1
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Sjövall A, Mustanoja E, Lyyski A, Auvinen P, Silvola J, Aarnisalo A, Pätäri-Sampo A, Laulajainen-Hongisto A. Microbiome of the External Auditory Canal: Changes After Long-Term Hearing Aid Use. Otol Neurotol 2024; 45:696-702. [PMID: 38769078 DOI: 10.1097/mao.0000000000004198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
OBJECTIVE To investigate the microbial changes of long-term hearing aid use culture independently. STUDY DESIGN Cross-sectional study. PATIENTS Fifty long-term hearing aid users and 80 volunteer controls with asymptomatic ears. INTERVENTION External auditory canal (EAC) sampling with DNA-free swabs. MAIN OUTCOME MEASURES Microbial communities in the samples were investigated with amplicon sequencing of the 16S rRNA gene. RESULTS The final analysis contained 48 hearing aid users, 59 controls. Twenty-four samples were excluded because of low sequence count, recent use of antimicrobials and/or corticosteroids, recent cold, or missing health status. The groups showed significant differences in bacterial diversity (beta div., p = 0.011), and hearing aid users showed lower species richness than the control group (alpha div., p < 0.01). The most frequent findings in both groups were Staphylococcus auricularis , Alloiococcus otitis , Cutibacterium acnes , Corynebacterium otitidis , and Staphylococcus unclassified sp. Hearing aid users' samples presented more Corynebacterium tuberculostearicum than the control samples. Common EAC pathogens, such as Staphylococcus aureus or Pseudomonas aeruginosa were rare. CONCLUSION Long-term hearing aid use lowers bacterial diversity and modulates the EAC microbiome. The changes mostly affect commensals. Lowered diversity may predispose individuals to EAC conditions and needs more research.
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Affiliation(s)
- Atte Sjövall
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
| | - Ella Mustanoja
- Institute of Biotechnology, HiLIFE, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Annina Lyyski
- Institute of Biotechnology, HiLIFE, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, HiLIFE, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | | | - Antti Aarnisalo
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
| | - Anu Pätäri-Sampo
- Department of Clinical Microbiology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anu Laulajainen-Hongisto
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
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2
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Jokelainen O, Rintala TJ, Fortino V, Pasonen-Seppänen S, Sironen R, Nykopp TK. Differential expression analysis identifies a prognostically significant extracellular matrix-enriched gene signature in hyaluronan-positive clear cell renal cell carcinoma. Sci Rep 2024; 14:10626. [PMID: 38724670 PMCID: PMC11082176 DOI: 10.1038/s41598-024-61426-3] [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: 10/28/2023] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
Hyaluronan (HA) accumulation in clear cell renal cell carcinoma (ccRCC) is associated with poor prognosis; however, its biology and role in tumorigenesis are unknown. RNA sequencing of 48 HA-positive and 48 HA-negative formalin-fixed paraffin-embedded (FFPE) samples was performed to identify differentially expressed genes (DEG). The DEGs were subjected to pathway and gene enrichment analyses. The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) data and DEGs were used for the cluster analysis. In total, 129 DEGs were identified. HA-positive tumors exhibited enhanced expression of genes related to extracellular matrix (ECM) organization and ECM receptor interaction pathways. Gene set enrichment analysis showed that epithelial-mesenchymal transition-associated genes were highly enriched in the HA-positive phenotype. A protein-protein interaction network was constructed, and 17 hub genes were discovered. Heatmap analysis of TCGA-KIRC data identified two prognostic clusters corresponding to HA-positive and HA-negative phenotypes. These clusters were used to verify the expression levels and conduct survival analysis of the hub genes, 11 of which were linked to poor prognosis. These findings enhance our understanding of hyaluronan in ccRCC.
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Affiliation(s)
- Otto Jokelainen
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio Campus, P.O. Box 1627, 70211, Kuopio, Finland.
- Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland.
| | - Teemu J Rintala
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | | | - Reijo Sironen
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio Campus, P.O. Box 1627, 70211, Kuopio, Finland
- Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Timo K Nykopp
- Department of Surgery, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Surgery, University of Eastern Finland, Kuopio, Finland
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3
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Kang S, Choi P, Maile-Moskowitz A, Brown CL, Gonzalez RA, Pruden A, Vikesland PJ. Highly Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification and Nanopore Sequencing (LAMPore) for Wastewater-Based Surveillance. ACS ES&T WATER 2024; 4:1629-1636. [PMID: 38633369 PMCID: PMC11019537 DOI: 10.1021/acsestwater.3c00690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/19/2024]
Abstract
Wastewater-based surveillance (WBS) has gained attention as a strategy to monitor and provide an early warning for disease outbreaks. Here, we applied an isothermal gene amplification technique, reverse-transcription loop-mediated isothermal amplification (RT-LAMP), coupled with nanopore sequencing (LAMPore) as a means to detect SARS-CoV-2. Specifically, we combined barcoding using both an RT-LAMP primer and the nanopore rapid barcoding kit to achieve highly multiplexed detection of SARS-CoV-2 in wastewater. RT-LAMP targeting the SARS-CoV-2 N region was conducted on 96 reactions including wastewater RNA extracts and positive and no-target controls. The resulting amplicons were pooled and subjected to nanopore sequencing, followed by demultiplexing based on barcodes that differentiate the source of each SARS-CoV-2 N amplicon derived from the 96 RT-LAMP products. The criteria developed and applied to establish whether SARS-CoV-2 was detected by the LAMPore assay indicated high consistency with polymerase chain reaction-based detection of the SARS-CoV-2 N gene, with a sensitivity of 89% and a specificity of 83%. We further profiled sequence variations on the SARS-CoV-2 N amplicons, revealing a number of mutations on a sample collected after viral variants had emerged. The results demonstrate the potential of the LAMPore assay to facilitate WBS for SARS-CoV-2 and the emergence of viral variants in wastewater.
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Affiliation(s)
- Seju Kang
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Petra Choi
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Ayella Maile-Moskowitz
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Connor L. Brown
- Department
of Genetics, Bioinformatics, and Computational Biology, Blacksburg, Virginia 24061, United States
| | - Raul A. Gonzalez
- Hampton
Roads Sanitation District, Virginia Beach ,Virginia23455, United States
| | - Amy Pruden
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Peter J. Vikesland
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
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4
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Brandt E, Koivisto A, Pereira P, Mustanoja E, Auvinen P, Saari T, Lehtola JM, Hannonen S, Rusanen M, Leinonen V, Scheperjans F, Kärkkäinen V. Gut Microbiome Changes in Patients With Idiopathic Normal Pressure Hydrocephalus. Alzheimer Dis Assoc Disord 2024; 38:133-139. [PMID: 38602449 PMCID: PMC11132091 DOI: 10.1097/wad.0000000000000613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/20/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND The gut microbiome is a complex system within the human gastrointestinal tract. The bacteria play a significant role in human health, and some can promote inflammation and pathologic processes through chemical interactions or metabolites. Gut microbiome dysbiosis has been linked to some neurological and other diseases. Here we aimed to examine microbiome differences between patients with a progressive neurological disorder, idiopathic normal pressure hydrocephalus (iNPH), compared with healthy controls (CO). METHODS We recruited 37 neurologically healthy CO and 10 patients with shunted iNPH. We evaluated these participants' cognition using the CERAD-NB test battery and CDR test, and collected a variety of information, including about dietary habits and health. We also collected fecal samples, which were subjected to 16S amplicon sequencing to analyze differences in gut microbiome composition. RESULTS We found that the iNPH group exhibited significantly different abundances of 10 bacterial genera compared with the CO group. The Escherichia/Shigella and Anaeromassilibacillus genera were most remarkably increased. Other increased genera were Butyrivibrio , Duncaniella , and an unidentified genus. The decreased genera were Agathobaculum , Paramuribaculum , Catenibacterium , and 2 unidentified genera. CONCLUSIONS Here we report the first identified microbiome differences in iNPH patients compared with healthy controls.
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Affiliation(s)
- Emilia Brandt
- Departments of Neurology
- NeuroCenter, Kuopio University Hospital, Kuopio
| | - Anne Koivisto
- NeuroCenter, Kuopio University Hospital, Kuopio
- Department of Neurosciences, Faculty of Medicine
- Department of Geriatrics, Helsinki University Hospital Helsinki
| | | | - Ella Mustanoja
- Institute of Biotechnology, University of Helsinki, Helsinki Institute of Life Sciences
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki Institute of Life Sciences
| | - Toni Saari
- Institute of Biotechnology, University of Helsinki, Helsinki Institute of Life Sciences
| | - Juha-Matti Lehtola
- Departments of Neurology
- Department of Psychiatry, Turku University Hospital, Turku, Finland
| | - Sanna Hannonen
- Departments of Neurology
- NeuroCenter, Kuopio University Hospital, Kuopio
| | - Minna Rusanen
- Departments of Neurology
- NeuroCenter, Kuopio University Hospital, Kuopio
| | - Ville Leinonen
- Neurosurgery, Institute of Clinical Medicine, School of Medicine, University of Eastern Finland
- NeuroCenter, Kuopio University Hospital, Kuopio
| | - Filip Scheperjans
- Clinicum, University of Helsinki
- Neurology, Helsinki University Hospital, Helsinki
| | - Virve Kärkkäinen
- Neurosurgery, Institute of Clinical Medicine, School of Medicine, University of Eastern Finland
- NeuroCenter, Kuopio University Hospital, Kuopio
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5
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Maurer DP, Vu M, Schmidt AG. Antigenic drift expands viral escape pathways from imprinted host humoral immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585891. [PMID: 38562862 PMCID: PMC10983950 DOI: 10.1101/2024.03.20.585891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
An initial virus exposure can imprint antibodies such that future responses to antigenically drifted strains are dependent on the identity of the imprinting strain. Subsequent exposure to antigenically distinct strains followed by affinity maturation can guide immune responses toward generation of cross-reactive antibodies. How viruses evolve in turn to escape these imprinted broad antibody responses is unclear. Here, we used clonal antibody lineages from two human donors recognizing conserved influenza virus hemagglutinin (HA) epitopes to assess viral escape potential using deep mutational scanning. We show that even though antibody affinity maturation does restrict the number of potential escape routes in the imprinting strain through repositioning the antibody variable domains, escape is still readily observed in drifted strains and attributed to epistatic networks within HA. These data explain how influenza virus continues to evolve in the human population by escaping even broad antibody responses.
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6
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Turunen J, Tejesvi MV, Paalanne N, Pokka T, Amatya SB, Mishra S, Kaisanlahti A, Reunanen J, Tapiainen T. Investigating prenatal and perinatal factors on meconium microbiota: a systematic review and cohort study. Pediatr Res 2024; 95:135-145. [PMID: 37591927 PMCID: PMC10798900 DOI: 10.1038/s41390-023-02783-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/30/2023] [Accepted: 07/29/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND The first-pass meconium has been suggested as a proxy for the fetal gut microbiota because it is formed in utero. This systematic review and cohort study investigated how pre- and perinatal factors influence the composition of the meconium microbiota. METHODS We performed the systematic review using Covidence by searching PubMed, Scopus, and Web of Science databases with the search terms "meconium microbiome" and "meconium microbiota". In the cohort study, we performed 16 S rRNA gene sequencing on 393 meconium samples and analyzed the sequencing data using QIIME2. RESULTS Our systematic review identified 69 studies exploring prenatal factors, immediate perinatal factors, and microbial composition in relation to subsequent health of infants but gave only limited comparative evidence regarding factors related to the composition of the meconium microbiota. The cohort study pointed to a low-biomass microbiota consisting of the phyla Firmicutes, Proteobacteria and Actinobacteriota and the genera Staphylococcus, Escherichia-Shigella and Lactobacillus, and indicated that immediate perinatal factors affected the composition of the meconium microbiota more than did prenatal factors. CONCLUSIONS This finding supports the idea that the meconium microbiota mostly starts developing during delivery. IMPACT It is unclear when the first-pass meconium microbiota develops, and what are the sources of the colonization. In this systematic review, we found 69 studies exploring prenatal factors, immediate perinatal factors, and microbial composition relative to subsequent health of infants, but there was no consensus on the factors affecting the meconium microbiota development. In this cohort study, immediate perinatal factors markedly affected the meconium microbiota development while prenatal factors had little effect on it. As the meconium microbiota composition was influenced by immediate perinatal factors, the present study supports the idea that the initial gut microbiota develops mainly during delivery.
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Affiliation(s)
- Jenni Turunen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland.
- Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Mysore V Tejesvi
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
| | - Niko Paalanne
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Tytti Pokka
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Research Service Unit, Oulu University Hospital, Oulu, Finland
| | - Sajeen Bahadur Amatya
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Surbhi Mishra
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Anna Kaisanlahti
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Justus Reunanen
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Terhi Tapiainen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
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7
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Quan N, Eguchi Y, Geiler-Samerotte K. Intra- FCY1: a novel system to identify mutations that cause protein misfolding. Front Genet 2023; 14:1198203. [PMID: 37745845 PMCID: PMC10512024 DOI: 10.3389/fgene.2023.1198203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Protein misfolding is a common intracellular occurrence. Most mutations to coding sequences increase the propensity of the encoded protein to misfold. These misfolded molecules can have devastating effects on cells. Despite the importance of protein misfolding in human disease and protein evolution, there are fundamental questions that remain unanswered, such as, which mutations cause the most misfolding? These questions are difficult to answer partially because we lack high-throughput methods to compare the destabilizing effects of different mutations. Commonly used systems to assess the stability of mutant proteins in vivo often rely upon essential proteins as sensors, but misfolded proteins can disrupt the function of the essential protein enough to kill the cell. This makes it difficult to identify and compare mutations that cause protein misfolding using these systems. Here, we present a novel in vivo system named Intra-FCY1 that we use to identify mutations that cause misfolding of a model protein [yellow fluorescent protein (YFP)] in Saccharomyces cerevisiae. The Intra-FCY1 system utilizes two complementary fragments of the yeast cytosine deaminase Fcy1, a toxic protein, into which YFP is inserted. When YFP folds, the Fcy1 fragments associate together to reconstitute their function, conferring toxicity in media containing 5-fluorocytosine and hindering growth. But mutations that make YFP misfold abrogate Fcy1 toxicity, thus strains possessing misfolded YFP variants rise to high frequency in growth competition experiments. This makes such strains easier to study. The Intra-FCY1 system cancels localization of the protein of interest, thus can be applied to study the relative stability of mutant versions of diverse cellular proteins. Here, we confirm this method can identify novel mutations that cause misfolding, highlighting the potential for Intra-FCY1 to illuminate the relationship between protein sequence and stability.
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Affiliation(s)
- N. Quan
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Y. Eguchi
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
| | - K. Geiler-Samerotte
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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8
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Rahman A, Manci M, Nadon C, Perez IA, Farsamin WF, Lampe MT, Le TH, Torres Martínez L, Weisberg AJ, Chang JH, Sachs JL. Competitive interference among rhizobia reduces benefits to hosts. Curr Biol 2023; 33:2988-3001.e4. [PMID: 37490853 DOI: 10.1016/j.cub.2023.06.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/31/2023] [Accepted: 06/29/2023] [Indexed: 07/27/2023]
Abstract
The capacity of beneficial microbes to compete for host infection-and the ability of hosts to discriminate among them-introduces evolutionary conflict that is predicted to destabilize mutualism. We investigated fitness outcomes in associations between legumes and their symbiotic rhizobia to characterize fitness impacts of microbial competition. Diverse Bradyrhizobium strains varying in their capacity to fix nitrogen symbiotically with a common host plant, Acmispon strigosus, were tested in full-factorial coinoculation experiments involving 28 pairwise strain combinations. We analyzed the effects of interstrain competition and host discrimination on symbiotic-interaction outcomes by relativizing fitness proxies to clonally infected and uninfected controls. More than one thousand root nodules of coinoculated plants were genotyped to quantify strain occupancy, and the Bradyrhizobium strain genome sequences were analyzed to uncover the genetic bases of interstrain competition outcomes. Strikingly, interstrain competition favored a fast-growing, minimally beneficial rhizobia strain. Host benefits were significantly diminished in coinoculation treatments relative to expectations from clonally inoculated controls, consistent with competitive interference among rhizobia that reduced both nodulation and plant growth. Competition traits appear polygenic, linked with inter-strain allelopathic interactions in the rhizosphere. This study confirms that competition among strains can destabilize mutualism by favoring microbes that are superior in colonizing host tissues but provide minimal benefits to host plants. Moreover, our findings help resolve the paradox that despite efficient host control post infection, legumes nonetheless encounter rhizobia that vary in their nitrogen fixation.
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Affiliation(s)
- Arafat Rahman
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Max Manci
- Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Cassandra Nadon
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Ivan A Perez
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Warisha F Farsamin
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew T Lampe
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Tram H Le
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Lorena Torres Martínez
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, St. Mary's College of Maryland, St. Mary's City, MD 20686, USA
| | - Alexandra J Weisberg
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Jeff H Chang
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Joel L Sachs
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA; Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
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9
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Tejesvi MV, Turunen J, Salmi S, Reunanen J, Paalanne N, Tapiainen T. Delivery Mode and Perinatal Antibiotics Influence the Infant Gut Bacteriome and Mycobiome: A Network Analysis. J Fungi (Basel) 2023; 9:718. [PMID: 37504707 PMCID: PMC10381809 DOI: 10.3390/jof9070718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023] Open
Abstract
Both exposure to antibiotics at birth and delivery via Caesarean section influence the gut bacteriome's development in infants. Using 16S rRNA and internal transcribed spacer sequencing on the Ion Torrent platform, we employed network analysis to investigate the bacterial and fungal interkingdom relationships in the gut microbiome from birth to age 18 months in a prospective cohort study of 140 infants. The gut microbiome at ages six and 18 months revealed distinctive microbial interactions, including both positive and negative associations between bacterial and fungal genera in the gut ecosystem. Perinatal factors, delivery mode and intrapartum antibiotic exposure affected the associations between bacterial and fungal species. In infants exposed and unexposed to perinatal antibiotics, the gut microbiome formed distinct networks for the bacteriome and mycobiome. The fungi Saccharomyces, Trichosporon, Pezoloma, Cystofilobasidium, Rigidoporus and Fomitopsis were strongly associated with exposure to antibiotics at birth. Hyaloscypha, Trichosporon, Fomitopsis and Vishniacozyma were strongly associated with the control group that was not exposed to antibiotics. Five distinct networks were formed according to delivery mode. The present study confirms that bacteria and fungi clearly interact in the infant gut ecosystem. Furthermore, perinatal factors appear to influence the relationships between bacteria and fungi in the developing gut microbiome.
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Affiliation(s)
- Mysore V Tejesvi
- Research Unit of Clinical Medicine, University of Oulu, 90014 Oulu, Finland
- Ecology and Genetics, Faculty of Science, University of Oulu, 90014 Oulu, Finland
| | - Jenni Turunen
- Research Unit of Clinical Medicine, University of Oulu, 90014 Oulu, Finland
- Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
| | - Sonja Salmi
- Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, 90014 Oulu, Finland
- Disease Networks Research Unit, University of Oulu, 90014 Oulu, Finland
| | - Justus Reunanen
- Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, 90014 Oulu, Finland
| | - Niko Paalanne
- Research Unit of Clinical Medicine, University of Oulu, 90014 Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, 90014 Oulu, Finland
| | - Terhi Tapiainen
- Research Unit of Clinical Medicine, University of Oulu, 90014 Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, 90014 Oulu, Finland
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10
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Wirth J, Huber N, Yin K, Brood S, Chang S, Martinez-Jimenez CP, Meier M. Spatial transcriptomics using multiplexed deterministic barcoding in tissue. Nat Commun 2023; 14:1523. [PMID: 36934108 PMCID: PMC10024691 DOI: 10.1038/s41467-023-37111-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/02/2023] [Indexed: 03/20/2023] Open
Abstract
Spatially resolved transcriptomics of tissue sections enables advances in fundamental and applied biomedical research. Here, we present Multiplexed Deterministic Barcoding in Tissue (xDBiT) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm2 with a 50 µm resolution. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared to previous reports. Furthermore, the introduction of alignment markers allowed seamless registration of images and spatial transcriptomic spots. Together with technological advances, we provide an open-source computational pipeline to prepare raw sequencing data for downstream analysis. The functionality of xDBiT was demonstrated by acquiring 16 spatially resolved transcriptomic datasets from five different murine organs, including the cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of spatial transcriptomes allowed for in-depth characterization of the murine kidney.
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Affiliation(s)
- Johannes Wirth
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Nina Huber
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Kelvin Yin
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Sophie Brood
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Simon Chang
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Celia P Martinez-Jimenez
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany.
- TUM School of Medicine, Technical University of Munich, Munich, Germany.
| | - Matthias Meier
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany.
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany.
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11
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Löytynoja A, Rastas P, Valtonen M, Kammonen J, Holm L, Olsen MT, Paulin L, Jernvall J, Auvinen P. Fragmented habitat compensates for the adverse effects of genetic bottleneck. Curr Biol 2023; 33:1009-1018.e7. [PMID: 36822202 DOI: 10.1016/j.cub.2023.01.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/01/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023]
Abstract
In the face of the human-caused biodiversity crisis, understanding the theoretical basis of conservation efforts of endangered species and populations has become increasingly important. According to population genetics theory, population subdivision helps organisms retain genetic diversity, crucial for adaptation in a changing environment. Habitat topography is thought to be important for generating and maintaining population subdivision, but empirical cases are needed to test this assumption. We studied Saimaa ringed seals, landlocked in a labyrinthine lake and recovering from a drastic bottleneck, with additional samples from three other ringed seal subspecies. Using whole-genome sequences of 145 seals, we analyzed the distribution of variation and genetic relatedness among the individuals in relation to the habitat shape. Despite a severe history of genetic bottlenecks with prevalent homozygosity in Saimaa ringed seals, we found evidence for the population structure mirroring the subregions of the lake. Our genome-wide analyses showed that the subpopulations had retained unique variation and largely complementary patterns of homozygosity, highlighting the significance of habitat connectivity in conservation biology and the power of genomic tools in understanding its impact. The central role of the population substructure in preserving genetic diversity at the metapopulation level was confirmed by simulations. Integration of genetic analyses in conservation decisions gives hope to Saimaa ringed seals and other endangered species in fragmented habitats.
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Affiliation(s)
- Ari Löytynoja
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland.
| | - Pasi Rastas
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Mia Valtonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Juhana Kammonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Liisa Holm
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland; Organismal and Evolutionary Biology Research Program, Faculty of Biosciences, University of Helsinki, Helsinki 00014, Finland
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute and University of Copenhagen, Copenhagen 1350, Denmark
| | - Lars Paulin
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Jukka Jernvall
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland; Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Petri Auvinen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
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12
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Boertien JM, Murtomäki K, Pereira PAB, van der Zee S, Mertsalmi TH, Levo R, Nojonen T, Mäkinen E, Jaakkola E, Laine P, Paulin L, Pekkonen E, Kaasinen V, Auvinen P, Scheperjans F, van Laar T. Fecal microbiome alterations in treatment-naive de novo Parkinson's disease. NPJ Parkinsons Dis 2022; 8:129. [PMID: 36216843 PMCID: PMC9551094 DOI: 10.1038/s41531-022-00395-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
Gut microbiota alterations in Parkinson's disease (PD) have been found in several studies and are suggested to contribute to the pathogenesis of PD. However, previous results could not be adequately adjusted for a potential confounding effect of PD medication and disease duration, as almost all PD participants were already using dopaminergic medication and were included several years after diagnosis. Here, the gut microbiome composition of treatment-naive de novo PD subjects was assessed compared to healthy controls (HC) in two large independent case-control cohorts (n = 136 and 56 PD, n = 85 and 87 HC), using 16S-sequencing of fecal samples. Relevant variables such as technical batches, diet and constipation were assessed for their potential effects. Overall gut microbiome composition differed between PD and HC in both cohorts, suggesting gut microbiome alterations are already present in de novo PD subjects at the time of diagnosis, without the possible confounding effect of dopaminergic medication. Although no differentially abundant taxon could be replicated in both cohorts, multiple short chain fatty acids (SCFA) producing taxa were decreased in PD in both cohorts. In particular, several taxa belonging to the family Lachnospiraceae were decreased in abundance. Fewer taxonomic differences were found compared to previous studies, indicating smaller effect sizes in de novo PD.
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Affiliation(s)
- Jeffrey M. Boertien
- grid.4494.d0000 0000 9558 4598Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Kirsi Murtomäki
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Pedro A. B. Pereira
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Sygrid van der Zee
- grid.4494.d0000 0000 9558 4598Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Tuomas H. Mertsalmi
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Reeta Levo
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Tanja Nojonen
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Elina Mäkinen
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland ,grid.410552.70000 0004 0628 215XClinical Neurosciences, University of Turku and Neurocenter, Turku University Hospital, Turku, Finland
| | - Elina Jaakkola
- grid.410552.70000 0004 0628 215XClinical Neurosciences, University of Turku and Neurocenter, Turku University Hospital, Turku, Finland
| | - Pia Laine
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Eero Pekkonen
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Valtteri Kaasinen
- grid.410552.70000 0004 0628 215XClinical Neurosciences, University of Turku and Neurocenter, Turku University Hospital, Turku, Finland
| | - Petri Auvinen
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Filip Scheperjans
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Teus van Laar
- grid.4494.d0000 0000 9558 4598Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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13
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Plavec Z, Domanska A, Liu X, Laine P, Paulin L, Varjosalo M, Auvinen P, Wolf SG, Anastasina M, Butcher SJ. SARS-CoV-2 Production, Purification Methods and UV Inactivation for Proteomics and Structural Studies. Viruses 2022; 14:v14091989. [PMID: 36146795 PMCID: PMC9505060 DOI: 10.3390/v14091989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 is the causative agent of COVID-19. During the pandemic of 2019–2022, at least 500 million have been infected and over 6.3 million people have died from COVID-19. The virus is pleomorphic, and due to its pathogenicity is often handled in very restrictive biosafety containments laboratories. We developed two effective and rapid purification methods followed by UV inactivation that allow easy downstream handling of the virus. We monitored the purification through titering, sequencing, mass spectrometry and electron cryogenic microscopy. Although pelleting through a sucrose cushion, followed by gentle resuspension overnight gave the best particle recovery, infectivity decreased, and the purity was significantly worse than if using the size exclusion resin Capto Core. Capto Core can be used in batch mode, and was seven times faster than the pelleting method, obviating the need for ultracentrifugation in the containment laboratory, but resulting in a dilute virus. UV inactivation was readily optimized to allow handling of the inactivated samples under standard operating conditions. When containment laboratory space is limited, we recommend the use of Capto Core for purification and UV for inactivation as a simple, rapid workflow prior, for instance, to electron cryogenic microscopy or cell activation experiments.
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Affiliation(s)
- Zlatka Plavec
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Aušra Domanska
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Pia Laine
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Sharon G. Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maria Anastasina
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
- Correspondence: (M.A.); (S.J.B.); Tel.: +358-5044-84629 (M.A.); +358-5041-55492 (S.J.B.)
| | - Sarah J. Butcher
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
- Correspondence: (M.A.); (S.J.B.); Tel.: +358-5044-84629 (M.A.); +358-5041-55492 (S.J.B.)
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14
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Patarroyo MA, Patarroyo ME, Pabón L, Alba MP, Bermudez A, Rugeles MT, Díaz-Arevalo D, Zapata-Builes W, Zapata MI, Reyes C, Suarez CF, Agudelo W, López C, Aza-Conde J, Melo M, Escamilla L, Oviedo J, Guzmán F, Silva Y, Forero M, Flórez-Álvarez L, Aguilar-Jimenez W, Moreno-Vranich A, Garry J, Avendaño C. SM-COLSARSPROT: Highly Immunogenic Supramutational Synthetic Peptides Covering the World's Population. Front Immunol 2022; 13:859905. [PMID: 35693819 PMCID: PMC9175637 DOI: 10.3389/fimmu.2022.859905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Fifty ~20-amino acid (aa)-long peptides were selected from functionally relevant SARS-CoV-2 S, M, and E proteins for trial B-21 and another 53 common ones, plus some new ones derived from the virus' main genetic variants for complementary trial C-21. Peptide selection was based on tremendous SARS-CoV-2 genetic variability for analysing them concerning vast human immunogenetic polymorphism for developing the first supramutational, Colombian SARS-protection (SM-COLSARSPROT), peptide mixture. Specific physicochemical rules were followed, i.e., aa predilection for polyproline type II left-handed (PPIIL) formation, replacing β-branched, aromatic aa, short-chain backbone H-bond-forming residues, π-π interactions (n→π* and π-CH), aa interaction with π systems, and molecular fragments able to interact with them, disrupting PPIIL propensity formation. All these modified structures had PPIIL formation propensity to enable target peptide interaction with human leukocyte antigen-DRβ1* (HLA-DRβ1*) molecules to mediate antigen presentation and induce an appropriate immune response. Such modified peptides were designed for human use; however, they induced high antibody titres against S, M, and E parental mutant peptides and neutralising antibodies when suitably modified and chemically synthesised for immunising 61 major histocompatibility complex class II (MHCII) DNA genotyped Aotus monkeys (matched with their corresponding HLA-DRβ1* molecules), predicted to cover 77.5% to 83.1% of the world's population. Such chemically synthesised peptide mixture represents an extremely pure, stable, reliable, and cheap vaccine for COVID-19 pandemic control, providing a new approach for a logical, rational, and soundly established methodology for other vaccine development.
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Affiliation(s)
- Manuel A. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Manuel E. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Laura Pabón
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha P. Alba
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Adriana Bermudez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Diana Díaz-Arevalo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - María Isabel Zapata
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - César Reyes
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carlos F. Suarez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - William Agudelo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carolina López
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jorge Aza-Conde
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Miguel Melo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Luis Escamilla
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jairo Oviedo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Fanny Guzmán
- Núcleo de Biotecnología, Pontificia U. Católica de Valparaíso, Valparaíso, Chile
| | - Yolanda Silva
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha Forero
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Armando Moreno-Vranich
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jason Garry
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Catalina Avendaño
- Facultad de Ciencias Agropecualrias, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
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15
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Janjic A, Wange LE, Bagnoli JW, Geuder J, Nguyen P, Richter D, Vieth B, Vick B, Jeremias I, Ziegenhain C, Hellmann I, Enard W. Prime-seq, efficient and powerful bulk RNA sequencing. Genome Biol 2022; 23:88. [PMID: 35361256 PMCID: PMC8969310 DOI: 10.1186/s13059-022-02660-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/23/2022] [Indexed: 12/21/2022] Open
Abstract
Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it performs equivalently to TruSeq, a standard bulk RNA-seq method, but is fourfold more cost-efficient due to almost 50-fold cheaper library costs. We also validate a direct RNA isolation step, show that intronic reads are derived from RNA, and compare cost-efficiencies of available protocols. We conclude that prime-seq is currently one of the best options to set up an early barcoding bulk RNA-seq protocol from which many labs would profit.
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Affiliation(s)
- Aleksandar Janjic
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
- Graduate School of Systemic Neurosciences, Faculty of Biology, Ludwig-Maximilians University, Martinsried, Germany
| | - Lucas E Wange
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Johannes W Bagnoli
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Johanna Geuder
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Phong Nguyen
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Daniel Richter
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Beate Vieth
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ines Hellmann
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany.
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16
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Ogawa Y, Katsuyama Y, Ohnishi Y. Engineering of the Ligand Specificity of Transcriptional Regulator XylS by Deep Mutational Scanning. ACS Synth Biol 2022; 11:473-485. [PMID: 34964613 DOI: 10.1021/acssynbio.1c00564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deep mutational scanning is a method for protein engineering. Here, we applied it to alter the ligand specificity of the transcriptional regulator XylS from Pseudomonas putida to recognize p-toluic acid instead of the native ligand m-toluic acid. For this purpose, we used an antibiotic resistance gene-based dual screening system, which was constructed for the directed evolution of XylS toward the above-mentioned ligand specificity. We constructed a xylS mutant library in which each codon for the amino acid residue of the putative ligand-binding domain (residues 1-213, except 7th residue) was randomized to generate all possible single amino acid-substituted XylS variants and introduced it into Escherichia coli harboring the selection plasmid for the screening system. The cells were cultured in the presence of appropriate antibiotics and m-toluic acid or p-toluic acid, and the frequency of each mutation present in the library was examined using a next-generation sequencer before and after cultivation. Heatmaps showing the enrichment score of each XylS variant were obtained. By searching for a p-toluic-acid-specific heatmap pattern, we focused on G71 and H77. Analysis of the ligand specificities of G71- or H77-substituted XylS variants revealed that several G71-substituted XylS variants responded specifically to p-toluic acid. Thus, the 71st residue was found to be an unprecedented residue that is important for switching ligand specificity. Our study demonstrated the usefulness of deep mutational scanning in engineering the ligand specificity of a transcriptional regulator without structural information. We also discussed the advantages and disadvantages of deep mutational scanning compared with directed evolution.
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Affiliation(s)
- Yuki Ogawa
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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17
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Walker AR, Shields RC. Identification and Analysis of Essential Genes in Streptococcus mutans with Transposon Sequencing. Methods Mol Biol 2022; 2377:237-258. [PMID: 34709620 DOI: 10.1007/978-1-0716-1720-5_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Transposon sequencing (Tn-seq) has greatly accelerated the rate at which gene function can be profiled in microbial organisms. This technique has been applied to the study of the dental caries pathogen Streptococcus mutans where it has been used to generate large transposon mutant libraries. Coupled with high-throughput sequencing and bioinformatics tools, culture of these transposon mutant libraries has facilitated the identification of essential and conditional essential genes. In this chapter, we describe a procedure for performing Tn-seq studies in S. mutans that covers pooled transposon mutant construction, in vitro culture, and DNA library sequencing and data analysis.
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Affiliation(s)
- Alejandro R Walker
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Robert C Shields
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA.
- Department of Biological Sciences, College of Sciences and Mathematics, Arkansas State University, Jonesboro, AR, USA.
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18
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Mousavi SA, Gao Y, Penttinen P, Frostegård Å, Paulin L, Lindström K. Using amplicon sequencing of rpoB for identification of inoculant rhizobia from peanut nodules. Lett Appl Microbiol 2021; 74:204-211. [PMID: 34753197 DOI: 10.1111/lam.13599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/22/2021] [Accepted: 10/28/2021] [Indexed: 12/16/2022]
Abstract
To improve the nitrogen fixation, legume crops are often inoculated with selected effective rhizobia. However, there is large variation in how well the inoculant strains compete with the indigenous microflora in soil. To assess the success of the inoculant, it is necessary to distinguish it from other, closely related strains. Methods used until now have generally been based either on fingerprinting methods or on the use of reporter genes. Nevertheless, these methods have their shortcomings, either because they do not provide sufficiently specific information on the identity of the inoculant strain, or because they use genetically modified organisms that need prior authorization to be applied in the field or other uncontained environments. Another possibility is to target a gene that is naturally present in the bacterial genomes. Here we have developed a method that is based on amplicon sequencing of the bacterial housekeeping gene rpoB, encoding the beta-subunit of the RNA polymerase, which has been proposed as an alternative to the 16S rRNA gene to study the diversity of rhizobial populations in soils. We evaluated the method under laboratory and field conditions. Peanut seeds were inoculated with various Bradyrhizobium strains. After nodule development, DNA was extracted from selected nodules and the nodulating rhizobia were analysed by amplicon sequencing of the rpoB gene. The analyses of the sequence data showed that the method reliably identified bradyrhizobial strains in nodules, at least at the species level, and could be used to assess the competitiveness of the inoculant compared to other bradyrhizobia.
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Affiliation(s)
- S A Mousavi
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland.,Division of Ecology and Evolutionary Biology, Department of Biology, University of Turku, Turku, Finland
| | - Y Gao
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland.,Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway.,International Research and Development Center, Kingenta Ecological Engineering Group Co. Ltd, Linyi, China
| | - P Penttinen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Å Frostegård
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
| | - L Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - K Lindström
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland
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19
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Herholt A, Sahoo VK, Popovic L, Wehr MC, Rossner MJ. Dissecting intercellular and intracellular signaling networks with barcoded genetic tools. Curr Opin Chem Biol 2021; 66:102091. [PMID: 34644670 DOI: 10.1016/j.cbpa.2021.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/25/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022]
Abstract
The power of next-generation sequencing has stimulated the development of many analysis techniques for transcriptomics and genomics. More recently, the concept of 'molecular barcoding' has broadened the spectrum of sequencing-based applications to dissect different aspects of intracellular and intercellular signaling. In these assay formats, barcode reporters replace standard reporter genes. The virtually infinitive number of expressed barcode sequences allows high levels of multiplexing, hence accelerating experimental progress. Furthermore, reporter barcodes are used to quantitatively monitor a variety of biological events in living cells which has already provided much insight into complex cellular signaling and will further increase our knowledge in the future.
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Affiliation(s)
- Alexander Herholt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Vivek K Sahoo
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Luksa Popovic
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Michael C Wehr
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany.
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20
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Patarroyo ME, Patarroyo MA, Alba MP, Pabon L, Rugeles MT, Aguilar-Jimenez W, Florez L, Bermudez A, Rout AK, Griesinger C, Suarez CF, Aza-Conde J, Reyes C, Avendaño C, Samacá J, Camargo A, Silva Y, Forero M, Gonzalez E. The First Chemically-Synthesised, Highly Immunogenic Anti-SARS-CoV-2 Peptides in DNA Genotyped Aotus Monkeys for Human Use. Front Immunol 2021; 12:724060. [PMID: 34539660 PMCID: PMC8446425 DOI: 10.3389/fimmu.2021.724060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Thirty-five peptides selected from functionally-relevant SARS-CoV-2 spike (S), membrane (M), and envelope (E) proteins were suitably modified for immunising MHC class II (MHCII) DNA-genotyped Aotus monkeys and matched with HLA-DRβ1* molecules for use in humans. This was aimed at producing the first minimal subunit-based, chemically-synthesised, immunogenic molecules (COLSARSPROT) covering several HLA alleles. They were predicted to cover 48.25% of the world’s population for 6 weeks (short-term) and 33.65% for 15 weeks (long-lasting) as they induced very high immunofluorescent antibody (IFA) and ELISA titres against S, M and E parental native peptides, SARS-CoV-2 neutralising antibodies and host cell infection. The same immunological methods that led to identifying new peptides for inclusion in the COLSARSPROT mixture were used for antigenicity studies. Peptides were analysed with serum samples from patients suffering mild or severe SARS-CoV-2 infection, thereby increasing chemically-synthesised peptides’ potential coverage for the world populations up to 62.9%. These peptides’ 3D structural analysis (by 1H-NMR acquired at 600 to 900 MHz) suggested structural-functional immunological association. This first multi-protein, multi-epitope, minimal subunit-based, chemically-synthesised, highly immunogenic peptide mixture highlights such chemical synthesis methodology’s potential for rapidly obtaining very pure, highly reproducible, stable, cheap, easily-modifiable peptides for inducing immune protection against COVID-19, covering a substantial percentage of the human population.
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Affiliation(s)
- Manuel E Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,Universidad Santo Tomás, Bogotá, Colombia
| | - Manuel A Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha P Alba
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Laura Pabon
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - María T Rugeles
- Grupo Inmunovirología, Universidad de Antioquia, Medellín, Colombia
| | | | - Lizdany Florez
- Grupo Inmunovirología, Universidad de Antioquia, Medellín, Colombia
| | - Adriana Bermudez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Ashok K Rout
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carlos F Suarez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jorge Aza-Conde
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - César Reyes
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Catalina Avendaño
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
| | - Jhoan Samacá
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Anny Camargo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Yolanda Silva
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha Forero
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Edgardo Gonzalez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
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21
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Heinzel S, Aho VTE, Suenkel U, von Thaler AK, Schulte C, Deuschle C, Paulin L, Hantunen S, Brockmann K, Eschweiler GW, Maetzler W, Berg D, Auvinen P, Scheperjans F. Gut Microbiome Signatures of Risk and Prodromal Markers of Parkinson Disease. Ann Neurol 2021; 90:E1-E12. [PMID: 34021620 DOI: 10.1002/ana.26128] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/14/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Alterations of the gut microbiome in Parkinson disease (PD) have been repeatedly demonstrated. However, little is known about whether such alterations precede disease onset and how they relate to risk and prodromal markers of PD. We investigated associations of these features with gut microbiome composition. METHODS Established risk and prodromal markers of PD as well as factors related to diet/lifestyle, bowel function, and medication were studied in relation to bacterial α-/β-diversity, enterotypes, and differential abundance in stool samples of 666 elderly TREND (Tübingen Evaluation of Risk Factors for Early Detection of Neurodegeneration) study participants. RESULTS Among risk and prodromal markers, physical inactivity, occupational solvent exposure, and constipation showed associations with α-diversity. Physical inactivity, sex, constipation, possible rapid eye movement sleep behavior disorder (RBD), and smoking were associated with β-diversity. Subthreshold parkinsonism and physical inactivity showed an interaction effect. Among other factors, age and urate-lowering medication were associated with α- and β-diversity. Constipation was highest in individuals with the Firmicutes-enriched enterotype, and physical inactivity was most frequent in the Bacteroides-enriched enterotype. Constipation was lowest and subthreshold parkinsonism least frequent in individuals with the Prevotella-enriched enterotype. Differentially abundant taxa were linked to constipation, physical inactivity, possible RBD, smoking, and subthreshold parkinsonism. Substantia nigra hyperechogenicity, olfactory loss, depression, orthostatic hypotension, urinary/erectile dysfunction, PD family history, and the prodromal PD probability showed no significant microbiome associations. INTERPRETATION Several risk and prodromal markers of PD are associated with gut microbiome composition. However, the impact of the gut microbiome on PD risk and potential microbiome-dependent subtypes in the prodrome of PD need further investigation based on prospective clinical and (multi)omics data in incident PD cases. ANN NEUROL 2021;90:E1-E12.
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Affiliation(s)
- Sebastian Heinzel
- Department of Neurology, Christian-Albrechts University, Kiel, Germany
| | - Velma T E Aho
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Helsinki, Finland
| | - Ulrike Suenkel
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Anna-Katharina von Thaler
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Schulte
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Christian Deuschle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sari Hantunen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Kathrin Brockmann
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Gerhard W Eschweiler
- Department of Psychiatry and Psychotherapy, Geriatric Center, Tübingen University Hospital, Tübingen, Germany
- Geriatric Center, Tübingen University Hospital, Tübingen, Germany
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts University, Kiel, Germany
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts University, Kiel, Germany
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Filip Scheperjans
- Department of Neurology, Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Helsinki, Finland
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22
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Salonen IS, Chronopoulou PM, Nomaki H, Langlet D, Tsuchiya M, Koho KA. 16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes in Deep-Sea Benthic Foraminifera. Front Microbiol 2021; 12:694406. [PMID: 34385987 PMCID: PMC8353385 DOI: 10.3389/fmicb.2021.694406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Foraminifera are unicellular eukaryotes that are an integral part of benthic fauna in many marine ecosystems, including the deep sea, with direct impacts on benthic biogeochemical cycles. In these systems, different foraminiferal species are known to have a distinct vertical distribution, i.e., microhabitat preference, which is tightly linked to the physico-chemical zonation of the sediment. Hence, foraminifera are well-adapted to thrive in various conditions, even under anoxia. However, despite the ecological and biogeochemical significance of foraminifera, their ecology remains poorly understood. This is especially true in terms of the composition and diversity of their microbiome, although foraminifera are known to harbor diverse endobionts, which may have a significant meaning to each species' survival strategy. In this study, we used 16S rRNA gene metabarcoding to investigate the microbiomes of five different deep-sea benthic foraminiferal species representing differing microhabitat preferences. The microbiomes of these species were compared intra- and inter-specifically, as well as with the surrounding sediment bacterial community. Our analysis indicated that each species was characterized with a distinct, statistically different microbiome that also differed from the surrounding sediment community in terms of diversity and dominant bacterial groups. We were also able to distinguish specific bacterial groups that seemed to be strongly associated with particular foraminiferal species, such as the family Marinilabiliaceae for Chilostomella ovoidea and the family Hyphomicrobiaceae for Bulimina subornata and Bulimina striata. The presence of bacterial groups that are tightly associated to a certain foraminiferal species implies that there may exist unique, potentially symbiotic relationships between foraminifera and bacteria that have been previously overlooked. Furthermore, the foraminifera contained chloroplast reads originating from different sources, likely reflecting trophic preferences and ecological characteristics of the different species. This study demonstrates the potential of 16S rRNA gene metabarcoding in resolving the microbiome composition and diversity of eukaryotic unicellular organisms, providing unique in situ insights into enigmatic deep-sea ecosystems.
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Affiliation(s)
- Iines S Salonen
- Ecosystems and Environment Research Program, University of Helsinki, Helsinki, Finland.,SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Hidetaka Nomaki
- SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Dewi Langlet
- SUGAR, X-star, Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.,UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, Université de Lille - CNRS, Université du Littoral Côte d'Opale, Station Marine de Wimereux, Lille, France.,Evolution, Cell Biology, and Symbiosis Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Masashi Tsuchiya
- Research Institute for Global Change (RIGC), Japan Agency of Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Karoliina A Koho
- Ecosystems and Environment Research Program, University of Helsinki, Helsinki, Finland
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23
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Duru IC, Bucur FI, Andreevskaya M, Nikparvar B, Ylinen A, Grigore-Gurgu L, Rode TM, Crauwels P, Laine P, Paulin L, Løvdal T, Riedel CU, Bar N, Borda D, Nicolau AI, Auvinen P. High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes. BMC Genomics 2021; 22:117. [PMID: 33579201 PMCID: PMC7881616 DOI: 10.1186/s12864-021-07407-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
Background High-pressure processing (HPP) is a commonly used technique in the food industry to inactivate pathogens, including L. monocytogenes. It has been shown that L. monocytogenes is able to recover from HPP injuries and can start to grow again during long-term cold storage. To date, the gene expression profiling of L. monocytogenes during HPP damage recovery at cooling temperature has not been studied. In order identify key genes that play a role in recovery of the damage caused by HPP treatment, we performed RNA-sequencing (RNA-seq) for two L. monocytogenes strains (barotolerant RO15 and barosensitive ScottA) at nine selected time points (up to 48 h) after treatment with two pressure levels (200 and 400 MPa). Results The results showed that a general stress response was activated by SigB after HPP treatment. In addition, the phosphotransferase system (PTS; mostly fructose-, mannose-, galactitol-, cellobiose-, and ascorbate-specific PTS systems), protein folding, and cobalamin biosynthesis were the most upregulated genes during HPP damage recovery. We observed that cell-division-related genes (divIC, dicIVA, ftsE, and ftsX) were downregulated. By contrast, peptidoglycan-synthesis genes (murG, murC, and pbp2A) were upregulated. This indicates that cell-wall repair occurs as a part of HPP damage recovery. We also observed that prophage genes, including anti-CRISPR genes, were induced by HPP. Interestingly, a large amount of RNA-seq data (up to 85%) was mapped to Rli47, which is a non-coding RNA that is upregulated after HPP. Thus, we predicted that Rli47 plays a role in HPP damage recovery in L. monocytogenes. Moreover, gene-deletion experiments showed that amongst peptidoglycan biosynthesis genes, pbp2A mutants are more sensitive to HPP. Conclusions We identified several genes and mechanisms that may play a role in recovery from HPP damage of L. monocytogenes. Our study contributes to new information on pathogen inactivation by HPP. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07407-6.
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Affiliation(s)
- Ilhan Cem Duru
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Florentina Ionela Bucur
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
| | | | - Bahareh Nikparvar
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anne Ylinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Leontina Grigore-Gurgu
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
| | - Tone Mari Rode
- Department of Process Technology, Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, N-4068, Stavanger, Norway
| | - Peter Crauwels
- Institute of Microbiology and Biotechnology, Ulm, University, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
| | - Pia Laine
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Trond Løvdal
- Department of Process Technology, Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, N-4068, Stavanger, Norway
| | - Christian U Riedel
- Institute of Microbiology and Biotechnology, Ulm, University, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
| | - Nadav Bar
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Daniela Borda
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
| | - Anca Ioana Nicolau
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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24
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Low-complexity and highly robust barcodes for error-rich single molecular sequencing. 3 Biotech 2021; 11:78. [PMID: 33505833 DOI: 10.1007/s13205-020-02607-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/23/2020] [Indexed: 12/28/2022] Open
Abstract
DNA barcodes are frequently corrupted due to insertion, deletion, and substitution errors during DNA synthesis, amplification and sequencing, resulting in index hopping. In this paper, we propose a new DNA barcode construction scheme that combines a cyclic block code with a predetermined pseudo-random sequence bit by bit to form bit pairs, and then converts the bit pairs to bases, i.e., the DNA barcodes. Then, we present a barcode identification scheme for noisy sequencing reads, which uses a combination of cyclic shifting and traditional dynamic programming to mark the insertion and deletion positions, and then performs erasure-and-error-correction decoding on the corrupted codewords. Furthermore, we verify the identification error rate of barcodes for multiple errors and evaluate the reliability of the barcodes in DNA context. This method can be easily generalized for constructing long barcodes, which may be used in scenarios with serious errors. Simulation results show that the bit error rate after identifying insertions/deletions is greatly reduced using the combination of cyclic shift and dynamic programming compared to using dynamic programming only. It indicates that the proposed method can effectively improve the accuracy for estimating insertion/deletion errors. And the overall identification error rate of the proposed method is lower than 10 - 5 when the probability of each base mutation is less than 0.1, which is the typical scenario in third-generation sequencing.
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25
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Holmer J, Aho V, Eriksdotter M, Paulin L, Pietiäinen M, Auvinen P, Schultzberg M, Pussinen PJ, Buhlin K. Subgingival microbiota in a population with and without cognitive dysfunction. J Oral Microbiol 2021; 13:1854552. [PMID: 33537116 PMCID: PMC7833025 DOI: 10.1080/20002297.2020.1854552] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/29/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022] Open
Abstract
Aim: The aim of this study was to compare the subgingival microbiota of people with Alzheimer´s disease (AD), mild cognitive impairment (MCI), subjective cognitive decline (SCD) and cognitively healthy individuals. Materials and methods: The study population was recruited from 2013 to 2017 and comprised 132 cases recently diagnosed with AD (n = 46), MCI (n = 40) or SCD (n = 46), and 63 cognitively healthy controls. Subgingival samples were collected, and the microbiotas were characterized by 16S rRNA gene sequencing. Results: The relative abundance of the ten most common genera did not differ between the cases and control groups. However, the microbial richness and evenness were higher in cases than in controls and differed across the four groups. The variables with the greatest influence on the microbial community composition were related to periodontal disease followed by body mass index, study group affiliation and smoking. Ten taxa exhibited significant differences between case participants and controls. Two Operational Taxonomic Units were particularly abundant in AD compared to controls: Slackia exigua, which was also associated with deep periodontal pockets, and a Lachnospiraceae [G-7] bacterium. Conclusion: It is concluded that in individuals with cognitive impairment or AD, the subgingival microbiota exhibits shifts typical of periodontal disease.
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Affiliation(s)
- Jacob Holmer
- Unit of Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Velma Aho
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Maria Eriksdotter
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
- Theme Aging, Karolinska University Hospital, Huddinge, Sweden
| | - Lars Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Milla Pietiäinen
- Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Marianne Schultzberg
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Pirkko J. Pussinen
- Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kåre Buhlin
- Unit of Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
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26
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Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria. BMC Genomics 2021; 22:28. [PMID: 33413101 PMCID: PMC7788899 DOI: 10.1186/s12864-020-07338-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq for Le. gelidum, Lc. piscium, and P. oligofermentans at 0 °C, 4 °C, 14 °C, 25 °C, and 28 °C. RESULTS We observed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene in all three species. Our results indicated that DEAD-box RNA helicase genes (cshA, cshB) also play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species, indicating that these genes could be part of the cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species. We identified transcription binding site motifs for heat-shock response genes in Le. gelidum and Lc. piscium. Finally, we showed that food spoilage-related genes were upregulated at cold temperatures. CONCLUSIONS The results of this study provide new insights on the cold- and heat-shock response of psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as targets for future studies.
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Lecomte A, Barateau L, Pereira P, Paulin L, Auvinen P, Scheperjans F, Dauvilliers Y. Gut microbiota composition is associated with narcolepsy type 1. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2020; 7:7/6/e896. [PMID: 33037102 PMCID: PMC7577550 DOI: 10.1212/nxi.0000000000000896] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/31/2020] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects. METHODS Thirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1. RESULTS We found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI. CONCLUSION We provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.
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Affiliation(s)
- Alexandre Lecomte
- From the Institute of Biotechnology (A.L., P.P., L.P., P.A.), University of Helsinki, Finland; Sleep-Wake Disorders Unit (L.B., Y.D.), Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier; National Reference Network for Narcolepsy (L.B., Y.D.), CHU Montpellier; PSNREC (L.B., Y.D.), University of Montpellier, INSERM, France; and Department of Neurology (P.P., F.S.), Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Finland
| | - Lucie Barateau
- From the Institute of Biotechnology (A.L., P.P., L.P., P.A.), University of Helsinki, Finland; Sleep-Wake Disorders Unit (L.B., Y.D.), Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier; National Reference Network for Narcolepsy (L.B., Y.D.), CHU Montpellier; PSNREC (L.B., Y.D.), University of Montpellier, INSERM, France; and Department of Neurology (P.P., F.S.), Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Finland
| | - Pedro Pereira
- From the Institute of Biotechnology (A.L., P.P., L.P., P.A.), University of Helsinki, Finland; Sleep-Wake Disorders Unit (L.B., Y.D.), Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier; National Reference Network for Narcolepsy (L.B., Y.D.), CHU Montpellier; PSNREC (L.B., Y.D.), University of Montpellier, INSERM, France; and Department of Neurology (P.P., F.S.), Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Finland
| | - Lars Paulin
- From the Institute of Biotechnology (A.L., P.P., L.P., P.A.), University of Helsinki, Finland; Sleep-Wake Disorders Unit (L.B., Y.D.), Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier; National Reference Network for Narcolepsy (L.B., Y.D.), CHU Montpellier; PSNREC (L.B., Y.D.), University of Montpellier, INSERM, France; and Department of Neurology (P.P., F.S.), Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Finland
| | - Petri Auvinen
- From the Institute of Biotechnology (A.L., P.P., L.P., P.A.), University of Helsinki, Finland; Sleep-Wake Disorders Unit (L.B., Y.D.), Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier; National Reference Network for Narcolepsy (L.B., Y.D.), CHU Montpellier; PSNREC (L.B., Y.D.), University of Montpellier, INSERM, France; and Department of Neurology (P.P., F.S.), Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Finland
| | - Filip Scheperjans
- From the Institute of Biotechnology (A.L., P.P., L.P., P.A.), University of Helsinki, Finland; Sleep-Wake Disorders Unit (L.B., Y.D.), Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier; National Reference Network for Narcolepsy (L.B., Y.D.), CHU Montpellier; PSNREC (L.B., Y.D.), University of Montpellier, INSERM, France; and Department of Neurology (P.P., F.S.), Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Finland
| | - Yves Dauvilliers
- From the Institute of Biotechnology (A.L., P.P., L.P., P.A.), University of Helsinki, Finland; Sleep-Wake Disorders Unit (L.B., Y.D.), Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier; National Reference Network for Narcolepsy (L.B., Y.D.), CHU Montpellier; PSNREC (L.B., Y.D.), University of Montpellier, INSERM, France; and Department of Neurology (P.P., F.S.), Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Finland.
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Aykanat T, Rasmussen M, Ozerov M, Niemelä E, Paulin L, Vähä JP, Hindar K, Wennevik V, Pedersen T, Svenning MA, Primmer CR. Life-history genomic regions explain differences in Atlantic salmon marine diet specialization. J Anim Ecol 2020; 89:2677-2691. [PMID: 33460064 DOI: 10.1111/1365-2656.13324] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 07/14/2020] [Indexed: 01/04/2023]
Abstract
Animals employ various foraging strategies along their ontogeny to acquire energy, and with varying degree of efficiencies, to support growth, maturation and subsequent reproduction events. Individuals that can efficiently acquire energy early are more likely to mature at an earlier age, as a result of faster energy gain which can fuel maturation and reproduction. We aimed to test the hypothesis that heritable resource acquisition variation that covaries with efficiency along the ontogeny would influence maturation timing of individuals. To test this hypothesis, we utilized Atlantic salmon as a model which exhibits a simple, hence trackable, genetic control of maturation age. We then monitored the variation in diet acquisition (quantified as stomach fullness and composition) of individuals with different ages, and linked it with genomic regions (haploblocks) that were previously identified to be associated with age-at-maturity. Consistent with the hypothesis, we demonstrated that one of the life-history genomic regions tested (six6) was indeed associated with age-dependent differences in stomach fullness. Prey composition was marginally linked to six6, and suggestively (but non-significantly) to vgll3 genomic regions. We further showed Atlantic salmon switched to the so-called 'feast and famine' strategy along the ontogeny, where older age groups exhibited heavier stomach content, but that came at the expense of running on empty more often. These results suggest genetic variation underlying resource utilization may explain the genetic basis of age structure in Atlantic salmon. Given that ontogenetic diet has a genetic component and the strong spatial diversity associated with these genomic regions, we predict populations with diverse maturation age will have diverse evolutionary responses to future changes in marine food web structures.
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Affiliation(s)
- Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Martin Rasmussen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mikhail Ozerov
- Department of Biology, University of Turku, Turku, Finland.,Kevo Subarctic Research Institute, University of Turku, Turku, Finland
| | - Eero Niemelä
- Department of Biology, University of Turku, Turku, Finland.,Natural Resources Institute Finland (Luke), Oulu, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juha-Pekka Vähä
- Association for Water and Environment of Western Uusimaa, Lohja, Finland
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | | | - Torstein Pedersen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Martin-A Svenning
- Arctic Ecology Department, Norwegian Institute for Nature Research (NINA), Tromsø, Norway
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Host Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and Function. Curr Biol 2020; 30:3260-3266.e5. [PMID: 32679100 DOI: 10.1016/j.cub.2020.06.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 01/08/2023]
Abstract
The composition of host-associated microbiomes can have important consequences for host health and fitness [1-3]. Yet we still lack understanding of many fundamental processes that determine microbiome composition [4, 5]. There is mounting evidence that historical contingency during microbiome assembly may overshadow more deterministic processes, such as the selective filters imposed by host traits [6-8]. More specifically, species arrival order has been frequently shown to affect microbiome composition [9-12], a phenomenon known as priority effects [13-15]. However, it is less clear whether priority effects during microbiome assembly are consequential for the host [16] or whether intraspecific variation in host traits can alter the trajectory of microbiome assembly under priority effects. In a greenhouse inoculation experiment using the black cottonwood (Populus trichocarpa) foliar microbiome, we manipulated host genotype and the colonization order of common foliar fungi. We quantified microbiome assembly outcomes using fungal marker gene sequencing and measured susceptibility of the colonized host to a leaf rust pathogen, Melampsora × columbiana. We found that the effect of species arrival order on microbiome composition, and subsequent disease susceptibility, depended on the host genotype. Additionally, we found that microbiome assembly history can affect host disease susceptibility independent of microbiome composition at the time of pathogen exposure, suggesting that the interactive effects of species arrival order and host genotype can decouple community composition and function. Overall, these results highlight the importance of a key process underlying stochasticity in microbiome assembly while also revealing which hosts are most likely to experience these effects.
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30
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Heinzel S, Aho VTE, Suenkel U, von Thaler AK, Schulte C, Deuschle C, Paulin L, Hantunen S, Brockmann K, Eschweiler GW, Maetzler W, Berg D, Auvinen P, Scheperjans F. Gut Microbiome Signatures of Risk and Prodromal Markers of Parkinson Disease. Ann Neurol 2020; 88:320-331. [PMID: 32441370 DOI: 10.1002/ana.25788] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Alterations of the gut microbiome in Parkinson disease (PD) have been repeatedly demonstrated. However, little is known about whether such alterations precede disease onset and how they relate to risk and prodromal markers of PD. We investigated associations of these features with gut microbiome composition. METHODS Established risk and prodromal markers of PD as well as factors related to diet/lifestyle, bowel function, and medication were studied in relation to bacterial α-/β-diversity, enterotypes, and differential abundance in stool samples of 666 elderly TREND (Tübingen Evaluation of Risk Factors for Early Detection of Neurodegeneration) study participants. RESULTS Among risk and prodromal markers, physical activity, occupational solvent exposure, and constipation showed associations with α-diversity. Physical activity, sex, constipation, possible rapid eye movement sleep behavior disorder (RBD), and smoking were associated with β-diversity. Subthreshold parkinsonism and physical activity showed an interaction effect. Among other factors, age and urate-lowering medication were associated with α- and β-diversity. Physical inactivity and constipation were highest in individuals with the Firmicutes-enriched enterotype. Constipation was lowest and subthreshold parkinsonism least frequent in individuals with the Prevotella-enriched enterotype. Differentially abundant taxa were linked to constipation, physical activity, possible RBD, smoking, and subthreshold parkinsonism. Substantia nigra hyperechogenicity, olfactory loss, depression, orthostatic hypotension, urinary/erectile dysfunction, PD family history, and the prodromal PD probability showed no significant microbiome associations. INTERPRETATION Several risk and prodromal markers of PD are associated with gut microbiome composition. However, the impact of the gut microbiome on PD risk and potential microbiome-dependent subtypes in the prodrome of PD need further investigation based on prospective clinical and (multi)omics data in incident PD cases. ANN NEUROL 2020;88:320-331.
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Affiliation(s)
- Sebastian Heinzel
- Department of Neurology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Velma T E Aho
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Neurology, Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Helsinki, Finland
| | - Ulrike Suenkel
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Anna-Katharina von Thaler
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Schulte
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Christian Deuschle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sari Hantunen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Kathrin Brockmann
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Gerhard W Eschweiler
- Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany.,Geriatric Center at the University Hospital Tübingen, Tübingen, Germany
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts University of Kiel, Kiel, Germany.,Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Filip Scheperjans
- Department of Neurology, Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Helsinki, Finland
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31
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Enrichment of intracellular sulphur cycle -associated bacteria in intertidal benthic foraminifera revealed by 16S and aprA gene analysis. Sci Rep 2019; 9:11692. [PMID: 31406214 PMCID: PMC6690927 DOI: 10.1038/s41598-019-48166-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 07/30/2019] [Indexed: 12/21/2022] Open
Abstract
Benthic foraminifera are known to play an important role in marine carbon and nitrogen cycles. Here, we report an enrichment of sulphur cycle -associated bacteria inside intertidal benthic foraminifera (Ammonia sp. (T6), Haynesina sp. (S16) and Elphidium sp. (S5)), using a metabarcoding approach targeting the 16S rRNA and aprA -genes. The most abundant intracellular bacterial groups included the genus Sulfurovum and the order Desulfobacterales. The bacterial 16S OTUs are likely to originate from the sediment bacterial communities, as the taxa found inside the foraminifera were also present in the sediment. The fact that 16S rRNA and aprA -gene derived intracellular bacterial OTUs were species-specific and significantly different from the ambient sediment community implies that bacterivory is an unlikely scenario, as benthic foraminifera are known to digest bacteria only randomly. Furthermore, these foraminiferal species are known to prefer other food sources than bacteria. The detection of sulphur-cycle related bacterial genes in this study suggests a putative role for these bacteria in the metabolism of the foraminiferal host. Future investigation into environmental conditions under which transcription of S-cycle genes are activated would enable assessment of their role and the potential foraminiferal/endobiont contribution to the sulphur-cycle.
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32
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Trébeau C, Boutet de Monvel J, Wong Jun Tai F, Petit C, Etournay R. DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments. Bioinformatics 2019; 35:2690-2691. [PMID: 30576403 PMCID: PMC6662285 DOI: 10.1093/bioinformatics/bty1030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/19/2018] [Accepted: 12/17/2018] [Indexed: 11/17/2022] Open
Abstract
Summary Using adequate DNA barcodes is essential to unambiguously identify each DNA library within a multiplexed set of libraries sequenced using next-generation sequencers. We introduce DNABarcodeCompatibility, an R-package that allows one to design single or dual-barcoding multiplex experiments by imposing desired constraints on the barcodes (including sequencer chemistry, barcode pairwise minimal distance and nucleotide content), while optimizing barcode frequency usage, thereby allowing one to both facilitate the demultiplexing step and spare expensive library-preparation kits. The package comes with a user-friendly interface and a web app developed in Java and Shiny (https://dnabarcodecompatibility.pasteur.fr), respectively, with the aim to help bridge the expertise of core facilities with the experimental needs of non-experienced users. Availability and implementation DNABarcodeCompatibility can be easily extended to fulfil specific project needs. The source codes of the R-package and its user interfaces are publicly available along with documentation at [https://github.com/comoto-pasteur-fr] under the GPL-2 licence. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Céline Trébeau
- Unité de Génétique et Physiologie de l'Audition, Département Neuroscience, Institut Pasteur, Paris, France.,UMRS 1120, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Sorbonne Université, Paris, France
| | - Jacques Boutet de Monvel
- Unité de Génétique et Physiologie de l'Audition, Département Neuroscience, Institut Pasteur, Paris, France.,UMRS 1120, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Sorbonne Université, Paris, France
| | - Fabienne Wong Jun Tai
- Unité de Génétique et Physiologie de l'Audition, Département Neuroscience, Institut Pasteur, Paris, France.,UMRS 1120, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Sorbonne Université, Paris, France
| | - Christine Petit
- Unité de Génétique et Physiologie de l'Audition, Département Neuroscience, Institut Pasteur, Paris, France.,UMRS 1120, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Sorbonne Université, Paris, France.,Collège de France, Paris, France. 5Institut de la Vision, Paris, France.,Institut de la Vision, Paris, France
| | - Raphaël Etournay
- Unité de Génétique et Physiologie de l'Audition, Département Neuroscience, Institut Pasteur, Paris, France.,UMRS 1120, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Sorbonne Université, Paris, France
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Chronopoulou PM, Salonen I, Bird C, Reichart GJ, Koho KA. Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera. Front Microbiol 2019; 10:1169. [PMID: 31191490 PMCID: PMC6547873 DOI: 10.3389/fmicb.2019.01169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/07/2019] [Indexed: 12/29/2022] Open
Abstract
Foraminifera are ubiquitous marine protists with an important role in the benthic carbon cycle. However, morphological observations often fail to resolve their exact taxonomic placement and there is a lack of field studies on their particular trophic preferences. Here, we propose the application of metabarcoding as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene. Living foraminiferal specimens were collected from two intertidal mudflats of the Wadden Sea and DNA was extracted from foraminiferal individuals and from the surrounding sediments. Molecular analysis allowed us to confirm that our foraminiferal specimens belong to three genetic types: Ammonia sp. T6, Elphidium sp. S5 and Haynesina sp. S16. Foraminiferal intracellular eukaryote communities reflected to an extent those of the surrounding sediments but at different relative abundances. Unlike sediment eukaryote communities, which were largely determined by the sampling site, foraminiferal intracellular eukaryote communities were driven by foraminiferal species, followed by sediment depth. Our data suggests that Ammonia sp. T6 can predate on metazoan classes, whereas Elphidium sp. S5 and Haynesina sp. S16 are more likely to ingest diatoms. These observations, alongside the use of metabarcoding in similar ecological studies, significantly contribute to our overall understanding of the ecological roles of these protists in intertidal benthic environments and their position and function in the benthic food webs.
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Affiliation(s)
- Panagiota-Myrsini Chronopoulou
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Iines Salonen
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Clare Bird
- Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom
| | - Gert-Jan Reichart
- Department of Ocean Systems, NIOZ-Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, Netherlands
| | - Karoliina A Koho
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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