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Branton WG, Fernandes JP, Mohammadzadeh N, Doan MAL, Laman JD, Gelman BB, Fagrouch Z, Kondova I, Mooij P, Koopman G, Power C. Microbial molecule ingress promotes neuroinflammation and brain CCR5 expression in persons with HIV-associated neurocognitive disorders. Brain Behav Immun 2023; 107:110-123. [PMID: 36202168 DOI: 10.1016/j.bbi.2022.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Systemic inflammation accompanies HIV-1 infection, resulting in microbial translocation from different tissues. We investigated interactions between lentivirus infections, neuroinflammation and microbial molecule presence in the brain. METHODS Brain tissues from adult humans with (n = 22) and without HIV-1 (n = 11) infection as well as adult nonhuman primates (NHPs) with (n = 11) and without (n = 4) SIVmac251 infection were investigated by RT-PCR/ddPCR, immunofluorescence and western blotting. Studies of viral infectivity, host immune gene expression and viability were performed in primary human neural cells. FINDINGS Among NHPs, SIV DNA quantitation in brain showed increased levels among animals with SIV encephalitis (n = 5) that was associated with bacterial genomic copy number as well as CCR5 and CASP1 expression in brain. Microbial DnaK and peptidoglycan were immunodetected in brains from uninfected and SIV-infected animals, chiefly in glial cells. Human microglia infected by HIV-1 showed increased p24 production after exposure to peptidoglycan that was associated CCR5 induction. HIV-1 Vpr application to human neurons followed by peptidoglycan exposure resulted in reduced mitochondrial function and diminished beta-III tubulin expression. In human brains, bacterial genome copies (250-550 copies/gm of tissue), were correlated with increased bacterial rRNA and GroEL transcript levels in patients with HIV-associated neurocognitive disorders (HAND). Glial cells displayed microbial GroEL and peptidoglycan immunoreactivity accompanied by CCR5 induction in brains from patients with HAND. INTERPRETATION Increased microbial genomes and proteins were evident in brain tissues from lentivirus-infected humans and animals and associated with neurological disease. Microbial molecule translocation into the brain might exacerbate neuroinflammatory disease severity and represent a driver of lentivirus-associated brain disease.
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Affiliation(s)
- William G Branton
- Departments of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Jason P Fernandes
- Medical Microbiology & Immunology, University of Alberta, Edmonton, AB, Canada
| | | | - Mathew A L Doan
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| | - Jon D Laman
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
| | - Benjamin B Gelman
- Departments of Pathology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Zahra Fagrouch
- Department of Virology and Animal Science Department, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ivanela Kondova
- Department of Virology and Animal Science Department, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Petra Mooij
- Department of Virology and Animal Science Department, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Gerrit Koopman
- Department of Virology and Animal Science Department, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Christopher Power
- Departments of Medicine, University of Alberta, Edmonton, AB, Canada; Medical Microbiology & Immunology, University of Alberta, Edmonton, AB, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada.
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Correcting the Estimation of Viral Taxa Distributions in Next-Generation Sequencing Data after Applying Artificial Neural Networks. Genes (Basel) 2021; 12:genes12111755. [PMID: 34828361 PMCID: PMC8624964 DOI: 10.3390/genes12111755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Estimating the taxonomic composition of viral sequences in a biological samples processed by next-generation sequencing is an important step in comparative metagenomics. Mapping sequencing reads against a database of known viral reference genomes, however, fails to classify reads from novel viruses whose reference sequences are not yet available in public databases. Instead of a mapping approach, and in order to classify sequencing reads at least to a taxonomic level, the performance of artificial neural networks and other machine learning models was studied. Taxonomic and genomic data from the NCBI database were used to sample labelled sequencing reads as training data. The fitted neural network was applied to classify unlabelled reads of simulated and real-world test sets. Additional auxiliary test sets of labelled reads were used to estimate the conditional class probabilities, and to correct the prior estimation of the taxonomic distribution in the actual test set. Among the taxonomic levels, the biological order of viruses provided the most comprehensive data base to generate training data. The prediction accuracy of the artificial neural network to classify test reads to their viral order was considerably higher than that of a random classification. Posterior estimation of taxa frequencies could correct the primary classification results.
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Draft Genome Sequence of Phocine Herpesvirus 1 Isolated from the Brain of a Harbor Seal. Microbiol Resour Announc 2019; 8:8/14/e00210-19. [PMID: 30948468 PMCID: PMC6449559 DOI: 10.1128/mra.00210-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Phocine herpesvirus 1 (PhHV-1) is a viral pathogen with high prevalence, morbidity, and mortality in harbor seals. In this study, we used a metagenomic approach to assemble the PhHV-1 genome from the brain tissue of a harbor seal. Phocine herpesvirus 1 (PhHV-1) is a viral pathogen with high prevalence, morbidity, and mortality in harbor seals. In this study, we used a metagenomic approach to assemble the PhHV-1 genome from the brain tissue of a harbor seal. Here, we present a 119-kb draft genome of PhHV-1 comprising 76 open reading frames.
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Fakhour S, Ambroise J, Renoz F, Foray V, Gala JL, Hance T. A large-scale field study of bacterial communities in cereal aphid populations across Morocco. FEMS Microbiol Ecol 2019; 94:4810747. [PMID: 29346623 DOI: 10.1093/femsec/fiy003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/15/2018] [Indexed: 11/13/2022] Open
Abstract
Insects are frequently associated with bacteria that can have significant ecological and evolutionary impacts on their hosts. To date, few studies have examined the influence of environmental factors to microbiome composition of aphids. The current work assessed the diversity of bacterial communities of five cereal aphid species (Sitobion avenae, Rhopalosiphum padi, R. maidis, Sipha maydis and Diuraphis noxia) collected across Morocco, covering a wide range of environmental conditions. We aimed to test whether symbiont combinations are host or environment specific. Deep 16S rRNA sequencing enabled us to identify 17 bacterial operational taxonomic units (OTUs). The obligate symbiont Buchnera aphidicola was represented by five OTUs with multiple haplotypes in many single samples. Facultative endosymbionts were presented by a high prevalence of Regiella insecticola and Serratia symbiotica in S. avenae and Si. maydis, respectively. In addition to these symbiotic partners, Pseudomonas, Acinetobacter, Pantoea, Erwinia and Staphyloccocus were also identified in aphids, suggesting that the aphid microbiome is not limited to the presence of endosymbiotic bacteria. Beside a significant association between host species and bacterial communities, an inverse correlation was also found between altitude and α-diversity. Overall, our results support that symbiont combinations are mainly host specific.
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Affiliation(s)
- Samir Fakhour
- National Institute of Agronomic Research (INRA), Km 18, 23000 Béni-Mellal, Morocco.,Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, 1348 Louvain-La-Neuve, Belgium
| | - Jérôme Ambroise
- Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, 1200 Woluwe-Saint-Lambert, Belgium
| | - François Renoz
- Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, 1348 Louvain-La-Neuve, Belgium
| | - Vincent Foray
- Centre de Recherche de Biologie cellulaire de Montpellier, (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, Montpellier 34293, France
| | - Jean-Luc Gala
- Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain, 1200 Woluwe-Saint-Lambert, Belgium
| | - Thierry Hance
- Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, 1348 Louvain-La-Neuve, Belgium
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Shen H, Zang Y, Song K, Ma Y, Dai T, Serwadda A. A Meta-Transcriptomics Survey Reveals Changes in the Microbiota of the Chinese Mitten Crab Eriocheir sinensis Infected with Hepatopancreatic Necrosis Disease. Front Microbiol 2017; 8:732. [PMID: 28491058 PMCID: PMC5405120 DOI: 10.3389/fmicb.2017.00732] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/10/2017] [Indexed: 12/19/2022] Open
Abstract
Infection of the freshwater Chinese mitten crab Eriocheir sinensis with hepatopancreatic necrosis disease (HPND) has been a major problem in the crab-cultivated Chinese Province of Jiangsu since 2015. To explore the etiology of HPND, meta-transcriptomic libraries of the hepatopancreata from crabs with and without HPND were constructed. Comparison analyses showed that there were no statistically significant differences in viral and microsporidial communities in the hepatopancreata of diseased and healthy crabs. Bacteroidetes, Proteobacteria, and Firmicutes were the most dominant bacterial phyla in the hepatopancreata of healthy crabs, with a combined prevalence of 93%. However, a decrease in bacterial diversity and a striking shift in the microbial composition were found in the hepatopancreata of crabs infected with HPND. Tenericutes was the most prevalent bacterial phylum in diseased crabs (31.82%), whereas its prevalence was low in healthy crabs (0.02%). By contrast, the prevalence of Bacteroidetes was significantly lower in crabs with HPND (3.49%) than in crabs without HPND (41.04%). We also found that the prevalence of Actinobacteria was higher in crabs with HPND (16.70%) than in crabs without the disease (4.03%). The major bacterial family within the Tenericutes phylum in crabs with HPND was detected by polymerase chain reaction and determined to be Mycoplasmataceae. In conclusion, there were striking changes in the microbiota of diseased and healthy crabs. Specifically, the prevalence of bacteria belonging to Tenericutes and Actinobacteria phyla increased, whereas the prevalence of bacteria belonging to the Bacteroidetes phylum decreased in crabs with HPND, clearly pointing to an association with HPND.
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Affiliation(s)
- Huaishun Shen
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesWuxi, China.,Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Yanan Zang
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Kun Song
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Yuanchao Ma
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Tianhao Dai
- Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
| | - Ali Serwadda
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesWuxi, China.,Wuxi Fisheries College, Nanjing Agricultural UniversityNanjing, China
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Rosales SM, Vega Thurber RL. Brain transcriptomes of harbor seals demonstrate gene expression patterns of animals undergoing a metabolic disease and a viral infection. PeerJ 2016; 4:e2819. [PMID: 28028481 PMCID: PMC5182994 DOI: 10.7717/peerj.2819] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/22/2016] [Indexed: 11/20/2022] Open
Abstract
Diseases of marine mammals can be difficult to diagnose because of their life history and protected status. Stranded marine mammals have been a particularly useful resource to discover and comprehend the diseases that plague these top predators. Additionally, advancements in high-throughput sequencing (HTS) has contributed to the discovery of novel pathogens in marine mammals. In this study, we use a combination of HTS and stranded harbor seals (Phoca vitulina) to better understand a known and unknown brain disease. To do this, we used transcriptomics to evaluate brain tissues from seven neonatal harbor seals that expired from an unknown cause of death (UCD) and compared them to four neonatal harbor seals that had confirmed phocine herpesvirus (PhV-1) infections in the brain. Comparing the two disease states we found that UCD animals showed a significant abundance of fatty acid metabolic transcripts in their brain tissue, thus we speculate that a fatty acid metabolic dysregulation contributed to the death of these animals. Furthermore, we were able to describe the response of four young harbor seals with PhV-1 infections in the brain. PhV-1 infected animals showed a significant ability to mount an innate and adaptive immune response, especially to combat viral infections. Our data also suggests that PhV-1 can hijack host pathways for DNA packaging and exocytosis. This is the first study to use transcriptomics in marine mammals to understand host and viral interactions and assess the death of stranded marine mammals with an unknown disease. Furthermore, we show the value of applying transcriptomics on stranded marine mammals for disease characterization.
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Affiliation(s)
- Stephanie M Rosales
- Department of Microbiology, Oregon State University , Corvallis , OR , United States
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Branton WG, Lu JQ, Surette MG, Holt RA, Lind J, Laman JD, Power C. Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis. Sci Rep 2016; 6:37344. [PMID: 27892518 PMCID: PMC5125007 DOI: 10.1038/srep37344] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/26/2016] [Indexed: 12/14/2022] Open
Abstract
Microbial communities reside in healthy tissues but are often disrupted during disease. Bacterial genomes and proteins are detected in brains from humans, nonhuman primates, rodents and other species in the absence of neurological disease. We investigated the composition and abundance of microbiota in frozen and fixed autopsied brain samples from patients with multiple sclerosis (MS) and age- and sex-matched nonMS patients as controls, using neuropathological, molecular and bioinformatics tools. 16s rRNA sequencing revealed Proteobacteria to be the dominant phylum with restricted diversity in cerebral white matter (WM) from MS compared to nonMS patients. Both clinical groups displayed 1,200–1,400 bacterial genomes/cm3 and low bacterial rRNA:rDNA ratios in WM. RNAseq analyses showed a predominance of Proteobacteria in progressive MS patients’ WM, associated with increased inflammatory gene expression, relative to a broader range of bacterial phyla in relapsing-remitting MS patients’ WM. Although bacterial peptidoglycan (PGN) and RNA polymerase beta subunit immunoreactivities were observed in all patients, PGN immunodetection was correlated with demyelination and neuroinflammation in MS brains. Principal component analysis revealed that demyelination, PGN and inflammatory gene expression accounted for 86% of the observed variance. Thus, inflammatory demyelination is linked to an organ-specific dysbiosis in MS that could contribute to underlying disease mechanisms.
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Affiliation(s)
- W G Branton
- Department of Medicine, University of Alberta, Edmonton AB Canada.,Department of Laboratory Medicine &Pathology, University of Alberta, Edmonton AB Canada
| | - J Q Lu
- Department of Laboratory Medicine &Pathology, University of Alberta, Edmonton AB Canada.,Department of Psychiatry, University of Alberta, Edmonton AB Canada
| | - M G Surette
- Department of Medicine, McMaster University, Hamilton ON Canada
| | - R A Holt
- Genome Sciences Centre, Vancouver BC, Canada
| | - J Lind
- Department of Neurosciences, Section of Medical Physiology, Faculty of Medical Sciences, University Medical Center Groningen, University of Groningen, Groningen Netherlands
| | - J D Laman
- Multiple Sclerosis Centre, University of Alberta, Edmonton AB Canada
| | - C Power
- Department of Medicine, University of Alberta, Edmonton AB Canada.,Department of Laboratory Medicine &Pathology, University of Alberta, Edmonton AB Canada.,Department of Neurosciences, Section of Medical Physiology, Faculty of Medical Sciences, University Medical Center Groningen, University of Groningen, Groningen Netherlands
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Rosales SM, Vega Thurber R. Correction: Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event. PLoS One 2015; 10:e0146208. [PMID: 26713443 PMCID: PMC4699895 DOI: 10.1371/journal.pone.0146208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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