC 27101, USA
- Correspondence:
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135
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Zhang L, Li C, Zhai Y, Feng L, Bai K, Zhang Z, Huang Y, Li T, Li D, Li H, Cui P, Chen D, Wang H, Yang X. Analysis of the vaginal microbiome of giant pandas using metagenomics sequencing. Microbiologyopen 2020; 9:e1131. [PMID: 33205903 PMCID: PMC7755806 DOI: 10.1002/mbo3.1131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/16/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/30/2022] Open
Abstract
In this study, a total of 14 vaginal samples (GPV1‐14) from giant pandas were analyzed. These vaginal samples were divided into two groups as per the region and age of giant pandas. All the vaginal samples were analyzed using metagenomic sequencing. As per the outcomes of metagenomic analysis, Proteobacteria (39.04%), Firmicutes (5.27%), Actinobacteria (2.94%), and Basidiomycota (2.77%) were found to be the dominant phyla in the microbiome of the vaginal samples. At the genus level, Pseudomonas (21.90%) was found to be the most dominant genus, followed by Streptococcus (3.47%), Psychrobacter (1.89%), and Proteus (1.38%). Metastats analysis of the microbial species in the vaginal samples of giant pandas from Wolong Nature Reserve, Dujiangyan and Ningbo Youngor Zoo, and Ya'an Bifengxia Nature Reserve was found to be significantly different (p < 0.05). Age groups, that is, AGE1 (5‐10 years old) and AGE2 (11‐16 years old), also demonstrated significantly different inter‐group microbial species (p < 0.05). For the first time, Chlamydia and Neisseria gonorrhoeae were detected in giant pandas’ reproductive tract. GPV3 vaginal sample (2.63%) showed highest Chlamydia content followed by GPV14 (0.91%), and GPV7 (0.62%). GPV5 vaginal sample (7.17%) showed the highest Neisseria gonorrhoeae content, followed by GPV14 (7.02%), and GPV8 (6.50%). Furthermore, we employed eggNOG, CAZy, KEGG, and NCBI databases to investigate the functional significance of giant panda's vaginal microbial community. The outcomes indicated that giant panda's vaginal microbes were involved in biological processes. The data from this study will help in improving the reproductive health of giant pandas.
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Affiliation(s)
- Lan Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Caiwu Li
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, PR China
| | - Yaru Zhai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Lan Feng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Keke Bai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Zhizhong Zhang
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, PR China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, PR China
| | - Ti Li
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, PR China
| | - Desheng Li
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, PR China
| | - Hao Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Pengfei Cui
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Danyu Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Xin Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, PR China
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136
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Baldan R, Sendi P. Precision Medicine in the Diagnosis and Management of Orthopedic Biofilm Infections. Front Med (Lausanne) 2020; 7:580671. [PMID: 33240905 PMCID: PMC7683765 DOI: 10.3389/fmed.2020.580671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/22/2020] [Indexed: 01/02/2023] Open
Abstract
Orthopedic biofilm infections are difficult to treat and require a multidisciplinary approach to diagnostics and management. Recent advances in the field include methods to disrupt biofilm, sequencing tools, and antibiotic susceptibility tests for bacteria residing in biofilm. The observation of interclonal differences in biofilm properties of the causative microorganisms, together with considerations of comorbidities and polypharmacy in a growing aging population, calls for a personalized approach to treat these infections. In this article, we highlight aspects of precision medicine that may open new perspectives in the diagnosis and management of orthopedic biofilm infections.
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Affiliation(s)
- Rossella Baldan
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Centre for Musculoskeletal Infections, University Hospital Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, Departments of Medicine and Clinical Research, University Hospital Basel, Basel, Switzerland.,Department of Orthopaedic and Trauma Surgery, University Hospital Basel, Basel, Switzerland
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137
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Goll R, Johnsen PH, Hjerde E, Diab J, Valle PC, Hilpusch F, Cavanagh JP. Effects of fecal microbiota transplantation in subjects with irritable bowel syndrome are mirrored by changes in gut microbiome. Gut Microbes 2020; 12:1794263. [PMID: 32991818 PMCID: PMC7583512 DOI: 10.1080/19490976.2020.1794263] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a common disorder of the lower gastrointestinal tract. The pathophysiology is far from settled, but a gut microbial dysbiosis is hypothesized to be a contributing factor. We earlier published a randomized double-blind placebo-controlled clinical trial on fecal microbiota transplantation (FMT) for IBS - the REFIT trial. The present data set describes the engraftment and includes participants from the study who received active FMT; 14 participants with effect of FMT (Effect) and 8 without (No effect). Samples were collected at baseline, after 6 and 12 months. Samples from the transplants (Donor) served as a comparator. In total 66 recipient samples and 17 donor samples were subjected to deep metagenomic sequencing, and taxonomic and functional analyses were performed. Alpha diversity measures showed a significantly increased diversity and evenness in the IBS groups compared to the donors. Taxonomic profiles showed higher relative abundance of phylum Firmicutes, and lower relative abundance of phylum Bacteroidetes, compared to donors at baseline. This profile was shifted toward the donor profile following FMT. Imputed growth rates showed that the resulting growth pattern was a conglomerate of donor and recipient activity. Thirty-four functional subclasses showed distinct differences between baseline samples and donors, most of which were shifted toward a donor-like profile after FMT. All of these changes were less pronounced in the No effect group. We conclude that FMT induces long-term changes in gut microbiota, and these changes mirror the clinical effect of the treatment. The study was registered in ClinicalTrials.gov (NCT02154867).
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Affiliation(s)
- Rasmus Goll
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, UiT the Arctic University of Norway, Tromsø, Norway,Department of Gastroenterology, Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway,CONTACT Rasmus Goll Department of Gastroenterology, Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Peter Holger Johnsen
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, UiT the Arctic University of Norway, Tromsø, Norway,Department of Internal Medicine, University Hospital of North Norway, Harstad, Norway
| | - Erik Hjerde
- Institute of Chemistry, UiT the Arctic University of Norway, Tromsø, Norway
| | - Joseph Diab
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, UiT the Arctic University of Norway, Tromsø, Norway
| | - Per Christian Valle
- Department of Internal Medicine, University Hospital of North Norway, Harstad, Norway
| | | | - Jorunn Pauline Cavanagh
- Pediatric Infections Group. Department of Pediatrics, University Hospital of North Norway, Tromsø, Norway,Pediatric Infections Group. Department of Clinical Medicine, UiT the Arctic University of Norway, Tromsø, Norway
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138
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Doster E, Thomas KM, Weinroth MD, Parker JK, Crone KK, Arthur TM, Schmidt JW, Wheeler TL, Belk KE, Morley PS. Metagenomic Characterization of the Microbiome and Resistome of Retail Ground Beef Products. Front Microbiol 2020; 11:541972. [PMID: 33240224 PMCID: PMC7677504 DOI: 10.3389/fmicb.2020.541972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 03/11/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Ground beef can be a reservoir for a variety of bacteria, including spoilage organisms, and pathogenic foodborne bacteria. These bacteria can exhibit antimicrobial resistance (AMR) which is a public health concern if resistance in pathogens leads to treatment failure in humans. Culture-dependent techniques are commonly used to study individual bacterial species, but these techniques are unable to describe the whole community of microbial species (microbiome) and the profile of AMR genes they carry (resistome), which is critical for getting a holistic perspective of AMR. The objective of this study was to characterize the microbiome and resistome of retail ground beef products labeled as coming from conventional or raised without antibiotics (RWA) production systems. Sixteen ground beef products were purchased from 6 retail grocery outlets in Fort Collins, CO, half of which were labeled as produced from cattle raised conventionally and half of products were from RWA production. Total DNA was extracted and isolated from each sample and subjected to 16S rRNA amplicon sequencing for microbiome characterization and target-enriched shotgun sequencing to characterize the resistome. Differences in the microbiome and resistome of RWA and conventional ground beef were analyzed using the R programming software. Our results suggest that the resistome and microbiome of retail ground beef products with RWA packaging labels do not differ from products that do not carry claims regarding antimicrobial drug exposures during cattle production. The resistome predominantly consisted of tetracycline resistance making up more than 90% of reads mapped to resistance gene accessions in our samples. Firmicutes and Proteobacteria predominated in the microbiome of all samples (69.6% and 29.0%, respectively), but Proteobacteria composed a higher proportion in ground beef from conventionally raised cattle. In addition, our results suggest that product management, such as packaging type, could exert a stronger influence on the microbiome than the resistome in consumer-ready products. Metagenomic analyses of ground beef is a promising tool to investigate community-wide shifts in retail ground beef. Importantly, however, results from metagenomic sequencing must be carefully considered in parallel with traditional methods to better characterize the risk of AMR in retail products.
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Affiliation(s)
- Enrique Doster
- Texas A&M University, VERO Program, Canyon, TX, United States.,Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States.,Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Kevin M Thomas
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Maggie D Weinroth
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Jennifer K Parker
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Kathryn K Crone
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Terrance M Arthur
- U.S. Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - John W Schmidt
- U.S. Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Tommy L Wheeler
- U.S. Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Keith E Belk
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Paul S Morley
- Texas A&M University, VERO Program, Canyon, TX, United States.,Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
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139
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Abstract
Cardiovascular disease (CVD) is the number one leading cause for human mortality. Besides genetics and environmental factors, in recent years, gut microbiota has emerged as a new factor influencing CVD. Although cause-effect relationships are not clearly established, the reported associations between alterations in gut microbiota and CVD are prominent. Therefore, we hypothesized that machine learning (ML) could be used for gut microbiome-based diagnostic screening of CVD. To test our hypothesis, fecal 16S ribosomal RNA sequencing data of 478 CVD and 473 non-CVD human subjects collected through the American Gut Project were analyzed using 5 supervised ML algorithms including random forest, support vector machine, decision tree, elastic net, and neural networks. Thirty-nine differential bacterial taxa were identified between the CVD and non-CVD groups. ML modeling using these taxonomic features achieved a testing area under the receiver operating characteristic curve (0.0, perfect antidiscrimination; 0.5, random guessing; 1.0, perfect discrimination) of ≈0.58 (random forest and neural networks). Next, the ML models were trained with the top 500 high-variance features of operational taxonomic units, instead of bacterial taxa, and an improved testing area under the receiver operating characteristic curves of ≈0.65 (random forest) was achieved. Further, by limiting the selection to only the top 25 highly contributing operational taxonomic unit features, the area under the receiver operating characteristic curves was further significantly enhanced to ≈0.70. Overall, our study is the first to identify dysbiosis of gut microbiota in CVD patients as a group and apply this knowledge to develop a gut microbiome-based ML approach for diagnostic screening of CVD.
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Affiliation(s)
- Sachin Aryal
- Bioinformatics & Artificial Intelligence Laboratory, Center for Hypertension and Precision Medicine, Program in Physiological Genomics, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Ahmad Alimadadi
- Bioinformatics & Artificial Intelligence Laboratory, Center for Hypertension and Precision Medicine, Program in Physiological Genomics, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Ishan Manandhar
- Bioinformatics & Artificial Intelligence Laboratory, Center for Hypertension and Precision Medicine, Program in Physiological Genomics, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Bina Joe
- Bioinformatics & Artificial Intelligence Laboratory, Center for Hypertension and Precision Medicine, Program in Physiological Genomics, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xi Cheng
- Bioinformatics & Artificial Intelligence Laboratory, Center for Hypertension and Precision Medicine, Program in Physiological Genomics, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
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140
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Chen J, Hilt EE, Li F, Wu H, Jiang Z, Zhang Q, Wang J, Wang Y, Li Z, Tang J, Yang S. Epidemiological and Genomic Analysis of SARS-CoV-2 in 10 Patients From a Mid-Sized City Outside of Hubei, China in the Early Phase of the COVID-19 Outbreak. Front Public Health 2020; 8:567621. [PMID: 33072702 PMCID: PMC7531217 DOI: 10.3389/fpubh.2020.567621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/30/2020] [Accepted: 08/14/2020] [Indexed: 12/28/2022] Open
Abstract
A novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing Coronavirus Disease 2019 (COVID-19) pandemic. In this study, we performed a comprehensive epidemiological and genomic analysis of SARS-CoV-2 genomes from 10 patients in Shaoxing (Zhejiang Province), a mid-sized city outside of the epicenter Hubei province, China, during the early stage of the outbreak (late January to early February, 2020). We obtained viral genomes with >99% coverage and a mean depth of 296X demonstrating that viral genomic analysis is feasible via metagenomics sequencing directly on nasopharyngeal samples with SARS-CoV-2 Real-time PCR Ct values <28. We found that a cluster of four patients with travel history to Hubei shared the exact same virus with patients from Wuhan, Taiwan, Belgium, and Australia, highlighting how quickly this virus spread to the globe. The virus from another cluster of two family members living together without travel history but with a sick contact of a confirmed case from another city outside of Hubei accumulated significantly more mutations (9 SNPs vs. average 4 SNPs), suggesting a complex and dynamic nature of this outbreak. Our findings add to the growing knowledge of the epidemiological and genomic characteristics of SARS-CoV-2 and offers a glimpse into the early phase of this viral infection outside of Hubei, China.
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Affiliation(s)
- Jinkun Chen
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Evann E Hilt
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Fan Li
- Three Coin Analytics, Inc., Pleasanton, CA, United States
| | - Huan Wu
- IngeniGen XunMinKang Biotechnology Inc., Shaoxing, China
| | - Zhuojing Jiang
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Qinchao Zhang
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Jiling Wang
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Yifang Wang
- IngeniGen XunMinKang Biotechnology Inc., Shaoxing, China
| | - Ziqin Li
- Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, China
| | - Jialiang Tang
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, China
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141
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Schreiber PW, Kufner V, Hübel K, Schmutz S, Zagordi O, Kaur A, Bayard C, Greiner M, Zbinden A, Capaul R, Böni J, Hirsch HH, Mueller TF, Mueller NJ, Trkola A, Huber M. Metagenomic Virome Sequencing in Living Donor and Recipient Kidney Transplant Pairs Revealed JC Polyomavirus Transmission. Clin Infect Dis 2020; 69:987-994. [PMID: 30508036 PMCID: PMC7108204 DOI: 10.1093/cid/ciy1018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 08/16/2018] [Accepted: 11/29/2018] [Indexed: 12/29/2022] Open
Abstract
Background Before kidney transplantation, donors and recipients are routinely screened for viral pathogens using specific tests. Little is known about unrecognized viruses of the urinary tract that potentially result in transmission. Using an open metagenomic approach, we aimed to comprehensively assess virus transmission in living-donor kidney transplantation. Methods Living kidney donors and their corresponding recipients were enrolled at the time of transplantation. Follow-up study visits for recipients were scheduled 4–6 weeks and 1 year thereafter. At each visit, plasma and urine samples were collected and transplant recipients were evaluated for signs of infection or other transplant-related complications. For metagenomic analysis, samples were enriched for viruses, amplified by anchored random polymerase chain reaction (PCR), and sequenced using high-throughput metagenomic sequencing. Viruses detected by sequencing were confirmed using real-time PCR. Results We analyzed a total of 30 living kidney donor and recipient pairs, with a follow-up of at least 1 year. In addition to viruses commonly detected during routine post-transplant virus monitoring, metagenomic sequencing detected JC polyomavirus (JCPyV) in the urine of 7 donors and their corresponding recipients. Phylogenetic analysis confirmed infection with the donor strain in 6 cases, suggesting transmission from the transplant donor to the recipient, despite recipient seropositivity for JCPyV at the time of transplantation. Conclusions Metagenomic sequencing identified frequent transmission of JCPyV from kidney transplant donors to recipients. Considering the high incidence rate, future studies within larger cohorts are needed to define the relevance of JCPyV infection and the donor’s virome for transplant outcomes.
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Affiliation(s)
- Peter W Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Verena Kufner
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Kerstin Hübel
- Department of Nephrology, University Hospital Zurich, and University of Zurich
| | - Stefan Schmutz
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Osvaldo Zagordi
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Amandeep Kaur
- Department of Biomedicine, University of Basel, Switzerland
| | - Cornelia Bayard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Michael Greiner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Andrea Zbinden
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Riccarda Capaul
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Jürg Böni
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Hans H Hirsch
- Department of Biomedicine, University of Basel, Switzerland
| | - Thomas F Mueller
- Department of Nephrology, University Hospital Zurich, and University of Zurich
| | - Nicolas J Mueller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
| | - Alexandra Trkola
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
| | - Michael Huber
- Institute of Medical Virology, University Hospital Zurich, and University of Zurich
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142
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Abstract
The human microbiota exerts multiple physiological functions such as the regulation of metabolic and inflammatory processes. High-throughput sequencing techniques such as next-generation sequencing have become widely available in preclinical and clinical settings and have exponentially increased our knowledge about the microbiome and its interaction with host cells and organisms. There is now emerging evidence that microorganisms also contribute to inflammatory and neoplastic diseases of the pancreas. This review summarizes current clinical and translational microbiome studies in acute and chronic pancreatitis as well as pancreatic cancer and provides evidence that the microbiome has a high potential for biomarker discovery. Furthermore, the intestinal and pancreas-specific microbiome may also become an integrative part of diagnostic and therapeutic approaches of pancreatic diseases in the near future.
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Affiliation(s)
- Christoph Ammer-Herrmenau
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Centre Goettingen, Goettingen, Germany
| | - Nina Pfisterer
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Centre Goettingen, Goettingen, Germany
| | - Mark Fj Weingarten
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Centre Goettingen, Goettingen, Germany
| | - Albrecht Neesse
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Centre Goettingen, Goettingen, Germany
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143
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Schoster A, Weese JS, Gerber V, Nicole Graubner C. Dysbiosis is not present in horses with fecal water syndrome when compared to controls in spring and autumn. J Vet Intern Med 2020; 34:1614-1621. [PMID: 32588473 PMCID: PMC7379055 DOI: 10.1111/jvim.15778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Fecal water syndrome (FWS) is long-standing and common in horses, particularly in central Europe. No large epidemiological data sets exist, and the cause remains elusive. Dysbiosis could play a role in pathogenesis. OBJECTIVES To evaluate whether dysbiosis is present in horses with FWS when compared to stable-matched control horses in spring and autumn. ANIMALS Fecal samples were collected from horses with FWS (n = 16; 9 mares, 7 geldings) and controls (n = 15; 8 mares, 7 geldings). METHODS The bacterial microbiome of samples collected in spring and autumn of 2016 was analyzed using high-throughput sequencing. Differences in relative abundance of bacterial taxa, alpha diversity, and beta diversity indices were assessed between horses with FWS and controls based on season. RESULTS Differences in microbial community composition based on time point and health status were not observed on any taxonomic level. Limited differences were seen on linear discriminant analysis effect size analysis. No difference in alpha diversity indices was observed including richness, diversity based on health status, or time point. No effect of health status on microbial community membership structure was observed. CONCLUSIONS AND CLINICAL IMPORTANCE Limited differences were found in the bacterial microbiota of horses with and without FWS, regardless of season. Further research is needed to elucidate the role of microbiota in the development of FWS.
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Affiliation(s)
| | - J. Scott Weese
- University of Guelph, University of GuelphGuelphOntarioCanada
| | - Vinzenz Gerber
- Vetsuisse Faculty, University of BernDepartment of Veterinary MedicineBernSwitzerland
| | - Claudia Nicole Graubner
- Equine Clinic ‐ Vetsuisse Faculty, University of BernDepartment of Veterinary MedicineBerneSwitzerland
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Auffret MD, Stewart RD, Dewhurst RJ, Duthie CA, Watson M, Roehe R. Identification of Microbial Genetic Capacities and Potential Mechanisms Within the Rumen Microbiome Explaining Differences in Beef Cattle Feed Efficiency. Front Microbiol 2020; 11:1229. [PMID: 32582125 PMCID: PMC7292206 DOI: 10.3389/fmicb.2020.01229] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 01/17/2020] [Accepted: 05/14/2020] [Indexed: 12/15/2022] Open
Abstract
In this study, Bos Taurus cattle offered one high concentrate diet (92% concentrate-8% straw) during two independent trials allowed us to classify 72 animals comprising of two cattle breeds as "Low" or "High" feed efficiency groups. Digesta samples were taken from individual beef cattle at the abattoir. After metagenomic sequencing, the rumen microbiome composition and genes were determined. Applying a targeted approach based on current biological evidence, 27 genes associated with host-microbiome interaction activities were selected. Partial least square analysis enabled the identification of the most significant genes and genera of feed efficiency (VIP > 0.8) across years of the trial and breeds when comparing all potential genes or genera together. As a result, limited number of genes explained about 40% of the variability in both feed efficiency indicators. Combining information from rumen metagenome-assembled genomes and partial least square analysis results, microbial genera carrying these genes were determined and indicated that a limited number of important genera impacting on feed efficiency. In addition, potential mechanisms explaining significant difference between Low and High feed efficiency animals were analyzed considering, based on the literature, their gastrointestinal location of action. High feed efficiency animals were associated with microbial species including several Eubacterium having the genetic capacity to form biofilm or releasing metabolites like butyrate or propionate known to provide a greater contribution to cattle energy requirements compared to acetate. Populations associated with fucose sensing or hemolysin production, both mechanisms specifically described in the lower gut by activating the immune system to compete with pathogenic colonizers, were also identified to affect feed efficiency using rumen microbiome information. Microbial mechanisms associated with low feed efficiency animals involved potential pathogens within Proteobacteria and Spirochaetales, releasing less energetic substrates (e.g., acetate) or producing sialic acid to avoid the host immune system. Therefore, this study focusing on genes known to be involved in host-microbiome interaction improved the identification of rumen microbial genetic capacities and potential mechanisms significantly impacting on feed efficiency in beef cattle fed high concentrate diet.
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Affiliation(s)
| | - Robert D. Stewart
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Mick Watson
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
- Edinburgh Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Rainer Roehe
- Scotland’s Rural College (SRUC), Edinburgh, United Kingdom
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145
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Xue F, Wang Y, Zhao Y, Nan X, Hua D, Sun F, Yang L, Jiang L, Xiong B. Ruminal Methanogenic Responses to the Thiamine Supplementation in High-Concentrate Diets. Animals (Basel) 2020; 10:E935. [PMID: 32481707 PMCID: PMC7341502 DOI: 10.3390/ani10060935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Thiamine supplementation in high-concentrate diets (HC) was confirmed to attenuate ruminal subacute acidosis through promoting carbohydrate metabolism, however, whether thiamine supplementation in HC impacts methane metabolism is still unclear. Therefore, in the present study, thiamine was supplemented in the high-concentrate diets to investigate its effects on ruminal methanogens and methanogenesis process. METHODS an in vitro fermentation experiment which included three treatments: control diet (CON, concentrate/forage = 4:6; DM basis), high-concentrate diet (HC, concentrate/forage = 6:4; DM basis) and high-concentrate diet supplemented with thiamine (HCT, concentrate/forage = 6:4, DM basis; thiamine supplementation content = 180 mg/kg DM) was conducted. Each treatment concluded with four repeats, with three bottles in each repeat. The in vitro fermentation was sustained for 48h each time and repeated three times. At the end of fermentation, fermentable parameters, ruminal bacteria and methanogens community were measured. RESULTS HC significantly decreased ruminal pH, thiamine and acetate content, while significantly increasing propionate content compared with CON (p < 0.05). Conversely, thiamine supplementation significantly increased ruminal pH, acetate while significantly decreasing propionate content compared with HC treatment (p < 0.05). No significant difference of ruminal methanogens abundances among three treatments was observed. Thiamine supplementation significantly decreased methane production compared with CON, while no significant change was found in HCT compared with HC. CONCLUSION thiamine supplementation in the high-concentrate diet (HC) could efficiently reduce CH4 emissions compared with high-forage diets while without causing ruminal metabolic disorders compared with HC treatment. This study demonstrated that supplementation of proper thiamine in concentrate diets could be an effective nutritional strategy to decrease CH4 production in dairy cows.
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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; (F.X.); (Y.W.); (Y.Z.); (X.N.); (D.H.); (F.S.); (L.Y.)
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yue Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.X.); (Y.W.); (Y.Z.); (X.N.); (D.H.); (F.S.); (L.Y.)
| | - Yiguang Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.X.); (Y.W.); (Y.Z.); (X.N.); (D.H.); (F.S.); (L.Y.)
| | - Xuemei Nan
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.X.); (Y.W.); (Y.Z.); (X.N.); (D.H.); (F.S.); (L.Y.)
| | - Dengke Hua
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.X.); (Y.W.); (Y.Z.); (X.N.); (D.H.); (F.S.); (L.Y.)
| | - Fuyu Sun
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.X.); (Y.W.); (Y.Z.); (X.N.); (D.H.); (F.S.); (L.Y.)
| | - Liang Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.X.); (Y.W.); (Y.Z.); (X.N.); (D.H.); (F.S.); (L.Y.)
| | - Linshu Jiang
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing University of Agriculture, Beijing 102206, China
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.X.); (Y.W.); (Y.Z.); (X.N.); (D.H.); (F.S.); (L.Y.)
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146
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Arunasri K, Mahesh M, Sai Prashanthi G, Jayasudha R, Kalyana Chakravarthy S, Tyagi M, Pappuru RR, Shivaji S. Comparison of the Vitreous Fluid Bacterial Microbiomes between Individuals with Post Fever Retinitis and Healthy Controls. Microorganisms 2020; 8:E751. [PMID: 32429503 PMCID: PMC7285296 DOI: 10.3390/microorganisms8050751] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/23/2020] [Accepted: 05/04/2020] [Indexed: 12/21/2022] Open
Abstract
Ocular microbiome research has gained momentum in the recent past and has provided new insights into health and disease conditions. However, studies on sight threatening intraocular inflammatory diseases have remained untouched. In the present study, we attempted to identify the bacterial microbiome associated with post fever retinitis using a metagenomic sequencing approach. For this purpose, bacterial ocular microbiomes were generated from vitreous samples collected from control individuals (VC, n = 19) and individuals with post fever retinitis (PFR, n = 9), and analysed. The results revealed 18 discriminative genera in the microbiomes of the two cohorts out of which 16 genera were enriched in VC and the remaining two in PFR group. These discriminative genera were inferred to have antimicrobial, anti-inflammatory, and probiotic function. Only two pathogenic bacteria were differentially abundant in 20% of the PFR samples. PCoA and heatmap analysis showed that the vitreous microbiomes of VC and PFR formed two distinct clusters indicating dysbiosis in the vitreous bacterial microbiomes. Functional assignments and network analysis also revealed that the vitreous bacterial microbiomes in the control group exhibited more evenness in the bacterial diversity and several bacteria had antimicrobial function compared to the PFR group.
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Affiliation(s)
- Kotakonda Arunasri
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Malleswarapu Mahesh
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Gumpili Sai Prashanthi
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Sama Kalyana Chakravarthy
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Mudit Tyagi
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (M.T.); (R.R.P.)
| | - Rajeev R. Pappuru
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (M.T.); (R.R.P.)
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
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147
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Lu L, Robertson G, Ashworth J, Pham Hong A, Shi T, Ivens A, Thwaites G, Baker S, Woolhouse M. Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam. Front Microbiol 2020; 11:833. [PMID: 32499763 PMCID: PMC7242649 DOI: 10.3389/fmicb.2020.00833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 12/20/2019] [Accepted: 04/07/2020] [Indexed: 12/18/2022] Open
Abstract
Acute respiratory infections (ARIs) impose a major public health burden on fragile healthcare systems of developing Southeast Asian countries such as Vietnam. The epidemiology, genetic diversity and transmission patterns of respiratory viral pathogens that circulate in this region are not well characterized. We used RT-PCR to screen for 14 common respiratory viruses in nasal/throat samples from 4326 ARI patients from 5 sites in Vietnam during 2012-2016. 64% of patients tested positive for viruses; 14% tested positive multiple co-infecting viruses. The most frequently detected viruses were Respiratory syncytial virus (RSV, 23%), Human Rhinovirus (HRV, 13%), Influenza A virus (IAV, 11%) and Human Bocavirus (HBoV, 7%). RSV infections peaked in July to October, were relatively more common in children <1 year and in the northernmost hospital. IAV infections peaked in December to February and were relatively more common in patients >5 years in the central region. Coinfection with IAV or RSV was associated with increased disease severity compared with patients only infected with HBoV or HRV. Over a hundred genomes belonging to 13 families and 24 genera were obtained via metagenomic sequencing, including novel viruses and viruses less commonly associated with ARIs. Phylogenetic and phylogeographic analyses further indicated that neighboring countries were the most likely source of many virus lineages causing ARIs in Vietnam and estimated the period that specific lineages have been circulating. Our study illustrates the value of applying the state-of-the-art virus diagnostic methods (multiplex RT-PCR and metagenomic sequencing) and phylodynamic analyses at a national level to generate an integrated picture of viral ARI epidemiology.
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Affiliation(s)
- Lu Lu
- Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Gail Robertson
- Statistical Consultancy Unit, School of Mathematics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jordan Ashworth
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Anh Pham Hong
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ting Shi
- Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Alasdair Ivens
- Institute of Immunology and Infection Research, The University of Edinburgh, Edinburgh, United Kingdom
| | - Guy Thwaites
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Mark Woolhouse
- Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
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148
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Oude Munnink BB, Farag EABA, GeurtsvanKessel C, Schapendonk C, van der Linden A, Kohl R, Arron G, Ziglam H, Goravey WGM, Coyle PV, Ibrahim I, Mohran KA, Alrajhi MMS, Islam MM, Abdeen R, Al-Zeyara AAMAH, Younis NM, Al-Romaihi HE, Thani MHJA, Molenkamp R, Sikkema RS, Koopmans M. First molecular analysis of rabies virus in Qatar and clinical cases imported into Qatar, a case report. Int J Infect Dis 2020; 96:323-326. [PMID: 32376305 DOI: 10.1016/j.ijid.2020.04.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 04/23/2020] [Accepted: 04/25/2020] [Indexed: 11/27/2022] Open
Abstract
Identifying the origin of the rabies virus (RABV) infection may have significant implications for control measures. Here, we identified the source of a RABV infection of two Nepalese migrants in Qatar by comparing their RABV genomes with RABV genomes isolated from the brains of a RABV infected camel and fox from Qatar.
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Affiliation(s)
- Bas B Oude Munnink
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | | | - Corine GeurtsvanKessel
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Claudia Schapendonk
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Anne van der Linden
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Robert Kohl
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Georgina Arron
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | | | | | | | | | - Khaled A Mohran
- Department of Animal Resources, Ministry of Municipals and Environment, Doha, Qatar; Animal Health Research Institute, Biotechnology Departments ERC, Dokki, Egypt
| | | | - Md Mazharul Islam
- Department of Animal Resources, Ministry of Municipals and Environment, Doha, Qatar
| | - Randa Abdeen
- Department of Animal Resources, Ministry of Municipals and Environment, Doha, Qatar
| | | | - Nidal Mahmoud Younis
- Department of Animal Resources, Ministry of Municipals and Environment, Doha, Qatar
| | | | | | - Richard Molenkamp
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Marion Koopmans
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
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149
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Martin RM, Burke K, Verma D, Xie H, Langer J, Schlaberg R, Swaminathan S, Hanson KE. Contact Transmission of Vaccinia to an Infant Diagnosed by Viral Culture and Metagenomic Sequencing. Open Forum Infect Dis 2020; 7:ofaa111. [PMID: 32685604 PMCID: PMC7357282 DOI: 10.1093/ofid/ofaa111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/25/2020] [Indexed: 12/30/2022] Open
Abstract
Targeted molecular diagnostic tests and accurate immunoassays have transformed the landscape of clinical virology, calling into question the usefulness of traditional viral culture. Here we present a case where viral culture, followed by metagenomic sequencing, was central to the diagnosis of an unexpected viral infection, with significant clinical and public health implications.
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Affiliation(s)
- Rebekah M Martin
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.,Associated Regional and University Pathologists, Inc. (ARUP Laboratories), Salt Lake City, Utah, USA
| | - Kristina Burke
- Dermatology Clinic, Tripler Army Medical Center, Honolulu, Hawaii, USA
| | - Dinesh Verma
- Division of Infectious Diseases, Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Heng Xie
- IDbyDNA, Salt Lake City, Utah, USA
| | - Janine Langer
- Associated Regional and University Pathologists, Inc. (ARUP Laboratories), Salt Lake City, Utah, USA
| | - Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.,IDbyDNA, Salt Lake City, Utah, USA
| | - Sankar Swaminathan
- Division of Infectious Diseases, Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Kimberly E Hanson
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.,Associated Regional and University Pathologists, Inc. (ARUP Laboratories), Salt Lake City, Utah, USA.,Division of Infectious Diseases, Department of Medicine, University of Utah, Salt Lake City, Utah, USA
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150
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Naboka YL, Gudima IA, Mordanov SV, Krakhotkin DV, Ilyash AV, Kogan MI, Ibishev KS. [Virusuria as a component of the urine microbiota and its significance for assessing the health of the urinary tract: a descriptive clinical study]. Urologiia 2020:12-18. [PMID: 32190998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
AIM To determine the frequency of occurrence of oportunistic pathogenic bacterial flora and viral pathogens in the urine of healthy people with the establishment of the association between them. MATERIALS AND METHODS 40 healthy sexually active women and men were examined, which are divided by gender into equivalent groups: Group I - healthy women (n=19), Group II - healthy men (n=21). The age of the subjects ranged from 20 to 25 years, the average age was 22.4+/-1.2 years. In both groups, the average portion of morning urine was taken for a study after a proper hygienic procedure with self-urination of the subjects in a sterile plastic container (Sterile Uricol for urine sample collection "HiMedia"). In addition to the nutrient media regulated by the Clinical Guidelines, additional HiMedia chromogenic media were used to cultivate facultative anaerobic (FAB) and non-clostridial anaerobic bacteria (NAB). Detection of viruses was performed by PCR with detection in "real time". DNA isolation was carried out by the sorption method using the AmpliPrime DNA-Sorb-B ("NextBio") kit from urine samples, with preliminary concentration. RESULTS In all 40 cases, normative leukocyturia was detected in the urine. According to the results of bacteriological examination of urine, healthy men and women in all cases found aerobic-anaerobic associations. Coagulase-negative staphylococci (CNS) and Corynebacterium spp. Dominated in the cluster of aerobic taxa of microbiota. (75.0%, 55.0% respectively). The spectrum of CNS was represented by five species: S.epidermidis (30.0%), S.haemolyticus (27.5%), and S.warneri (25.0%), S.saprophyticus and S.lentus (15.0%). Enterococcus spp. were recorded in the urine in 32.5% of cases. Representatives of the Enterobacteriaceae family were represented by 4 taxa: E. coli (10.0%), Klebsiella spp., Proteus spp. (5.0% each), Enterobacter spp., Citrobacter spp. (2.5%). In a cluster of anaerobic bacteria in the urine, Eubacterium spp. (60.0%) and almost half of healthy individuals recorded Lactobacillus spp. and Peptococcus spp. (42.5% each). When analyzing the frequencies of detection of various microbiota taxa, it was found that women significantly more frequently recorded urine Corynebacterium spp., Eubacterium spp. and Lactobacillus spp., as well as Enterococcus spp. and Peptococcus spp. Peptostreptococcus spp. and Veillonella spp. were significantly more often determined (p<0.05) in the urine of men. HHV6 (10.0%), HPV18 and B19 parvovirus (2,5%) were determined in the urine of healthy people. It should be noted that the studied viruses were more often recorded in men, in particular, HPV18 and parvovirus B19 - only in men, and HHV6 more often in men (7.5%), less often in women (2.5%). Significant associations of some genera of microorganisms with the sex of the participants were revealed for E. faecalis and Lactobacillus spp., which were more often found in the urine of healthy women Reliably significant associations were found for three taxa: viruses HPV6, HPV18 and parvoviruses B19 (16.7%) were determined in the presence of Bacteroides spp., Bifidobacterium spp., and Prevotella spp., in urine. Accordingly, in 83.3% of cases, these viruses were detected in the absence of the above-listed taxa of microorganisms in the urine. CONCLUSIONS The normal urinary microbiota of healthy women and men has differences: Lactobacillus spp and Candida spp are absent in the urine of men while Streptococcus spp in urine of women. HHV6, HPV18, parvoviruses B19 are found in urine of healthy people and more often in men. Data about the virobiota and microbiota of urine in healthy people can highlight on the pathogenesis of urinary tract infections of various localization and develop targeted approaches in personalized therapy of this group of diseases.
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Affiliation(s)
- Yu L Naboka
- Rostov State Medical University, Rostov-on-Don, Russia
| | - I A Gudima
- Rostov State Medical University, Rostov-on-Don, Russia
| | - S V Mordanov
- Rostov State Medical University, Rostov-on-Don, Russia
| | | | - A V Ilyash
- Rostov State Medical University, Rostov-on-Don, Russia
| | - M I Kogan
- Rostov State Medical University, Rostov-on-Don, Russia
| | - Kh S Ibishev
- Rostov State Medical University, Rostov-on-Don, Russia
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