1
|
Nath A, Gadratagi BG, Maurya RP, Ullah F, Patil NB, Adak T, Govindharaj GPP, Ray A, Mahendiran A, Desneux N, Chandra Rath P. Sublethal phosphine fumigation induces transgenerational hormesis in a factitious host, Corcyra cephalonica. Pest Manag Sci 2023; 79:3548-3558. [PMID: 37183345 DOI: 10.1002/ps.7542] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/31/2023] [Accepted: 05/06/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND The rice moth, Corcyra cephalonica (Stainton) (Lepidoptera: Pyralidae) is a pest of stored grains and widely used as a factitious host during the mass rearing of several natural enemies of crop pests. Hormesis is well-documented in pest insects, to some extent in natural enemies of pests. RESULTS We report transgenerational stimulatory effects of the widely used fumigant, phosphine. The study reports the consequences of sublethal, low lethal and median lethal concentrations (LC5 , LC25 and LC50 ) and untreated control for two sequential generations of the species (G1 to G2 ). In this study, we investigated the life-history traits, nutrient reserves (protein, lipid and carbohydrate) and larval gut microbiome (using 16 s rRNA V3-V4 metagenomics sequencing) of C. cephalonica. Stimulatory effects were observed for various biological traits of C. cephalonica, notably adult longevity, emergence and increased egg hatchability when exposed to LC5 of phosphine. The total protein, lipid and carbohydrate contents of C. cephalonica also were found to be significantly increased by LC5 in both generations. The microbial diversity of LC5 treated larval gut was higher and found to be different from the rest of the treatments. This is the first report showing hormesis to a fumigant insecticide. CONCLUSION Our findings increase knowledge on the interaction between hormesis, nutrient reserves and gut bacteria in C. cephalonica exposed to insecticides. Overall, the present study establishes phosphine-induced hormesis at LC5 in the host C. cephalonica, which might help improve the quality of mass rearing of various natural enemies. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Anshuman Nath
- Department of Entomology, College of Agriculture, G.B. Pant University of Agriculture and Technology, Pantnagar, India
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | | | - Ravi Prakash Maurya
- Department of Entomology, College of Agriculture, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Farman Ullah
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
| | - Naveenkumar B Patil
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Totan Adak
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | | | - Aishwarya Ray
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
- Department of Entomology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Annamalai Mahendiran
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | | | - Prakash Chandra Rath
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| |
Collapse
|
2
|
Niyogisubizo J, Cai Y, Zhang L, Zhang X, Wei Y. Editorial: Computational solutions for microbiome and metagenomics sequencing analyses, Volume II. Front Mol Biosci 2023; 10:1253303. [PMID: 37529378 PMCID: PMC10390057 DOI: 10.3389/fmolb.2023.1253303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Affiliation(s)
- Jovial Niyogisubizo
- Centre for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Yunpeng Cai
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Xingyu Zhang
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Yanjie Wei
- Centre for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| |
Collapse
|
3
|
Liu Y, Yuan Y, Yuan H, Wang Y, Jin C, Zhang H, Tang J, Hu Y. Metagenomic Sequencing to Analyze Composition and Function of Top-Gray Chalky Grain Microorganisms from Hybrid Rice Seeds. Plants (Basel) 2023; 12:2358. [PMID: 37375983 DOI: 10.3390/plants12122358] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
The top-gray chalkiness of hybrid rice (Oryza sativa L.) seeds is a typical phenomenon in hybrid rice seeds. The chalky part of the grain is infected and is the inoculum to infect the normal seeds during storage and soaking. These seed-associated microorganisms were cultivated and sequenced using metagenomics shotgun sequencing to obtain more comprehensive information on the seed-associated microorganisms in this experiment. The results showed that fungi could grow well on the rice flour medium, similar to the ingredients of rice seed endosperms. After the assembly of metagenomic data, a gene catalog was established, comprising 250,918 genes. Function analysis showed that glycoside hydrolases were the dominant enzymes, and the genus Rhizopus accounted for the dominant microorganisms. The fungal species R. microspores, R. delemar, and R. oryzae were likely to be the candidate pathogens in the top-gray chalky grains of hybrid rice seeds. These results will provide a reference for improving hybrid rice processing after harvest.
Collapse
Affiliation(s)
- You Liu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Yuan Yuan
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
- Quality Inspection Department, Hunan Ava Seeds Co., Ltd., Changsha 410128, China
| | - Hui Yuan
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
- Quality Inspection Department, Baiyunshan Forest Farm of Shimen County, Changde 415312, China
| | - Yan Wang
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Chenzhong Jin
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Hao Zhang
- Quality Inspection Department, Hunan Ava Seeds Co., Ltd., Changsha 410128, China
| | - Jianliang Tang
- Quality Inspection Department, Hunan Ava Seeds Co., Ltd., Changsha 410128, China
| | - Yihong Hu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| |
Collapse
|
4
|
Stupak A, Kwaśniewski W. Evaluating Current Molecular Techniques and Evidence in Assessing Microbiome in Placenta-Related Health and Disorders in Pregnancy. Biomolecules 2023; 13:911. [PMID: 37371491 DOI: 10.3390/biom13060911] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
The microbiome is of great interest due to its potential influence on the occurrence and treatment of some human illnesses. It may be regarded as disruptions to the delicate equilibrium that humans ordinarily maintain with their microorganisms or the microbiota in their environment. The focus of this review is on the methodologies and current understanding of the functional microbiome in pregnancy outcomes. We present how novel techniques bring new insights to the contemporary field of maternal-fetal medicine with a critical analysis. The maternal microbiome in late pregnancy has been extensively studied, although data on maternal microbial changes during the first trimester are rare. Research has demonstrated that, in healthy pregnancies, the origin of the placental microbiota is oral (gut) rather than vaginal. Implantation, placental development, and maternal adaptation to pregnancy are complex processes in which fetal and maternal cells interact. Microbiome dysbiosis or microbial metabolites are rising as potential moderators of antenatal illnesses related to the placenta, such as fetal growth restriction, preeclampsia, and others, including gestational diabetes and preterm deliveries. However, because of the presence of antimicrobial components, it is likely that the bacteria identified in placental tissue are (fragments of) bacteria that have been destroyed by the placenta's immune cells. Using genomic techniques (metagenomics, metatranscriptomics, and metaproteomics), it may be possible to predict some properties of a microorganism's genome and the biochemical (epigenetic DNA modification) and physical components of the placenta as its environment. Despite the results described in this review, this subject needs further research on some major and crucial aspects. The phases of an in utero translocation of the maternal gut microbiota to the fetus should be explored. With a predictive knowledge of the impacts of the disturbance on microbial communities that influence human health and the environment, genomics may hold the answer to the development of novel therapies for the health of pregnant women.
Collapse
Affiliation(s)
- Aleksandra Stupak
- Department of Obstetrics and Pathology of Pregnancy, Medical University of Lublin, Staszica Str. 16, 20-081 Lublin, Poland
| | - Wojciech Kwaśniewski
- Department of Gynecological Oncology and Gynecology, Medical University of Lublin, 20-081 Lublin, Poland
| |
Collapse
|
5
|
Ferreira C, Otani S, Aarestrup FM, Manaia CM. Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage. FEMS Microbes 2023; 4:xtad008. [PMID: 37333442 PMCID: PMC10117749 DOI: 10.1093/femsmc/xtad008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/24/2023] [Accepted: 03/05/2023] [Indexed: 08/06/2023] Open
Abstract
The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches. In this study, we aimed to evaluate and compare the performance of these methods to screen antibiotic resistance genes in animal faecal, wastewater, and water samples. Water and wastewater samples were from hospital effluent, different treatment stages of two treatment plants, and of the receiving river at the discharge point. The animal samples were from pig and chicken faeces. Antibiotic resistance gene coverage, sensitivity, and usefulness of the quantitative information were analyzed and discussed. While both methods were able to distinguish the resistome profiles and detect gradient stepwise mixtures of pig and chicken faeces, qPCR presented higher sensitivity for the detection of a few antibiotic resistance genes in water/wastewater. In addition, the comparison of predicted and observed antibiotic resistance gene quantifications unveiled the higher accuracy of qPCR. Metagenomics analyses, while less sensitive, provided a markedly higher coverage of antibiotic resistance genes compared to qPCR. The complementarity of both methods and the importance of selecting the best method according to the study purpose are discussed.
Collapse
Affiliation(s)
| | | | - Frank Møller Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Célia M Manaia
- Corresponding author. Escola Superior de Biotecnologia Universidade Católica Portuguesa Rua de Diogo Botelho, 1327 4169-005 Porto, Portugal. E-mail:
| |
Collapse
|
6
|
Xi M, Na X, Ma X, Lan H, Sun T, Liu WH, Hung W, Zhao A. Maternal diet associated with infants' intestinal microbiota mediated by predominant long-chain fatty acid in breast milk. Front Microbiol 2023; 13:1004175. [PMID: 36687649 PMCID: PMC9852834 DOI: 10.3389/fmicb.2022.1004175] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/09/2022] [Indexed: 01/08/2023] Open
Abstract
Introduction Long-chain fatty acids in breast milk are affected by the mother's diet and play an important role in the growth, development, and immune construction of infants. This study aims to explore the correlation between maternal diet, breast milk fatty acids (FAs), and the infant intestinal flora. Methods We enrolled 56 paired mothers and their infants; both breast milk samples and infants' fecal samples were collected to determine the long-chain FA content of breast milk by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS), and metagenomic technology was applied to determine the microbial composition of infant feces. The maternal diet was also investigated using a 24-h dietary recall. Results The results indicated that the fat contribution rates of edible oils in the maternal diet are significantly positively correlated with the contents of certain long-chain fatty acids (C16:0, C18:1, C16:1, and C22:4) in breast milk, which mainly regulate the abundance of Lacticaseibacillus rhamnosus, Lacticaseibacillus fermentum, and Lacticaseibacillus paracasei in the infant gut. Through KEGG pathway analysis, our data revealed that the long-chain FAs in different groups of breast milk were significantly correlated with the pathways of biotin metabolism, glycerolipid metabolism, and starch and sucrose metabolism. Discussion The results of this study suggest a pathway in which the diets of lactating mothers may affect the composition of the infant intestinal microbiota by influencing breast milk FAs and then further regulating infant health.
Collapse
Affiliation(s)
- Menglu Xi
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Xiaona Na
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Xia Ma
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot, China,Yili Innovation Center, Inner Mongolia Yili Industrial Group Co., Ltd., Hohhot, China
| | - Hanglian Lan
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot, China,Yili Innovation Center, Inner Mongolia Yili Industrial Group Co., Ltd., Hohhot, China
| | - Ting Sun
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot, China,Yili Innovation Center, Inner Mongolia Yili Industrial Group Co., Ltd., Hohhot, China
| | - Wei-Hsien Liu
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot, China,Yili Innovation Center, Inner Mongolia Yili Industrial Group Co., Ltd., Hohhot, China
| | - Weilian Hung
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot, China,Yili Innovation Center, Inner Mongolia Yili Industrial Group Co., Ltd., Hohhot, China,*Correspondence: Weilian Hung,
| | - Ai Zhao
- Vanke School of Public Health, Tsinghua University, Beijing, China,Ai Zhao,
| |
Collapse
|
7
|
Bawaneh A, Shively CA, Tooze JA, Cook KL. Impact of gut permeability on the breast microbiome using a non-human primate model. Gut Microbiome (Camb) 2022; 3:e10. [PMID: 36891249 DOI: 10.1017/gmb.2022.9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We previously demonstrated in non-human primates (NHP) that Mediterranean diet consumption shifted the proportional abundance of Lactobacillus in the breast and gut. This data highlights a potential link about gut-breast microbiome interconnectivity. To address this question, we compared bacterial populations identified in matched breast and faecal samples from our NHP study. Dietary pattern concurrently shifted two species in both regions; Streptococcus lutetiensis and Ruminococcus torques. While we observe similar trends in Lactobacillus abundances in the breast and gut, the species identified in each region vary; Mediterranean diet increased Lactobacillus_unspecified species in breast but regulated L. animalis and L. reuteri in the gut.We also investigated the impact of gut permeability on the breast microbiome. Regardless of dietary pattern, subjects that displayed increased physiological measures of gut permeability (elevated plasma lipopolysaccharide, decreased villi length, and decreased goblet cells) displayed a significantly different breast microbiome. Gut barrier dysfunction was associated with increased α-diversity and significant different β-diversity in the breast tissue. Taken together our data supports the presence of a breast microbiome influenced by diet that largely varies from the gut microbiome population but is, however, sensitive to gut permeability.
Collapse
|
8
|
Peng X, Zhao Y, Lin T, Shu X, Hou L, Gao L, Wang H, Ge N, Yue J. [Research of relationship between frailty and gut microbiota on middle-aged and the aged patients with diabetes]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2021; 38:1126-1133. [PMID: 34970896 DOI: 10.7507/1001-5515.202101083] [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: 06/14/2023]
Abstract
Gut microbiota plays an important role in development of diabetes with frailty. Therefore, it is of great significance to study the structural and functional characteristics of gut microbiota in Chinese with frailty. Totally 30 middle-aged and the aged participants in communities with diabetes were enrolled in this study, and their feces were collected. At the same time, we developed a metagenome analysis to explore the different of the structural and functional characteristics between diabetes with frailty and diabetes without frailty. The results showed the alpha diversity of intestinal microbiota in diabetes with frailty was lower. Collinsella and Butyricimonas were more abundant in diabetes with frailty. The functional characteristics showed that histidine metabolism, Epstein-Barr virus infection, sulfur metabolism, and biosynthesis of type Ⅱ polyketide products were upregulated in diabetes with frailty. Otherwise, butanoate metabolism and phenylalanine metabolism were down-regulated in diabetes with frailty. This research provides theoretical basic for exploring the mechanism of the gut microbiota on the occurrence and development of diabetes with frailty, and provides a basic for prevention and intervention of it.
Collapse
Affiliation(s)
- Xuchao Peng
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, P.R.China
| | - Yanli Zhao
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, P.R.China
| | - Taiping Lin
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, P.R.China
| | - Xiaoyu Shu
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, P.R.China
| | - Lisha Hou
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, P.R.China
| | - Langli Gao
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, P.R.China
| | - Hui Wang
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, P.R.China
| | - Ning Ge
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, P.R.China
| | - Jirong Yue
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, P.R.China
| |
Collapse
|
9
|
Yu J, Zhang H, Chen L, Ruan Y, Chen Y, Liu Q. Disease-Associated Gut Microbiota Reduces the Profile of Secondary Bile Acids in Pediatric Nonalcoholic Fatty Liver Disease. Front Cell Infect Microbiol 2021; 11:698852. [PMID: 34568090 PMCID: PMC8459332 DOI: 10.3389/fcimb.2021.698852] [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: 06/16/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Children with nonalcoholic fatty liver disease (NAFLD) display an altered gut microbiota compared with healthy children. However, little is known about the fecal bile acid profiles and their association with gut microbiota dysbiosis in pediatric NAFLD. A total of 68 children were enrolled in this study, including 32 NAFLD patients and 36 healthy children. Fecal samples were collected and analyzed by metagenomic sequencing to determine the changes in the gut microbiota of children with NAFLD, and an ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) system was used to quantify the concentrations of primary and secondary bile acids. The associations between the gut microbiota and concentrations of primary and secondary bile acids in the fecal samples were then analyzed. We found that children with NAFLD exhibited reduced levels of secondary bile acids and alterations in bile acid biotransforming-related bacteria in the feces. Notably, the decrease in Eubacterium and Ruminococcaceae bacteria, which express bile salt hydrolase and 7α-dehydroxylase, was significantly positively correlated with the level of fecal lithocholic acid (LCA). However, the level of fecal LCA was negatively associated with the abundance of the potential pathogen Escherichia coli that was enriched in children with NAFLD. Pediatric NAFLD is characterized by an altered profile of gut microbiota and fecal bile acids. This study demonstrates that the disease-associated gut microbiota is linked with decreased concentrations of secondary bile acids in the feces. The disease-associated gut microbiota likely inhibits the conversion of primary to secondary bile acids.
Collapse
Affiliation(s)
- Jiake Yu
- Department of Pediatric Infectious Disease, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hu Zhang
- Department of Pediatric Infectious Disease, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liya Chen
- Department of Pediatric Infectious Disease, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yufei Ruan
- Department of Pediatric Infectious Disease, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yiping Chen
- Department of Pediatric Infectious Disease, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qi Liu
- Department of Pediatric Infectious Disease, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
10
|
Huang L, Hong B, Yang W, Wang L, Yu R. Snipe: highly sensitive pathogen detection from metagenomic sequencing data. Brief Bioinform 2021; 22:6210456. [PMID: 33822895 DOI: 10.1093/bib/bbab064] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/05/2021] [Accepted: 02/08/2021] [Indexed: 01/24/2023] Open
Abstract
Metagenomics data provide rich information for the detection of foodborne pathogens from food and environmental samples that are mixed with complex background bacteria strains. While pathogen detection from metagenomic sequencing data has become an activity of increasing interest, shotgun sequencing of uncultured food samples typically produces data that contain reads from many different organisms, making accurate strain typing a challenging task. Particularly, as many pathogens may contain a common set of genes that are highly similar to those from normal bacteria in food samples, traditional strain-level abundance profiling approaches do not perform well at detecting pathogens of very low abundance levels. To overcome this limitation, we propose an abundance correction method based on species-specific genomic regions to achieve high sensitivity and high specificity in target pathogen detection at low abundance.
Collapse
Affiliation(s)
- Lihong Huang
- School of Informatics of Xiamen University, China
| | - Bin Hong
- Department of Computer Science, School of Informatics of Xiamen University, China
| | | | - Liansheng Wang
- Department of Computer Science, School of Informatics of Xiamen University, China
| | - Rongshan Yu
- Department of Computer Science, School of Informatics of Xiamen University, China
| |
Collapse
|
11
|
Xiao S, Zhang G, Jiang C, Liu X, Wang X, Li Y, Cheng M, Lv H, Xian F, Guo X, Tan Y. Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing. Front Cell Infect Microbiol 2021; 11:605825. [PMID: 33869074 PMCID: PMC8047475 DOI: 10.3389/fcimb.2021.605825] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 09/15/2020] [Accepted: 03/09/2021] [Indexed: 12/21/2022] Open
Abstract
Background Increasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking. Objectives To comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis. Methods DNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis. Results Compared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis. Conclusions A clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.
Collapse
Affiliation(s)
- Shiju Xiao
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Graduate School, Capital Medical University, Beijing, China
| | - Guangzhong Zhang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Chunyan Jiang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xin Liu
- Puyang Hospital of Traditional Chinese Medicine, Puyang, China
| | - Xiaoxu Wang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Graduate School, Capital Medical University, Beijing, China
| | - Yafan Li
- Beijing University of Chinese Medicine, Beijing, China
| | - Meijiao Cheng
- Beijing QuantiHealth Technology Co., Ltd, Beijing, China
| | - Hongpeng Lv
- Beijing University of Chinese Medicine, Beijing, China
| | - Fuyang Xian
- Beijing University of Chinese Medicine, Beijing, China
| | - Xinwei Guo
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Graduate School, Capital Medical University, Beijing, China.,Beijing Institute of Traditional Chinese Medicine, Beijing, China
| | - Yong Tan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| |
Collapse
|
12
|
Lu W, Feng Y, Jing F, Han Y, Lyu N, Liu F, Li J, Song X, Xie J, Qiu Z, Zhu T, Routy B, Routy JP, Li T, Zhu B. Association Between Gut Microbiota and CD4 Recovery in HIV-1 Infected Patients. Front Microbiol 2018; 9:1451. [PMID: 30034377 PMCID: PMC6043814 DOI: 10.3389/fmicb.2018.01451] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [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: 04/05/2018] [Accepted: 06/11/2018] [Indexed: 12/12/2022] Open
Abstract
Composition of the gut microbiota has been linked with human immunedeficiency virus (HIV)-infected patients on antiretroviral therapy (ART). Evidence suggests that ART-treated patients with poor CD4+ T-cell recovery have higher levels of microbial translocation and immune activation. However, the association of the gut microbiota and immune recovery remains unclear. We performed a cross-sectional study on 30 healthy controls (HC) and 61 HIV-infected individuals, including 15 immunological ART responders (IRs), 20 immunological ART non-responders (INRs) and 26 untreated individuals (VU). IR and INR groups were classified by CD4+ T-cell counts of ≥350 cells/mm3 and <350 cells/mm3 after 2 years of ART, respectively. Each subject’s gut microbiota composition was analyzed by metagenomics sequencing. Levels of CD4+ T cells, CD8+HLA-DR+ T cells and CD8+CD38+ T cells were measured by flow cytometry. We identified more Prevotella and fewer Bacteroides in HIV-infected individuals than in HC. Patients in INR group were enriched with Faecalibacterium prausnitzii, unclassified Subdoligranulum sp. and Coprococcus comes when compared with those in IR group. F. prausnitzii and unclassified Subdoligranulum sp. were overrepresented in individuals in VU group with CD4+ T-cell counts <350 cells/mm3. Moreover, we found that the relative abundance of unclassified Subdoligranulum sp. and C. comes were positively correlated with CD8+HLA-DR+ T-cell count and CD8+HLA-DR+/CD8+ percentage. Our study has shown that gut microbiota changes were associated with CD4+ T-cell counts and immune activation in HIV-infected subjects. Interventions to reverse gut dysbiosis and inhibit immune activation could be a new strategy for improving immune reconstitution of HIV-1-infected individuals.
Collapse
Affiliation(s)
- Wei Lu
- Department of Infectious Disease, Peking Union Medical College Hospital, Beijing, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuqing Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid School of Medicine, University of Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Fanhui Jing
- Department of Infectious Disease, Peking Union Medical College Hospital, Beijing, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Han
- Department of Infectious Disease, Peking Union Medical College Hospital, Beijing, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Na Lyu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Fei Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Xiaojing Song
- Department of Infectious Disease, Peking Union Medical College Hospital, Beijing, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Xie
- Department of Infectious Disease, Peking Union Medical College Hospital, Beijing, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhifeng Qiu
- Department of Infectious Disease, Peking Union Medical College Hospital, Beijing, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhu
- Department of Infectious Disease, Peking Union Medical College Hospital, Beijing, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bertrand Routy
- Division of Hematology and Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada.,Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illnesses Service Research Institute and Division of Hematology, McGill University Health Centre, Montreal, QC, Canada
| | - Taisheng Li
- Department of Infectious Disease, Peking Union Medical College Hospital, Beijing, China.,Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid School of Medicine, University of Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| |
Collapse
|