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Nong K, Qin X, Liu Z, Wang Z, Wu Y, Zhang B, Chen W, Fang X, Liu Y, Wang X, Zhang H. Potential effects and mechanism of flavonoids extract of Callicarpa nudiflora Hook on DSS-induced colitis in mice. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 128:155523. [PMID: 38489893 DOI: 10.1016/j.phymed.2024.155523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/27/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024]
Abstract
Callicarpa nudiflora Hook (C. nudiflora) is an anti-inflammatory, antimicrobial, antioxidant, and hemostatic ethnomedicine. To date, little has been reported regarding the activity of C. nudiflora against ulcerative colitis (UC). In this study, we investigated the effect of a flavonoid extract of C. nudiflora on Dextran Sulfate Sodium (DSS)-induced ulcerative colitis in mice. Mice in the treatment group (CNLF+DSS group) and drug-only (CNLF group) groups were administered 400 mg/kg of flavonoid extract of C. nudiflora leaf (CNLF), and drinking water containing 2.5 % DSS was given to the model and treatment groups. The symptoms of colitis were detected, relevant indicators were verified, intestinal barrier function was assessed, and the contents of the cecum were analyzed for intestinal microorganisms. The results showed that CNLF significantly alleviated the clinical symptoms and histological morphology of colitis in mice, inhibited the increase in pro-inflammatory factors (TNF-α, IL-6, IL-1β, and IFN-γ), and increased the level of IL-10. The expression of NF-κB and MAPK inflammatory signal pathway-related proteins (p-p65, p-p38, p-ERK, p-JNK) was regulated. The expression of tight junction proteins (ZO-1, OCLDN, and CLDN1) was increased, while the content of D-LA, DAO, and LPS was decreased. In addition, 16S rRNA sequencing showed that CNLF restored the gut microbial composition, and increased the relative abundance of Prevotellaceae, Intestinimonas butyriciproducens, and Barnesiella_intestinihominis. In conclusion, CNLF alleviated colitis by suppressing inflammation levels, improving intestinal barrier integrity, and modulating the intestinal microbiota, and therefore has promising future applications in the treatment of UC.
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Affiliation(s)
- Keyi Nong
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Xinyun Qin
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Zhineng Liu
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Zihan Wang
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Yijia Wu
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Bin Zhang
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Wanyan Chen
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Xin Fang
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Youming Liu
- Yibin Academy of Agricultural Sciences, Yibin 644600, China
| | - Xuemei Wang
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Haiwen Zhang
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China.
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Shi G, Zhu B, Wu Q, Dai J, Sheng N. Prenatal exposure to hexafluoropropylene oxide trimer acid (HFPO-TA) disrupts the maternal gut microbiome and fecal metabolome homeostasis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169330. [PMID: 38135079 DOI: 10.1016/j.scitotenv.2023.169330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Initially considered a "safe" substitute for perfluorooctanoic acid (PFOA), hexafluoropropylene oxide trimer acid (HFPO-TA) has been extensively used in the production of fluoropolymers for several years, leading to its environmental ubiquity and subsequent discovery of its significant bio-accumulative properties and toxicological effects. However, the specific impact of HFPO-TA on females, particularly those who are pregnant, remains unclear. In the present study, pregnant mice were exposed to 0.63 mg/kg/day HFPO-TA from gestational day (GD) 2 to GD 18. We then determined the potential effects of exposure on gut microbiota and fecal metabolites at GD 12 (mid-pregnancy) and GD 18 (late pregnancy). Our results revealed that, in addition to liver damage, HFPO-TA exposure during the specified window altered the structure and function of cecal gut microbiota. Notably, these changes showed the opposite trends at GD 12 and GD 18. Specifically, at GD 12, HFPO-TA exposure primarily resulted in the down-regulation of relative abundances within genera from the Bacteroidetes and Proteobacteria phyla, as well as associated Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. With extended exposure time, the down-regulated genera within Proteobacteria became significantly up-regulated, accompanied by corresponding up-regulation of human disease- and inflammation-associated pathways, suggesting that HFPO-TA exposure can induce intestinal inflammation and elevate the risk of infection during late pregnancy. Pearson correlation analysis revealed that disturbances in the gut microbiota were accompanied by abnormal fecal metabolite. Additionally, alterations in hormones related to the steroid hormone biosynthesis pathway at both sacrifice time indicated that HFPO-TA exposure might change the steroid hormone level of pregnant mice, but need further study. In conclusion, this study provides new insights into the mechanisms underlying HFPO-TA-induced adverse effects and increases awareness of potential persistent health risks to pregnant females.
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Affiliation(s)
- Guohui Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bao Zhu
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Sciences and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayin Dai
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Sciences and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Nan Sheng
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Sciences and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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Ishizaka A, Koga M, Mizutani T, Yamayoshi S, Iwatsuki-Horimoto K, Adachi E, Suzuki Y, Kawaoka Y, Yotsuyanagi H. Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV. BMC Microbiol 2024; 24:6. [PMID: 38172680 PMCID: PMC10763188 DOI: 10.1186/s12866-023-03157-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND People living with HIV (PLWH) with chronic inflammation may have an increasing risk for coronavirus disease 2019 (COVID-19) severity; however, the impact of their gut microbiota on COVID-19 is not fully elucidated. Here, we analyzed the temporal changes in the gut microbiota composition of hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (PLWH-CoV) and their correlation with COVID-19 severity. RESULT The 16S rRNA analysis results using stool samples (along the timeline from disease onset) from 12 hospitalized PLWH-CoV, whose median CD4 + T cell count was 671 cells/µl, were compared to those of 19 healthy people and 25 PLWH. Bacterial diversity in PLWH-CoV is not significantly different from that of healthy people and SARS-CoV-2 non-infected PLWH, but a significant difference in the microbiota diversity was observed in the classification according to the disease severity. Immediately after the disease onset, remarkable changes were observed in the gut microbiota of PLWH-CoV, and the changing with a decrease in some short-chain fatty acid-producing bacteria and an increase in colitis-related pathobiont. In the second week after disease onset, relative amounts of specific bacteria distinguished between disease severity. One month after the disease onset, dysbiosis of the gut microbiota persisted, and the number of Enterobacteriaceae, mainly Escherichia-Shigella, which is potentially pathogenic, increased and were enriched in patients who developed post-acute sequelae of COVID-19 (PASC). CONCLUSION The changes in the gut microbiota associated with SARS-CoV-2 infection observed in PLWH in this study indicated a persistent decrease in SCFA-producing bacteria and an intestinal environment with an increase in opportunistic pathogens associated with enteritis. This report demonstrates that the intestinal environment in PLWH tends to show delayed improvement even after COVID-19 recovery, and highlights the importance of the dysbiosis associated with SARS-CoV-2 infection as a potential factor in the COVID-19 severity and the PASC in PLWH.
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Affiliation(s)
- Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Taketoshi Mizutani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 6-2-3 Kashiwanoha, 277-0882, Kashiwa-shi, Chiba, Japan.
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Kiyoko Iwatsuki-Horimoto
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Pandemic Preparedness, Infection and Advanced Research Center, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan.
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, the University of Tokyo, Tokyo, Japan.
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan.
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Liu C, Pan K, Xu H, Song Y, Qi X, Lu Y, Jiang X, Liu H. The effects of enrofloxacin exposure on responses to oxidative stress, intestinal structure and intestinal microbiome community of largemouth bass (Micropterus salmoides). CHEMOSPHERE 2024; 348:140751. [PMID: 37992902 DOI: 10.1016/j.chemosphere.2023.140751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023]
Abstract
Antibiotic residues in the aquaculture environments may lead to antibiotic resistance, and potentially exert adverse effects on health of the non-target organisms and humans. In order to evaluate the effect of enrofloxacin of environmental concentrations on largemouth bass (Micropterus salmoides). Two hundred and seventy largemouth basses (with an average weight of 7.88 ± 0.60 g) were randomly divided into three groups, and separately exposed to 0, 1, 100 μg/L enrofloxacin (Control, ENR1, ENR100) for 30 days to detect the effect of enrofloxacin on the growth performance, oxidative stress, intestinal microbiota structure, inflammatory response and structure of the intestine. The results showed that ENR significantly reduced the final body weight (FBW) and weight gain rate (WGR), and increased feed conversion ratio (FCR) (P < 0.05). The histopathological analysis revealed that the villus width and muscular thickness of anterior intestine were significantly decreased with the increasing of enrofloxacin concentration. The activity of SOD was significantly increased at enrofloxacin stress, while CAT and POD activity were significantly decreased compared to control group (P < 0.05). The activities of lysozyme (LZM), alkaline phosphatase (AKP) and peroxidase (POD) in ENR1 was higher than that of control and ENR100 groups. Enrofloxacin treatment up-regulated the expression IL-1β and TNF-α, and down-regulated IL-10, and decreasing the expression level ZO-1, claudin-1, and occludin. Furthermore, the enrofloxacin treatment significantly decreased the intestinal bacterial diversity (P < 0.05). Exposure to 100 μg/L enrofloxacin obviously increased the relative abundance of Bacteroidota, Myxococcota, and Zixibacteria of fish gut, and reduced Firmicutes; 1 μg/L enrofloxacin considerably increased Bacteroidota, Myxococcota, and Actinobacteria, and reduced Firmicutes. The relative abundance of DTB120 and Elusimicrobiota was positively correlated with the occludin and claudin-1 gene. Taken together, exposure to enrofloxacin inhibited the growth of largemouth bass, influenced intestinal health, and induced dysbiosis of the intestinal microbiota.
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Affiliation(s)
- Chengrong Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kuiquan Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hongzhou Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanzhen Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoyu Qi
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yitong Lu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinxin Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Haixia Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Kong C, Pan T, Chen X, Junaid M, Liao H, Gao D, Wang Q, Liu W, Wang X, Wang J. Exposure to polystyrene nanoplastics and PCB77 induced oxidative stress, histopathological damage and intestinal microbiota disruption in white hard clam Meretrix lyrata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167125. [PMID: 37722427 DOI: 10.1016/j.scitotenv.2023.167125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
The toxic effects of organic pollutants and nanoplastics on fish have been extensively studied, but there is limited research available on their combined toxicity to bivalves. This research aimed to investigate the accumulation and ecotoxicological impacts such as antioxidant capacity, histopathology and intestinal microbiota in white hard clam Meretrix lyrata, resulting from 7 days of single and mixture exposure to 3,3',4,4'-tetrachlorobiphenyl (PCB77, 0.1 mg/L) and polystyrene nanoplastics (PS-NPs, 80 nm, 1 mg/L). Our findings revealed that PS-NPs accumulated in various tissues such as the intestine, gill, mantle, foot, and siphon. And when compared to the PCB-PSNPs (PP) co-exposure group, the intestinal fluorescence intensity mediated by plastic particles in the PS-NPs (PS group) was significantly higher. The gill, digestive gland, and intestine were all damaged to varying extent by single exposure to PS-NPs or PCB77, according to histopathological analysis, which was aggravated by PP group. Moreover, the co-exposure induced a higher level of oxidative stress, which reflected by increase of activities of superoxide dismutase, catalase, glutamate oxaloacetate transaminase and glutamic-pyruvic transaminase and malondialdehyde content. In addition, the intestine microbial composition was dramatically altered by the combined exposure, reducing the abundance of probiotics such as Firmicutes, thereby posing a great threat to the health and metabolism of M. lyrata. In conclusion, our findings showed that PS-NPs and PCB77 co-exposure induced a higher toxicity to M. lyrata, including histopathological changes, altered antioxidant capacity and intestinal microbiota disruption. This study provides novel insights into PCB77 and PS-NPs' combined toxicity to marine organisms and its underlying molecular mechanisms of ecotoxicological effects.
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Affiliation(s)
- Chunmiao Kong
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Ting Pan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xikun Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Junaid
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hongping Liao
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Dandan Gao
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qiuping Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Wanjing Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xu Wang
- Guangdong Provincial Key Laboratory of Quality&Safety Risk Assessment for Agro-products, Institute of Quality Standard and Monitoring Technology for Agro-products of Guangdong Academy of Agricultural Science, Guangzhou 510642, China.
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning 530007, China.
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Che Y, Wang N, Ma Q, Liu J, Xu Z, Li Q, Wang J, Sun Y. Microbial characterization of the nasal cavity in patients with allergic rhinitis and non-allergic rhinitis. Front Cell Infect Microbiol 2023; 13:1166389. [PMID: 37180436 PMCID: PMC10166850 DOI: 10.3389/fcimb.2023.1166389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction Although recent studies have shown that the human microbiome is involved in the pathogenesis of allergic diseases, the impact of microbiota on allergic rhinitis (AR) and non-allergic rhinitis (nAR) has not been elucidated. The aim of this study was to investigate the differences in the composition of the nasal flora in patients with AR and nAR and their role in the pathogenesis. Method From February to September 2022, 35 AR patients and 35 nAR patients admitted to Harbin Medical University's Second Affiliated Hospital, as well as 20 healthy subjects who underwent physical examination during the same period, were subjected to 16SrDNA and metagenomic sequencing of nasal flora. Results The microbiota composition of the three groups of study subjects differs significantly. The relative abundance of Vibrio vulnificus and Acinetobacter baumanni in the nasal cavity of AR patients was significantly higher when compared to nAR patients, while the relative abundance of Lactobacillus murinus, Lactobacillus iners, Proteobacteria, Pseudomonadales, and Escherichia coli was lower. In addition, Lactobacillus murinus and Lacttobacillus kunkeei were also negatively correlated with IgE, while Lacttobacillus kunkeei was positively correlated with age. The relative distribution of Faecalibacterium was higher in moderate than in severe AR patients. According to KEGG functional enrichment annotation, ICMT(protein-S-isoprenylcysteine O-methyltransferase,ICMT) is an AR microbiota-specific enzyme that plays a role, while glycan biosynthesis and metabolism are more active in AR microbiota. For AR, the model containing Parabacteroides goldstemii, Sutterella-SP-6FBBBBH3, Pseudoalteromonas luteoviolacea, Lachnospiraceae bacterium-615, and Bacteroides coprocola had the highest the area under the curve (AUC), which was 0.9733(95%CI:0.926-1.000) in the constructed random forest prediction model. The largest AUC for nAR is 0.984(95%CI:0.949-1.000) for the model containing Pseudomonas-SP-LTJR-52, Lachnospiraceae bacterium-615, Prevotella corporis, Anaerococcus vaginalis, and Roseburia inulinivorans. Conclusion In conclusion, patients with AR and nAR had significantly different microbiota profiles compared to healthy controls. The results suggest that the nasal microbiota may play a key role in the pathogenesis and symptoms of AR and nAR, providing us with new ideas for the treatment of AR and nAR.
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Affiliation(s)
| | | | | | | | | | | | | | - Yanan Sun
- *Correspondence: Jingting Wang, ; Yanan Sun,
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DeSantis TZ, Cardona C, Narayan NR, Viswanatham S, Ravichandar D, Wee B, Chow CE, Iwai S. StrainSelect: A novel microbiome reference database that disambiguates all bacterial strains, genome assemblies and extant cultures worldwide. Heliyon 2023; 9:e13314. [PMID: 36814618 PMCID: PMC9939595 DOI: 10.1016/j.heliyon.2023.e13314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/01/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Motivation: Microbial metagenomic profiling software and databases are advancing rapidly for development of novel disease biomarkers and therapeutics yet three problems impede analyses: 1) the conflation of "genome assembly" and "strain" in reference databases; 2) difficulty connecting DNA biomarkers to a procurable strain for laboratory experimentation; and 3) absence of a comprehensive and unified strain-resolved reference database for integrating both shotgun metagenomics and 16S rRNA gene data. Results: We demarcated 681,087 strains, the largest collection of its kind, by filtering public data into a knowledge graph of vertices representing contiguous DNA sequences, genome assemblies, strain monikers and bio-resource center (BRC) catalog numbers then adding inter-vertex edges only for synonyms or direct derivatives. Surprisingly, for 10,043 important strains, we found replicate RefSeq genome assemblies obstructing interpretation of database searches. We organized each strain into eight taxonomic ranks with bootstrap confidence inversely correlated with genome assembly contamination. The StrainSelect database is suited for applications where a taxonomic, functional or procurement reference is needed for shotgun or amplicon metagenomics since 636,568 strains have at least one 16S rRNA gene, 245,005 have at least one annotated genome assembly, and 36,671 are procurable from at least one BRC. The database overcomes all three aforementioned problems since it disambiguates strains from assemblies, locates strains at BRCs, and unifies a taxonomic reference for both 16S rRNA and shotgun metagenomics. Availability: The StrainSelect database is available in igraph and tabular vertex-edge formats compatible with Neo4J. Dereplicated MinHash and fasta databases are distributed for sourmash and usearch pipelines at http://strainselect.secondgenome.com. Contact:todd.desantis@gmail.com. Supplementary information: Supplementary data are available online.
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Affiliation(s)
- Todd Z. DeSantis
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA,Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany,Corresponding author at: Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA.
| | - Cesar Cardona
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Nicole R. Narayan
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Satish Viswanatham
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Divya Ravichandar
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | - Brendan Wee
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
| | | | - Shoko Iwai
- Second Genome, Inc., 1000 Marina Blvd, Suite 500, Brisbane, CA, 94005, USA
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Wu Y, Peng X, Li X, Li D, Tan Z, Yu R. Sex hormones influence the intestinal microbiota composition in mice. Front Microbiol 2022; 13:964847. [PMID: 36386696 PMCID: PMC9659915 DOI: 10.3389/fmicb.2022.964847] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/26/2022] [Indexed: 08/26/2023] Open
Abstract
Sex hormone secretion difference is one of the main reasons for sexually dimorphic traits in animals, which affects the dimorphism of the intestinal microbiota; however, their interaction is still unknown. Intestinal mucosa-associated microbiota (MAM) and intestinal luminal content microbiota (LM) belong to two different habitats according to the difference in interactions between bacteria and host intestinal epithelium/nutrients. To clarify the sexually dimorphic characteristics of MAM and LM and their correlation with sex hormones, 12 specific pathogen-free (SPF) Kunming mice from the same nest were fed separately according to sex. After 8 weeks, samples from the male intestinal mucosa group (MM group), the female intestinal mucosa group (FM group), the male intestinal content group (MC group), and the female intestinal content group (FC group) were collected and then, the next-generation sequencing of 16S ribosomal ribonucleic acid (rRNA) gene was performed. Our results showed that the sexual dimorphism of MAM was more obvious than that of LM and the relative abundance of Muribaculaceae, Turicibacter, and Parasutterella was significantly higher in the FM group than in the MM group (p < 0.001, p < 0.05, p < 0.05). Next, we measured the level of serum sex hormones in mice and calculated the correlation coefficient between major bacteria and sex hormones. The results showed that the correlation between MAM and sex hormones was more prominent, and finally, three bacterial genera (Muribaculaceae, Turicibacter, and Parasutterella) were obtained, which could better represent the relationship between sexual dimorphism and sex hormones. The abundance of Parasutterella is positively and negatively correlated with estradiol and testosterone (T), respectively, which may be related to the differences in the metabolism of bile acid and glucose. A decrease in the abundance of Turicibacter is closely related to autism. Our results show that the abundance of Turicibacter is negatively and positively correlated with T and estradiol, respectively, which can provide a hint for the prevalence of male autism. In conclusion, it is proposed in our study that intestinal microbiota is probably the biological basis of physiological and pathological differences due to sex, and intestinal MAM can better represent the sexual dimorphism of mice.
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Affiliation(s)
- Yi Wu
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
- Hunan Key Laboratory of Chinese Medicine Prescription and Syndromes Translational Medicine, Changsha, China
| | - Xinxin Peng
- Department of Pediatrics, The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Xiaoya Li
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
- Hunan Key Laboratory of Chinese Medicine Prescription and Syndromes Translational Medicine, Changsha, China
| | - Dandan Li
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
- Hunan Key Laboratory of Chinese Medicine Prescription and Syndromes Translational Medicine, Changsha, China
| | - Zhoujin Tan
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
- Hunan Key Laboratory of Chinese Medicine Prescription and Syndromes Translational Medicine, Changsha, China
| | - Rong Yu
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
- Hunan Key Laboratory of Chinese Medicine Prescription and Syndromes Translational Medicine, Changsha, China
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Khorsand B, Asadzadeh Aghdaei H, Nazemalhosseini-Mojarad E, Nadalian B, Nadalian B, Houri H. Overrepresentation of Enterobacteriaceae and Escherichia coli is the major gut microbiome signature in Crohn’s disease and ulcerative colitis; a comprehensive metagenomic analysis of IBDMDB datasets. Front Cell Infect Microbiol 2022; 12:1015890. [PMID: 36268225 PMCID: PMC9577114 DOI: 10.3389/fcimb.2022.1015890] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Objectives A number of converging strands of research suggest that the intestinal Enterobacteriaceae plays a crucial role in the development and progression of inflammatory bowel disease (IBD), however, the changes in the abundance of Enterobacteriaceae species and their related metabolic pathways in Crohn’s disease (CD) and ulcerative colitis (UC) compared to healthy people are not fully explained by comprehensive comparative metagenomics analysis. In the current study, we investigated the alternations of the Enterobacterales population in the gut microbiome of patients with CD and UC compared to healthy subjects. Methods Metagenomic datasets were selected from the Integrative Human Microbiome Project (HMP2) through the Inflammatory Bowel Disease Multi’omics Database (IBDMDB). We performed metagenome-wide association studies on fecal samples from 191 CD patients, 132 UC patients, and 125 healthy controls (HCs). We used the metagenomics dataset to study bacterial community structure, relative abundance, differentially abundant bacteria, functional analysis, and Enterobacteriaceae-related biosynthetic pathways. Results Compared to the gut microbiome of HCs, six Enterobacteriaceae species were significantly elevated in both CD and UC patients, including Escherichia coli, Klebsiella variicola, Klebsiella quasipneumoniae, Klebsiella pneumoniae, Proteus mirabilis, Citrobacter freundii, and Citrobacter youngae, while Klebsiella oxytoca, Morganella morganii, and Citrobacter amalonaticus were uniquely differentially abundant and enriched in the CD cohort. Four species were uniquely differentially abundant and enriched in the UC cohort, including Citrobacter portucalensis, Citrobacter pasteurii, Citrobacter werkmanii, and Proteus hauseri. Our analysis also showed a dramatically increased abundance of E. coli in their intestinal bacterial community. Biosynthetic pathways of aerobactin siderophore, LPS, enterobacterial common antigen, nitrogen metabolism, and sulfur relay systems encoded by E. coli were significantly elevated in the CD samples compared to the HCs. Menaquinol biosynthetic pathways were associated with UC that belonged to K. pneumoniae strains. Conclusions In conclusion, compared with healthy people, the taxonomic and functional composition of intestinal bacteria in CD and UC patients was significantly shifted to Enterobacteriaceae species, mainly E. coli and Klebsiella species.
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Affiliation(s)
- Babak Khorsand
- Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahareh Nadalian
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Banafsheh Nadalian
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Houri
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Hamidreza Houri,
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10
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Watanabe Y, Mizushima T, Okumura R, Fujino S, Ogino T, Miyoshi N, Takahashi H, Uemura M, Matsuda C, Yamamoto H, Takeda K, Doki Y, Eguchi H. Fecal Stream Diversion Changes Intestinal Environment, Modulates Mucosal Barrier, and Attenuates Inflammatory Cells in Crohn's Disease. Dig Dis Sci 2022; 67:2143-2157. [PMID: 34041649 DOI: 10.1007/s10620-021-07060-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/11/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND The intestinal environment plays important roles in mucosal barrier homeostasis and intestinal inflammation, as clarified in studies using experimental animals but not in humans. AIMS We investigated whether environmental changes in the fecal stream cause phenotypic changes in the human mucosal barrier. METHODS We obtained human ileal samples after fecal stream diversions in patients with rectal cancer or Crohn's disease. We investigated the bacterial load and diversity in the human defunctioned ileum, defined as the anal side of the ileum relative to the ileostomy. We also examined the epithelium and lamina propria cell phenotypes in the defunctioned ileum. RESULTS After fecal stream diversion, bacterial loads decreased significantly in the defunctioned ileum. Based on the Chao1, Shannon, and observed species indices, the diversity of mucosa-associated microbiota was lower in the defunctioned ileum than in the functional ileum. Moreover, the healthy defunctioned ileum showed reductions in villous height, goblet cell numbers, and Ki-67+ cell numbers. Additionally, interferon-γ+, interleukin-17+, and immunoglobulin A+ cell abundance in the lamina propria decreased. After the intestinal environment was restored with an ileostomy closure, the impaired ileal homeostasis recovered. The defunctioned ileum samples from patients with Crohn's disease also showed reductions in interferon-γ+ and interleukin-17+ cell numbers. CONCLUSIONS Fecal stream diversion reduced the abundance and diversity of intestinal bacteria. It also altered the intestinal mucosal barrier, similar to the alterations observed in germ-free animals. In patients with Crohn's disease, Th1 and Th17 cell numbers were attenuated, which suggests that the host-microbiome interaction is important in disease pathogenesis.
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Affiliation(s)
- Yoshifumi Watanabe
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Department of Therapeutics for Inflammatory Bowel Diseases, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan. .,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 1-1 Yamadaoka, Suita, Osaka, Japan.
| | - Ryu Okumura
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan
| | - Shiki Fujino
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takayuki Ogino
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Norikatsu Miyoshi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hidekazu Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Chu Matsuda
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hirofumi Yamamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kiyoshi Takeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 1-1 Yamadaoka, Suita, Osaka, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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11
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Glover JS, Browning BD, Ticer TD, Engevik AC, Engevik MA. Acinetobacter calcoaceticus is Well Adapted to Withstand Intestinal Stressors and Modulate the Gut Epithelium. Front Physiol 2022; 13:880024. [PMID: 35685287 PMCID: PMC9170955 DOI: 10.3389/fphys.2022.880024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/12/2022] [Indexed: 12/22/2022] Open
Abstract
Background: The gastrointestinal tract has been speculated to serve as a reservoir for Acinetobacter, however little is known about the ecological fitness of Acinetobacter strains in the gut. Likewise, not much is known about the ability of Acinetobacter to consume dietary, or host derived nutrients or their capacity to modulate host gene expression. Given the increasing prevalence of Acinetobacter in the clinical setting, we sought to characterize how A. calcoaceticus responds to gut-related stressors and identify potential microbe-host interactions. Materials and Methods: To accomplish these aims, we grew clinical isolates and commercially available strains of A. calcoaceticus in minimal media with different levels of pH, osmolarity, ethanol and hydrogen peroxide. Utilization of nutrients was examined using Biolog phenotypic microarrays. To examine the interactions of A. calcoaceticus with the host, inverted murine organoids where the apical membrane is exposed to bacteria, were incubated with live A. calcoaceticus, and gene expression was examined by qPCR. Results: All strains grew modestly at pH 6, 5 and 4; indicating that these strains could tolerate passage through the gastrointestinal tract. All strains had robust growth in 0.1 and 0.5 M NaCl concentrations which mirror the small intestine, but differences were observed between strains in response to 1 M NaCl. Additionally, all strains tolerated up to 5% ethanol and 0.1% hydrogen peroxide. Biolog phenotypic microarrays revealed that A. calcoaceticus strains could use a range of nutrient sources, including monosaccharides, disaccharides, polymers, glycosides, acids, and amino acids. Interestingly, the commercially available A. calcoaceticus strains and one clinical isolate stimulated the pro-inflammatory cytokines Tnf, Kc, and Mcp-1 while all strains suppressed Muc13 and Muc2. Conclusion: Collectively, these data demonstrate that A. calcoaceticus is well adapted to dealing with environmental stressors of the gastrointestinal system. This data also points to the potential for Acinetobacter to influence the gut epithelium.
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Affiliation(s)
- Janiece S. Glover
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Brittney D. Browning
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Taylor D. Ticer
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States
| | - Amy C. Engevik
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Melinda A. Engevik
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States
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12
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Kenna JE, Chua EG, Bakeberg M, Tay A, McGregor S, Gorecki A, Horne M, Marshall B, Mastaglia FL, Anderton RS. Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson's Disease Cohort. Front Neurosci 2021; 15:756951. [PMID: 34776854 PMCID: PMC8588830 DOI: 10.3389/fnins.2021.756951] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/01/2021] [Indexed: 01/03/2023] Open
Abstract
Background: There has been increasing recognition of the importance of the gut microbiome in Parkinson's disease (PD), but the influence of geographic location has received little attention. The present study characterized the gut microbiota and associated changes in host metabolic pathways in an Australian cohort of people with PD (PwP). Methods: The study involved recruitment and assessment of 87 PwP from multiple Movement Disorders Clinics in Australia and 47 healthy controls. Illumina sequencing of the V3 and V4 regions of the 16S rRNA gene was used to distinguish inter-cohort differences in gut microbiota; KEGG analysis was subsequently performed to predict functional changes in host metabolic pathways. Results: The current findings identified significant differences in relative abundance and diversity of microbial operational taxonomic units (OTUs), and specific bacterial taxa between PwP and control groups. Alpha diversity was significantly reduced in PwP when compared to controls. Differences were found in two phyla (Synergistetes and Proteobacteria; both increased in PwP), and five genera (Colidextribacter, Intestinibacter, Kineothrix, Agathobaculum, and Roseburia; all decreased in PwP). Within the PD cohort, there was no association identified between microbial composition and gender, constipation or use of gastrointestinal medication. Furthermore, KEGG analysis identified 15 upregulated and 11 downregulated metabolic pathways which were predicted to be significantly altered in PwP. Conclusion: This study provides the first comprehensive characterization of the gut microbiome and predicted functional metabolic effects in a southern hemisphere PD population, further exploring the possible mechanisms whereby the gut microbiota may exert their influence on this disease, and providing evidence for the incorporation of such data in future individualized therapeutic strategies.
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Affiliation(s)
- Jade E Kenna
- School of Medicine, The University of Western Australia, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,Centre for Clinical Neurosciences and Neurological Research, St. Vincent's Hospital Melbourne, Fitzroy, VIC, Australia.,Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Eng Guan Chua
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.,Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, WA, Australia
| | - Megan Bakeberg
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,School of Medicine, University of Notre Dame Australia, Fremantle, WA, Australia
| | - Alfred Tay
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.,Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, WA, Australia
| | - Sarah McGregor
- Centre for Clinical Neurosciences and Neurological Research, St. Vincent's Hospital Melbourne, Fitzroy, VIC, Australia
| | - Anastazja Gorecki
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.,School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Malcolm Horne
- Centre for Clinical Neurosciences and Neurological Research, St. Vincent's Hospital Melbourne, Fitzroy, VIC, Australia.,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Barry Marshall
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.,Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, WA, Australia
| | - Frank L Mastaglia
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Ryan S Anderton
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,Institute for Health Research, University of Notre Dame Australia, Fremantle, WA, Australia.,School of Nursing, Midwifery, Health Sciences and Physiotherapy, The University of Notre Dame Australia, Fremantle, WA, Australia
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