1
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Hwang Y, Cornman AL, Kellogg EH, Ovchinnikov S, Girguis PR. Genomic language model predicts protein co-regulation and function. Nat Commun 2024; 15:2880. [PMID: 38570504 PMCID: PMC10991518 DOI: 10.1038/s41467-024-46947-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
Deciphering the relationship between a gene and its genomic context is fundamental to understanding and engineering biological systems. Machine learning has shown promise in learning latent relationships underlying the sequence-structure-function paradigm from massive protein sequence datasets. However, to date, limited attempts have been made in extending this continuum to include higher order genomic context information. Evolutionary processes dictate the specificity of genomic contexts in which a gene is found across phylogenetic distances, and these emergent genomic patterns can be leveraged to uncover functional relationships between gene products. Here, we train a genomic language model (gLM) on millions of metagenomic scaffolds to learn the latent functional and regulatory relationships between genes. gLM learns contextualized protein embeddings that capture the genomic context as well as the protein sequence itself, and encode biologically meaningful and functionally relevant information (e.g. enzymatic function, taxonomy). Our analysis of the attention patterns demonstrates that gLM is learning co-regulated functional modules (i.e. operons). Our findings illustrate that gLM's unsupervised deep learning of the metagenomic corpus is an effective and promising approach to encode functional semantics and regulatory syntax of genes in their genomic contexts and uncover complex relationships between genes in a genomic region.
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Affiliation(s)
- Yunha Hwang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | | | - Elizabeth H Kellogg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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2
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Yaeger LN, Ranieri MRM, Chee J, Karabelas-Pittman S, Rudolph M, Giovannoni AM, Harvey H, Burrows LL. A genetic screen identifies a role for oprF in Pseudomonas aeruginosa biofilm stimulation by subinhibitory antibiotics. NPJ Biofilms Microbiomes 2024; 10:30. [PMID: 38521769 PMCID: PMC10960818 DOI: 10.1038/s41522-024-00496-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/05/2024] [Indexed: 03/25/2024] Open
Abstract
Biofilms are surface-associated communities of bacteria that grow in a self-produced matrix of polysaccharides, proteins, and extracellular DNA (eDNA). Sub-minimal inhibitory concentrations (sub-MIC) of antibiotics induce biofilm formation, potentially as a defensive response to antibiotic stress. However, the mechanisms behind sub-MIC antibiotic-induced biofilm formation are unclear. We show that treatment of Pseudomonas aeruginosa with multiple classes of sub-MIC antibiotics with distinct targets induces biofilm formation. Further, addition of exogenous eDNA or cell lysate failed to increase biofilm formation to the same extent as antibiotics, suggesting that the release of cellular contents by antibiotic-driven bacteriolysis is insufficient. Using a genetic screen for stimulation-deficient mutants, we identified the outer membrane porin OprF and the ECF sigma factor SigX as important. Similarly, loss of OmpA - the Escherichia coli OprF homolog - prevented sub-MIC antibiotic stimulation of E. coli biofilms. Our screen also identified the periplasmic disulfide bond-forming enzyme DsbA and a predicted cyclic-di-GMP phosphodiesterase encoded by PA2200 as essential for biofilm stimulation. The phosphodiesterase activity of PA2200 is likely controlled by a disulfide bond in its regulatory domain, and folding of OprF is influenced by disulfide bond formation, connecting the mutant phenotypes. Addition of reducing agent dithiothreitol prevented sub-MIC antibiotic biofilm stimulation. Finally, activation of a c-di-GMP-responsive promoter follows treatment with sub-MIC antibiotics in the wild-type but not an oprF mutant. Together, these results show that antibiotic-induced biofilm formation is likely driven by a signaling pathway that translates changes in periplasmic redox state into elevated biofilm formation through increases in c-di-GMP.
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Affiliation(s)
- Luke N Yaeger
- Biochemistry and Biomedical Sciences and the Michael G. DeGroote Centre for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Michael R M Ranieri
- Biochemistry and Biomedical Sciences and the Michael G. DeGroote Centre for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Jessica Chee
- Biochemistry and Biomedical Sciences and the Michael G. DeGroote Centre for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Sawyer Karabelas-Pittman
- Biochemistry and Biomedical Sciences and the Michael G. DeGroote Centre for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Madeleine Rudolph
- Biochemistry and Biomedical Sciences and the Michael G. DeGroote Centre for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Alessio M Giovannoni
- Biochemistry and Biomedical Sciences and the Michael G. DeGroote Centre for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Hanjeong Harvey
- Biochemistry and Biomedical Sciences and the Michael G. DeGroote Centre for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Lori L Burrows
- Biochemistry and Biomedical Sciences and the Michael G. DeGroote Centre for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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3
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Bergfeldt N, Kırdök E, Oskolkov N, Mirabello C, Unneberg P, Malmström H, Fraser M, Sanchez-Quinto F, Jorgensen R, Skar B, Lidén K, Jakobsson M, Storå J, Götherström A. Identification of microbial pathogens in Neolithic Scandinavian humans. Sci Rep 2024; 14:5630. [PMID: 38453993 PMCID: PMC10920878 DOI: 10.1038/s41598-024-56096-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.
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Affiliation(s)
- Nora Bergfeldt
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
| | - Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey
| | - Nikolay Oskolkov
- Science for Life Laboratory, Department of Biology, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden
| | - Claudio Mirabello
- Science for Life Laboratory, Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden
| | - Per Unneberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | - Magdalena Fraser
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | | | - Roger Jorgensen
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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4
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Chirabhundhu N, Luk-In S, Phuadraksa T, Wichit S, Chatsuwan T, Wannigama DL, Yainoy S. Occurrence and mechanisms of tigecycline resistance in carbapenem- and colistin-resistant Klebsiella pneumoniae in Thailand. Sci Rep 2024; 14:5215. [PMID: 38433246 PMCID: PMC10909888 DOI: 10.1038/s41598-024-55705-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024] Open
Abstract
Tigecycline has been regarded as one of the most important last-resort antibiotics for the treatment of infections caused by extensively drug-resistant (XDR) bacteria, particularly carbapenem- and colistin-resistant Klebsiella pneumoniae (C-C-RKP). However, reports on tigecycline resistance have been growing. Overall, ~ 4000 K. pneumoniae clinical isolates were collected over a five-year period (2017-2021), in which 240 isolates of C-C-RKP were investigated. Most of these isolates (91.7%) were resistant to tigecycline. Notably, a high-risk clone of ST16 was predominantly identified, which was associated with the co-harboring of blaNDM-1 and blaOXA-232 genes. Their major mechanism of tigecycline resistance was the overexpression of efflux pump acrB gene and its regulator RamA, which was caused by mutations in RamR (M184V, Y59C, I141T, A28T, C99/C100 insertion), in RamR binding site (PI) of ramA gene (C139T), in MarR (S82G), and/or in AcrR (L154R, R13Q). Interestingly, four isolates of ST147 carried the mutated tet(A) efflux pump gene. To our knowledge, this is the first report on the prevalence and mechanisms of tigecycline resistance in C-C-RKP isolated from Thailand. The high incidence of tigecycline resistance observed among C-C-RKP in this study reflects an ongoing evolution of XDR bacteria against the last-resort antibiotics, which demands urgent action.
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Affiliation(s)
- Nachat Chirabhundhu
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Sirirat Luk-In
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Thanawat Phuadraksa
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Sineewanlaya Wichit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Dhammika Leshan Wannigama
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries, The University of Sheffield, Sheffield, UK
- Pathogen Hunter's Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Sakda Yainoy
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand.
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5
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Liu X, Tong X, Zou L, Ju Y, Liu M, Han M, Lu H, Yang H, Wang J, Zong Y, Liu W, Xu X, Jin X, Xiao L, Jia H, Guo R, Zhang T. A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome. Commun Biol 2024; 7:139. [PMID: 38291185 PMCID: PMC10828421 DOI: 10.1038/s42003-024-05822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024] Open
Abstract
The nasal cavity harbors diverse microbiota that contributes to human health and respiratory diseases. However, whether and to what extent the host genome shapes the nasal microbiome remains largely unknown. Here, by dissecting the human genome and nasal metagenome data from 1401 healthy individuals, we demonstrated that the top three host genetic principal components strongly correlated with the nasal microbiota diversity and composition. The genetic association analyses identified 63 genome-wide significant loci affecting the nasal microbial taxa and functions, of which 2 loci reached study-wide significance (p < 1.7 × 10-10): rs73268759 within CAMK2A associated with genus Actinomyces and family Actinomycetaceae; and rs35211877 near POM121L12 with Gemella asaccharolytica. In addition to respiratory-related diseases, the associated loci are mainly implicated in cardiometabolic or neuropsychiatric diseases. Functional analysis showed the associated genes were most significantly expressed in the nasal airway epithelium tissue and enriched in the calcium signaling and hippo signaling pathway. Further observational correlation and Mendelian randomization analyses consistently suggested the causal effects of Serratia grimesii and Yokenella regensburgei on cardiometabolic biomarkers (cystine, glutamic acid, and creatine). This study suggested that the host genome plays an important role in shaping the nasal microbiome.
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Affiliation(s)
- Xiaomin Liu
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Tong
- BGI Research, Shenzhen, 518083, China
| | | | - Yanmei Ju
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Mo Han
- BGI Research, Shenzhen, 518083, China
| | - Haorong Lu
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huanming Yang
- BGI Research, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Jian Wang
- BGI Research, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Yang Zong
- BGI Research, Shenzhen, 518083, China
| | | | - Xun Xu
- BGI Research, Shenzhen, 518083, China
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huijue Jia
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong, China.
- School of Life Sciences, Fudan University, Shanghai, China.
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6
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Shi J, Yi M, Xie S, Wang Z, Zhang X, Tan X, Tao D, Liu Y, Yang Y. Mendelian randomization study revealed a gut microbiota-neuromuscular junction axis in myasthenia gravis. Sci Rep 2024; 14:2473. [PMID: 38291090 PMCID: PMC10827739 DOI: 10.1038/s41598-024-52469-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024] Open
Abstract
A growing number of studies have implicated that gut microbiota abundance is associated with myasthenia gravis (MG). However, the causal relationship underlying the associations is still unclear. Here, we aim to investigate the causal effect of gut microbiota on MG using Mendelian randomization (MR) method. Publicly available Genome-wide association study (GWAS) summary-level data for gut microbiota and for MG were extracted. Inverse variance weighted was used as the main method to analyze causality. The robustness of the results was validated with sensitivity analyses. Our results indicated that genetically predicted increased phylum Lentisphaerae (OR = 1.319, p = 0.026), class Lentisphaerae (OR = 1.306, p = 0.044), order Victivallales (OR = 1.306, p = 0.044), order Mollicutes (OR = 1.424, p = 0.041), and genus Faecalibacterium (OR = 1.763, p = 0.002) were potentially associated with a higher risk of MG; while phylum Actinobacteria (OR = 0.602, p = 0.0124), class Gammaproteobacteria (OR = 0.587, p = 0.036), family Defluviitaleaceae (OR = 0.695, p = 0.047), family Peptococcaceae (OR = 0.698, p = 0.029), and family Family XIII (OR = 0.614, p = 0.017) were related to a lower risk of MG. The present study provides genetic evidence for the causal associations between gut microbiota and MG, thus suggesting novel insights into the gut microbiota-neuromuscular junction axis in the pathogenesis of MG.
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Affiliation(s)
- Jiaying Shi
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ming Yi
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shengyu Xie
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zhaokun Wang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xinyue Zhang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaolan Tan
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Dachang Tao
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
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7
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Zhang H, Ma J, Wu Z, Chen X, Qian Y, Chen W, Wang Z, Zhang Y, Zhu H, Huang X, Ji Q. BacPE: a versatile prime-editing platform in bacteria by inhibiting DNA exonucleases. Nat Commun 2024; 15:825. [PMID: 38280845 PMCID: PMC10821919 DOI: 10.1038/s41467-024-45114-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024] Open
Abstract
Prime editing allows precise installation of any single base substitution and small insertions and deletions without requiring homologous recombination or double-strand DNA breaks in eukaryotic cells. However, the applications in bacteria are hindered and the underlying mechanisms that impede efficient prime editing remain enigmatic. Here, we report the determination of vital cellular factors that affect prime editing in bacteria. Genetic screening of 129 Escherichia coli transposon mutants identified sbcB, a 3'→5' DNA exonuclease, as a key genetic determinant in impeding prime editing in E. coli, combinational deletions of which with two additional 3'→5' DNA exonucleases, xseA and exoX, drastically enhanced the prime editing efficiency by up to 100-fold. Efficient prime editing in wild-type E. coli can be achieved by simultaneously inhibiting the DNA exonucleases via CRISPRi. Our results pave the way for versatile applications of prime editing for bacterial genome engineering.
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Affiliation(s)
- Hongyuan Zhang
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Jiacheng Ma
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Zhaowei Wu
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Xiaoyang Chen
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Yangyang Qian
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Weizhong Chen
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Zhipeng Wang
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Ya Zhang
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Huanhu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xingxu Huang
- Zhejiang Lab, Hangzhou, Zhejiang, 311121, China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Quanjiang Ji
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China.
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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8
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Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye IM, Gomis J, Ndiop M, Sene D, Faye Paye M, MacInnis BL, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ. Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing. Nat Commun 2024; 15:747. [PMID: 38272885 PMCID: PMC10810818 DOI: 10.1038/s41467-024-44800-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024] Open
Abstract
The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
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Affiliation(s)
- Zoë C Levine
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, USA
| | - Aita Sene
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Winnie Mkandawire
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Awa B Deme
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Tolla Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Mouhamad Sy
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Amy Gaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Younouss Diedhiou
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Amadou M Mbaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Ibrahima M Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Jules Gomis
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Médoune Ndiop
- Programme National de lutte contre le Paludisme, Ministère de la Santé, Dakar Fann, Senegal
| | - Doudou Sene
- Programme National de lutte contre le Paludisme, Ministère de la Santé, Dakar Fann, Senegal
| | | | - Bronwyn L MacInnis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aida S Badiane
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Andres Colubri
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Mouhamadou Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Ngayo Sy
- Service de Lutte Anti Parasitaire, Thies, Senegal
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Daouda Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal.
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal.
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
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9
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Hu T, Chen J, Lin X, He W, Liang H, Wang M, Li W, Wu Z, Han M, Jin X, Kristiansen K, Xiao L, Zou Y. Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly. Sci Rep 2024; 14:1292. [PMID: 38221534 PMCID: PMC10788345 DOI: 10.1038/s41598-024-51725-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024] Open
Abstract
The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.
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Affiliation(s)
- Tongyuan Hu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Xiaoqian Lin
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Wenxin He
- BGI Research, Shenzhen, 518083, China
| | - Hewei Liang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Wenxi Li
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Zhinan Wu
- BGI Research, Shenzhen, 518083, China
| | - Mo Han
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Karsten Kristiansen
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen, 518083, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China.
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10
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Groussman RD, Blaskowski S, Coesel SN, Armbrust EV. MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes. Sci Data 2023; 10:926. [PMID: 38129449 PMCID: PMC10739892 DOI: 10.1038/s41597-023-02842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.
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Affiliation(s)
- R D Groussman
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA.
| | - S Blaskowski
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Molecular Engineering & Sciences Building 3946 W Stevens Way NE, Seattle, WA, 98195, USA
| | - S N Coesel
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA
| | - E V Armbrust
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA.
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11
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Medeot D, Sannazzaro A, Estrella MJ, Torres Tejerizo G, Contreras-Moreira B, Pistorio M, Jofré E. Unraveling the genome of Bacillus velezensis MEP 218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis. Sci Rep 2023; 13:22168. [PMID: 38092837 PMCID: PMC10719345 DOI: 10.1038/s41598-023-49194-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16-C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892 bp, with a total of 3474 coding sequences and a G + C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1-4 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16-C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.
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Affiliation(s)
- Daniela Medeot
- Instituto de Biotecnología Ambiental y Salud (INBIAS), CCT-CONICET-Córdoba, Universidad Nacional de Río Cuarto, 5800, Córdoba, Argentina
| | - Analía Sannazzaro
- Instituto Tecnológico de Chascomús (INTECH), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín (UNSAM), 7130, Chascomús, Argentina
| | - María Julia Estrella
- Instituto Tecnológico de Chascomús (INTECH), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín (UNSAM), 7130, Chascomús, Argentina
| | - Gonzalo Torres Tejerizo
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, 1900, La Plata, Argentina
| | | | - Mariano Pistorio
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, 1900, La Plata, Argentina
| | - Edgardo Jofré
- Instituto de Biotecnología Ambiental y Salud (INBIAS), CCT-CONICET-Córdoba, Universidad Nacional de Río Cuarto, 5800, Córdoba, Argentina.
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12
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Mohabati Mobarez A, Baseri N, Khalili M, Mostafavi E, Esmaeili S. Genotyping and phylogenetic analysis of Coxiella burnetii in domestic ruminant and clinical samples in Iran: insights into Q fever epidemiology. Sci Rep 2023; 13:20374. [PMID: 37990125 PMCID: PMC10663619 DOI: 10.1038/s41598-023-47920-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 11/20/2023] [Indexed: 11/23/2023] Open
Abstract
Coxiella burnetii, a zoonotic pathogen, is the causative agent of Q fever, an endemic disease in Iran. However, there is currently a lack of available data on the genotypes of C. burnetii in the country. Here, we typed 26 C. burnetii isolates detected in milk, abortion, cotylodon, and cardiac valve samples from various geographical areas and hosts (7 cattle, 8 goats, 10 sheep, and 1 human) using Multilocus Variable Number Tandem Repeat Analysis (MLVA/VNTR) with five loci:ms24, ms27, ms28, ms33, and ms34. As IS1111 was observed to be spontaneously inserted in locus ms23 across all of our examined C. burnetii samples, five loci were employed for MLVA/VNTR genotyping. Among the 26 C. burnetii strains, 22 distinct genotypes (A-V) were identified in the discriminative loci. In silico analysis categorized Iranian C. burnetii strains into five genomic groups along with seven singletons, representing 11 exiting clonal complexes worldwide. Clusters 10 and 11 exclusively consisted of Iranian samples. These findings revealed high genotyping diversity among C. burnetii isolates in Iran. The genotypes circulating in Iran differed significantly from those found in other regions worldwide. To gain a comprehensive understanding of Q fever epidemiology in Iran, it is crucial to conduct large-scale studies that assess the distribution of C. burnetii genotypes across different geographical areas, hosts, and sources.
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Affiliation(s)
- Ashraf Mohabati Mobarez
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Neda Baseri
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Epidemiology and Biostatics, Pasteur Institute of Iran, Tehran, Iran
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Disease, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran
| | - Mohammad Khalili
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ehsan Mostafavi
- Department of Epidemiology and Biostatics, Pasteur Institute of Iran, Tehran, Iran
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Disease, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran
| | - Saber Esmaeili
- Department of Epidemiology and Biostatics, Pasteur Institute of Iran, Tehran, Iran.
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Disease, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran.
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13
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Ma T, Huang W, Li Y, Jin H, Kwok LY, Sun Z, Zhang H. Author Correction: Probiotics alleviate constipation and inflammation in late gestating and lactating sows. NPJ Biofilms Microbiomes 2023; 9:88. [PMID: 37985655 PMCID: PMC10662089 DOI: 10.1038/s41522-023-00455-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Affiliation(s)
- Teng Ma
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Weiqiang Huang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Yalin Li
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Hao Jin
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
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14
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Teixeira IM, de Moraes Assumpção Y, Paletta ACC, Aguiar L, Guimarães L, da Silva IT, Côrtes MF, Botelho AMN, Jaeger LH, Ferreira RF, de Oliveira Ferreira E, Penna B. Investigation of antimicrobial susceptibility and genetic diversity among Staphylococcus pseudintermedius isolated from dogs in Rio de Janeiro. Sci Rep 2023; 13:20219. [PMID: 37980395 PMCID: PMC10657392 DOI: 10.1038/s41598-023-47549-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/15/2023] [Indexed: 11/20/2023] Open
Abstract
Staphylococcus pseudintermedius is an opportunistic pathogen causing a variety of infections that are difficult to treat, especially because of the development of antimicrobial resistance. It has a clonal distribution around the world. To have a better understanding of the MRSP population, we search the presence of MRSP in colonized or infected dogs. Samples from 99 dogs with infections and 35 from asymptomatic dogs were collected. Isolates were identified by mass spectrometry and Multiplex-PCR. The mecA gene was confirmed by conventional PCR. MRSP strains were analyzed by whole-genome sequencing. 75 S. pseudintermedius were identified, most from infection cases. The species were isolated from 70 out of the 135 dogs. Penicillin and Trimethoprim/Sulfamethoxazole presented higher resistance rates. Forty-seven strains were classified as multi-drug resistant (MDR), and were more isolated from dogs with infection (P < 0.05). Eighteen samples were classified as MRSP, representing 24.0% of the population. Six of 16 MRSP sequenced samples belonged to the world spread clone ST71; others belonged to unknown clones. Most samples carried the SCCmec type IIIA. Twenty-one different genetic resistance determinants were found among MRPS strains. MRSP is circulating among infected and colonized dogs in Rio de Janeiro, Brazil.
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Affiliation(s)
- Izabel Mello Teixeira
- Laboratório de Biologia de Anaeróbios, Departamento Microbiologia Médica, IMPPG, UFRJ, Rio de Janeiro, Brazil
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Yasmim de Moraes Assumpção
- Laboratório de Biologia de Anaeróbios, Departamento Microbiologia Médica, IMPPG, UFRJ, Rio de Janeiro, Brazil
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Ana Clara Cabral Paletta
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Louise Aguiar
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Luciana Guimarães
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Isabella Thomaz da Silva
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Marina F Côrtes
- Laboratório de Investigação Médica, Instituto de Medicina Tropical, USP, São Paulo, Brazil
| | - Ana Maria Nunes Botelho
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Lauren Hubert Jaeger
- Laboratório de Células-Tronco e Parasitologia Molecular, Departamento de Ciências Farmacêuticas, UFJF, Juiz de Fora, Brazil
| | | | - Eliane de Oliveira Ferreira
- Laboratório de Biologia de Anaeróbios, Departamento Microbiologia Médica, IMPPG, UFRJ, Rio de Janeiro, Brazil
| | - Bruno Penna
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil.
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15
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Rueff AS, van Raaphorst R, Aggarwal SD, Santos-Moreno J, Laloux G, Schaerli Y, Weiser JN, Veening JW. Synthetic genetic oscillators demonstrate the functional importance of phenotypic variation in pneumococcal-host interactions. Nat Commun 2023; 14:7454. [PMID: 37978173 PMCID: PMC10656556 DOI: 10.1038/s41467-023-43241-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Phenotypic variation is the phenomenon in which clonal cells display different traits even under identical environmental conditions. This plasticity is thought to be important for processes including bacterial virulence, but direct evidence for its relevance is often lacking. For instance, variation in capsule production in the human pathogen Streptococcus pneumoniae has been linked to different clinical outcomes, but the exact relationship between variation and pathogenesis is not well understood due to complex natural regulation. In this study, we use synthetic oscillatory gene regulatory networks (GRNs) based on CRISPR interference (CRISPRi) together with live cell imaging and cell tracking within microfluidics devices to mimic and test the biological function of bacterial phenotypic variation. We provide a universally applicable approach for engineering intricate GRNs using only two components: dCas9 and extended sgRNAs (ext-sgRNAs). Our findings demonstrate that variation in capsule production is beneficial for pneumococcal fitness in traits associated with pathogenesis providing conclusive evidence for this longstanding question.
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Affiliation(s)
- Anne-Stéphanie Rueff
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
| | - Renske van Raaphorst
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200, Brussels, Belgium
| | - Surya D Aggarwal
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Javier Santos-Moreno
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
- Pompeu Fabra University, Barcelona, Spain
| | - Géraldine Laloux
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200, Brussels, Belgium
| | - Yolanda Schaerli
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland
| | - Jeffrey N Weiser
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015, Lausanne, Switzerland.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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16
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Allard N, Collette A, Paquette J, Rodrigue S, Côté JP. Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids. Commun Biol 2023; 6:1172. [PMID: 37973843 PMCID: PMC10654706 DOI: 10.1038/s42003-023-05534-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.
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Affiliation(s)
- Nancy Allard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Arianne Collette
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Josianne Paquette
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
| | - Jean-Philippe Côté
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
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17
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Liu R, Zou Y, Wang WQ, Chen JH, Zhang L, Feng J, Yin JY, Mao XY, Li Q, Luo ZY, Zhang W, Wang DM. Gut microbial structural variation associates with immune checkpoint inhibitor response. Nat Commun 2023; 14:7421. [PMID: 37973916 PMCID: PMC10654443 DOI: 10.1038/s41467-023-42997-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023] Open
Abstract
The gut microbiota may have an effect on the therapeutic resistance and toxicity of immune checkpoint inhibitors (ICIs). However, the associations between the highly variable genomes of gut bacteria and the effectiveness of ICIs remain unclear, despite the fact that merely a few gene mutations between similar bacterial strains may cause significant phenotypic variations. Here, using datasets from the gut microbiome of 996 patients from seven clinical trials, we systematically identify microbial genomic structural variants (SVs) using SGV-Finder. The associations between SVs and response, progression-free survival, overall survival, and immune-related adverse events are systematically explored by metagenome-wide association analysis and replicated in different cohorts. Associated SVs are located in multiple species, including Akkermansia muciniphila, Dorea formicigenerans, and Bacteroides caccae. We find genes that encode enzymes that participate in glucose metabolism be harbored in these associated regions. This work uncovers a nascent layer of gut microbiome heterogeneity that is correlated with hosts' prognosis following ICI treatment and represents an advance in our knowledge of the intricate relationships between microbiota and tumor immunotherapy.
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Affiliation(s)
- Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China.
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China.
| | - You Zou
- Information and Network center, Central South University, Changsha, 410083, P.R. China
| | - Wei-Quan Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Jun-Hong Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Lei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Jia Feng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Xiao-Yuan Mao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Zhi-Ying Luo
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, PR China
- Institute of Clinical Pharmacy, Central South University, Changsha, PR China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China.
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China.
| | - Dao-Ming Wang
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, 9713AV, the Netherlands.
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, 9713AV, the Netherlands.
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18
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Song Z, Zhou S, Zhang H, Keller NP, Oakley BR, Liu X, Yin WB. Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex. Nat Commun 2023; 14:7351. [PMID: 37963872 PMCID: PMC10645843 DOI: 10.1038/s41467-023-43205-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 11/03/2023] [Indexed: 11/16/2023] Open
Abstract
Production of secondary metabolites is controlled by a complicated regulatory network in eukaryotic cells. Several layers of regulators are involved in this process, ranging from pathway-specific regulation, to epigenetic control, to global regulation. Here, we discover that interaction of an RNA-binding protein CsdA with a regulator RsdA coordinates fungal secondary metabolism. Employing a genetic deletion approach and transcriptome analysis as well as metabolomics analysis, we reveal that CsdA and RsdA synergistically regulate fungal secondary metabolism comprehensively. Mechanistically, comprehensive genetic and biochemical studies prove that RsdA and CsdA co-localize in the nucleus and physically interact to achieve their functions. In particular, we demonstrate that CsdA mediates rsdA expression by binding specific motif "GUCGGUAU" of its pre-mRNA at a post-transcriptional level. We thus uncover a mechanism in which RNA-binding protein physically interacts with, and controls the expression level of, the RsdA to coordinate fungal secondary metabolism.
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Affiliation(s)
- Zili Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, PR China
| | - Shuang Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Hongjiao Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, PR China
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China.
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, PR China.
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19
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Bloemen B, Gand M, Vanneste K, Marchal K, Roosens NHC, De Keersmaecker SCJ. Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance. Sci Rep 2023; 13:19656. [PMID: 37952062 PMCID: PMC10640560 DOI: 10.1038/s41598-023-46771-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/04/2023] [Indexed: 11/14/2023] Open
Abstract
Rapid, accurate and comprehensive diagnostics are essential for outbreak prevention and pathogen surveillance. Real-time, on-site metagenomics on miniaturized devices, such as Oxford Nanopore Technologies MinION sequencing, could provide a promising approach. However, current sample preparation protocols often require substantial equipment and dedicated laboratories, limiting their use. In this study, we developed a rapid on-site applicable DNA extraction and library preparation approach for nanopore sequencing, using portable devices. The optimized method consists of a portable mechanical lysis approach followed by magnetic bead-based DNA purification and automated sequencing library preparation, and resulted in a throughput comparable to a current optimal, laboratory-based protocol using enzymatic digestion to lyse cells. By using spike-in reference communities, we compared the on-site method with other workflows, and demonstrated reliable taxonomic profiling, despite method-specific biases. We also demonstrated the added value of long-read sequencing by recovering reads containing full-length antimicrobial resistance genes, and attributing them to a host species based on the additional genomic information they contain. Our method may provide a rapid, widely-applicable approach for microbial detection and surveillance in a variety of on-site settings.
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Affiliation(s)
- Bram Bloemen
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052, Ghent, Belgium
| | - Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium
| | - Sigrid C J De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, Rue Juliette Wytsman 14, 1050, Brussels, Belgium.
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20
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Sokolov S, Brovko F, Solonin A, Nikanova D, Fursova K, Artyemieva O, Kolodina E, Sorokin A, Shchannikova M, Dzhelyadin T, Ermakov A, Boziev K, Zinovieva N. Genomic analysis and assessment of pathogenic (toxicogenic) potential of Staphylococcus haemolyticus and Bacillus paranthracis consortia isolated from bovine mastitis in Russia. Sci Rep 2023; 13:18646. [PMID: 37903798 PMCID: PMC10616132 DOI: 10.1038/s41598-023-45643-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/22/2023] [Indexed: 11/01/2023] Open
Abstract
Three stable microbial consortia, each composed of Bacillus paranthracis and Staphylococcus haemolyticus strains, were isolated from milk of cows diagnosed with mastitis in three geographically remote regions of Russia. The composition of these consortia remained stable following multiple passages on culture media. Apparently, this stability is due to the structure of the microbial biofilms formed by the communities. The virulence of the consortia depended on the B. paranthracis strains. It seems plausible that the ability of the consortia to cause mastitis in cattle was affected by mutations of the cytK gene of B. paranthracis.
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Affiliation(s)
- Sergei Sokolov
- Laboratory of Microbiology, L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, 142132, Russia.
- Laboratory of Plasmid Biology, Federal Research Center "Pushchino Scientific Center for Biological Researches", G.K. Skryabin Institute of Biochemistry & Physiology of Microorganisms of the Russian Academy of Sciences, Pushchino, 142290, Russia.
| | - Fedor Brovko
- Laboratory of Microbiology, L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, 142132, Russia
- Laboratory of Immunochemistry, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Alexander Solonin
- Laboratory of Plasmid Biology, Federal Research Center "Pushchino Scientific Center for Biological Researches", G.K. Skryabin Institute of Biochemistry & Physiology of Microorganisms of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Daria Nikanova
- Laboratory of Microbiology, L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, 142132, Russia
| | - Ksenia Fursova
- Laboratory of Immunochemistry, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Olga Artyemieva
- Laboratory of Microbiology, L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, 142132, Russia
| | - Evgenia Kolodina
- Laboratory of Microbiology, L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, 142132, Russia
| | - Anatoly Sorokin
- Laboratory of Cell Genome Functioning Mechanisms, Federal Research Center "Pushchino Scientific Center for Biological Researches", Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Margarita Shchannikova
- Laboratory of Immunochemistry, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Timur Dzhelyadin
- Laboratory of Cell Genome Functioning Mechanisms, Federal Research Center "Pushchino Scientific Center for Biological Researches", Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Artem Ermakov
- Laboratory of Cell Genome Functioning Mechanisms, Federal Research Center "Pushchino Scientific Center for Biological Researches", Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Khanafy Boziev
- Laboratory of Immunochemistry, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Natalia Zinovieva
- Laboratory of Microbiology, L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, 142132, Russia
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21
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Jiang S, Zhang C, Han Z, Ma W, Wang S, Huo D, Cui W, Zhai Q, Huang S, Zhang J. Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut. NPJ Biofilms Microbiomes 2023; 9:80. [PMID: 37838684 PMCID: PMC10576824 DOI: 10.1038/s41522-023-00447-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
Probiotics often acquire potentially adaptive mutations in vivo, gaining new functional traits through gut selection. While both the host and microbiome can contribute to probiotics' genetic evolution, separating the microbiome and the host's contribution to such selective pressures remains challenging. Here, we introduced germ-free (GF) and specific pathogen-free (SPF) mouse models to track how probiotic strains, i.e., Lactiplantibacillus plantarum HNU082 (Lp082) and Bifidobacterium animalis subsp. lactis V9 (BV9), genetically evolved under selection pressures derived from host factors alone and both host and microbial ecological factors. Notably, compared to the genome of a probiotic strain before consumption, the host only elicited <15 probiotic mutations in probiotic genomes that emerged in the luminal environment of GF mice, while a total of 840 mutations in Lp082 mutants and 21,579 mutations in BV9 were found in SPF mice, <0.25% of those derived from both factors that were never captured by other experimental evolution studies, indicating that keen microbial competitions exhibited the predominant evolutionary force in shaping probiotic genetic composition (>99.75%). For a given probiotic, functional genes occurring in potentially adaptive mutations induced by hosts (GF mice) were all shared with those found in mutants of SPF mice. Collectively, the native microbiome consistently drove a more rapid and divergent genetic evolution of probiotic strains in seven days of colonization than host factors did. Our study further laid a theoretical foundation for genetically engineering probiotics for better gut adaptation through in vitro artificial gut ecosystems without the selection pressures derived from host factors.
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Affiliation(s)
- Shuaiming Jiang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Chengcheng Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhe Han
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Wenyao Ma
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Shunhe Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Dongxue Huo
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Weipeng Cui
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Qixiao Zhai
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China.
| | - Jiachao Zhang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China.
- One Health Institute, Hainan University, Haikou, Hainan, 570228, China.
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22
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Sünderhauf D, Klümper U, Gaze WH, Westra ER, van Houte S. Interspecific competition can drive plasmid loss from a focal species in a microbial community. ISME J 2023; 17:1765-1773. [PMID: 37558861 PMCID: PMC10504238 DOI: 10.1038/s41396-023-01487-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
Plasmids are key disseminators of antimicrobial resistance genes and virulence factors, and it is therefore critical to predict and reduce plasmid spread within microbial communities. The cost of plasmid carriage is a key metric that can be used to predict plasmids' ecological fate, and it is unclear whether plasmid costs are affected by growth partners in a microbial community. We carried out competition experiments and tracked plasmid maintenance using a model system consisting of a synthetic and stable five-species community and a broad host-range plasmid, engineered to carry different payloads. We report that both the cost of plasmid carriage and its long-term maintenance in a focal strain depended on the presence of competitors, and that these interactions were species specific. Addition of growth partners increased the cost of a high-payload plasmid to a focal strain, and accordingly, plasmid loss from the focal species occurred over a shorter time frame. We propose that the destabilising effect of interspecific competition on plasmid maintenance may be leveraged in clinical and natural environments to cure plasmids from focal strains.
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Affiliation(s)
- David Sünderhauf
- Centre for Ecology and Conservation, University of Exeter, Environment and Sustainability Institute, Penryn, TR10 9FE, UK.
| | - Uli Klümper
- Department Hydrosciences, Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn, TR10 9FE, UK
| | - Edze R Westra
- Centre for Ecology and Conservation, University of Exeter, Environment and Sustainability Institute, Penryn, TR10 9FE, UK
| | - Stineke van Houte
- Centre for Ecology and Conservation, University of Exeter, Environment and Sustainability Institute, Penryn, TR10 9FE, UK.
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23
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Hazarika DJ, Bora SS, Naorem RS, Sharma D, Boro RC, Barooah M. Genomic insights into Bacillus subtilis MBB3B9 mediated aluminium stress mitigation for enhanced rice growth. Sci Rep 2023; 13:16467. [PMID: 37777563 PMCID: PMC10542363 DOI: 10.1038/s41598-023-42804-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/14/2023] [Indexed: 10/02/2023] Open
Abstract
Aluminium (Al) toxicity in acid soil ecosystems is a major impediment to crop production as it drastically affects plant root growth, thereby acquisition of nutrients from the soil. Plant growth-promoting bacteria offers an interesting avenue for promoting plant growth under an Al-phytotoxic environment. Here, we report the plant growth-promoting activities of an acid-tolerant isolate of Bacillus subtilis that could ameliorate acid-induced Al-stress in rice (Oryza sativa L.). The whole genome sequence data identified the major genes and genetic pathways in B. subtilis MBB3B9, which contribute to the plant growth promotion in acidic pH. Genetic pathways for organic acid production, denitrification, urea metabolism, indole-3-acetic acid (IAA) production, and cytokinin biosynthesis were identified as major genetic machinery for plant growth promotion and mitigation of Al-stress in plants. The in-vitro analyses revealed the production of siderophores and organic acid production as primary mechanisms for mitigation of Al-toxicity. Other plant growth-promoting properties such as phosphate solubilization, zinc solubilization, and IAA production were also detected in significant levels. Pot experiments involving rice under acidic pH and elevated concentrations of aluminium chloride (AlCl3) suggested that soil treatment with bacterial isolate MBB3B9 could enhance plant growth and productivity compared to untreated plants. A significant increase in plant growth and productivity was recorded in terms of plant height, chlorophyll content, tiller number, panicle number, grain yield, root growth, and root biomass production.
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Affiliation(s)
- Dibya Jyoti Hazarika
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sudipta Sankar Bora
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Romen Singh Naorem
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Darshana Sharma
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Robin Chandra Boro
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
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24
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Fonseca PAS, Lam S, Chen Y, Waters SM, Guan LL, Cánovas A. Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency. Sci Rep 2023; 13:16209. [PMID: 37758745 PMCID: PMC10533831 DOI: 10.1038/s41598-023-43097-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log2(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle.
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Grants
- Beef Farmers of Ontario, Genome Canada and the Sustainable Beef and Forage Science Cluster funded by the Canadian Beef Cattle Check-Off, Beef Cattle Research Council (BCRC), Alberta Beef Producers, Alberta Cattle Feeders’ Association, Beef Farmers of Ontario, La Fédération des Productuers de bovins du Québec, and Agriculture and Agri-Food Canada’s Canadian Agricultural Partnership
- Ontario Ministry of Agriculture, Food, and Rural Affairs (OMAFRA), Ontario Ministry of Research and Innovation, and the Ontario Agri-Food Innovation Alliance
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Affiliation(s)
- P A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - S Lam
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Y Chen
- Livestock Gentec, Department of Agriculture, Food & Nutritional Science, University of Alberta, Edmonton, AB, T6H 2P5, Canada
| | - S M Waters
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, C15 PW93, Co. Meath, Ireland
| | - L L Guan
- Livestock Gentec, Department of Agriculture, Food & Nutritional Science, University of Alberta, Edmonton, AB, T6H 2P5, Canada
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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25
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Ma T, Huang W, Li Y, Jin H, Kwok LY, Sun Z, Zhang H. Probiotics alleviate constipation and inflammation in late gestating and lactating sows. NPJ Biofilms Microbiomes 2023; 9:70. [PMID: 37741814 PMCID: PMC10517943 DOI: 10.1038/s41522-023-00434-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/11/2023] [Indexed: 09/25/2023] Open
Abstract
Constipation and systemic inflammation are common in late pregnant and lactating sows, which cause health problems like uteritis, mastitis, dystocia, or even stillbirth, further influencing piglets' survival and growth. Probiotic supplementation can improve such issues, but the beneficial mechanism of relieving constipation and enhancing gut motility remains underexplored. This study aimed to investigate the effects and mechanism of probiotic supplementation in drinking water to late pregnant sows on constipation, inflammation, and piglets' growth performance. Seventy-four sows were randomly allocated to probiotic (n = 36) and control (n = 38) groups. Probiotic treatment significantly relieved sow constipation, enhanced serum IL-4 and IL-10 levels while reducing serum IL-1β, IL-12p40, and TNF-α levels, and increased piglet daily gain and weaning weight. Furthermore, probiotic administration reshaped the sow gut bacteriome and phageome structure/diversity, accompanied by increases in some potentially beneficial bacteria. At 113 days of gestation, the probiotic group was enriched in several gut microbial bioactive metabolites, multiple carbohydrate-active enzymes that degrade pectin and starch, fecal butyrate and acetate, and some serum metabolites involved in vitamin and amino acid metabolism. Our integrated correlation network analysis revealed that the alleviation of constipation and inflammation was associated with changes in the sow gut bacteriome, phageome, bioactive metabolic potential, and metabolism.
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Affiliation(s)
- Teng Ma
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Weiqiang Huang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Yalin Li
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Hao Jin
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
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26
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Suzuki S, Yokota K, Igimi S, Kajikawa A. Negative chemotaxis of Ligilactobacillus agilis BKN88 against gut-derived substances. Sci Rep 2023; 13:15632. [PMID: 37730901 PMCID: PMC10511705 DOI: 10.1038/s41598-023-42840-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023] Open
Abstract
Ligilactobacillus agilis is a motile lactic acid bacterium found in the gastrointestinal tracts of animals. The findings of our previous study suggest that the motility of L. agilis BKN88 enables gut colonization in murine models. However, the chemotactic abilities of motile lactobacilli remain unknown. This study aimed to identify the gut-derived chemoeffectors and their corresponding chemoreceptors in L. agilis BKN88. Chemotaxis assays with chemotactic and non-chemotactic (ΔcheA) L. agilis strains revealed that low pH, organic acids, and bile salts served as repellents. L. agilis BKN88 was more sensitive to bile and acid than the gut-derived non-motile lactobacilli, implying that L. agilis might utilize motility and chemotaxis instead of exhibiting stress tolerance/resistance. L. agilis BKN88 contains five putative chemoreceptor genes (mcp1-mcp5). Chemotaxis assays using a series of chemoreceptor mutants revealed that each of the five chemoreceptors could sense multiple chemoeffectors and that these chemoreceptors were functionally redundant. Mcp2 and Mcp3 sensed all tested chemoeffectors. This study provides further insights into the interactions between chemoreceptors and ligands of motile lactobacilli and the unique ecological and evolutionary features of motile lactobacilli, which may be distinct from those of non-motile lactobacilli.
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Affiliation(s)
- Shunya Suzuki
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Kenji Yokota
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Shizunobu Igimi
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Akinobu Kajikawa
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
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27
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Saini J, Deere TM, Lessner DJ. The minimal SUF system is not required for Fe-S cluster biogenesis in the methanogenic archaeon Methanosarcina acetivorans. Sci Rep 2023; 13:15120. [PMID: 37704679 PMCID: PMC10500019 DOI: 10.1038/s41598-023-42400-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023] Open
Abstract
Iron-sulfur (Fe-S) proteins are essential for the ability of methanogens to carry out methanogenesis and biological nitrogen fixation (diazotrophy). Nonetheless, the factors involved in Fe-S cluster biogenesis in methanogens remain largely unknown. The minimal SUF Fe-S cluster biogenesis system (i.e., SufBC) is postulated to serve as the primary system in methanogens. Here, the role of SufBC in Methanosarcina acetivorans, which contains two sufCB gene clusters, was investigated. The CRISPRi-dCas9 and CRISPR-Cas9 systems were utilized to repress or delete sufC1B1 and sufC2B2, respectively. Neither the dual repression of sufC1B1 and sufC2B2 nor the deletion of both sufC1B1 and sufC2B2 affected the growth of M. acetivorans under any conditions tested, including diazotrophy. Interestingly, deletion of only sufC1B1 led to a delayed-growth phenotype under all growth conditions, suggesting that the deletion of sufC2B2 acts as a suppressor mutation in the absence of sufC1B1. In addition, the deletion of sufC1B1 and/or sufC2B2 did not affect the total Fe-S cluster content in M. acetivorans cells. Overall, these results reveal that the minimal SUF system is not required for Fe-S cluster biogenesis in M. acetivorans and challenge the universal role of SufBC in Fe-S cluster biogenesis in methanogens.
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Affiliation(s)
- Jasleen Saini
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA
| | - Thomas M Deere
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA
| | - Daniel J Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA.
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28
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Huang J, Dai X, Wu Z, Hu X, Sun J, Tang Y, Zhang W, Han P, Zhao J, Liu G, Wang X, Mao S, Wang Y, Call DR, Liu J, Wang L. Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes. ISME J 2023; 17:1467-1481. [PMID: 37369704 PMCID: PMC10432423 DOI: 10.1038/s41396-023-01463-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Prophages play important roles in the transduction of various functional traits, including virulence factors, but remain debatable in harboring and transmitting antimicrobial resistance genes (ARGs). Herein we characterize a prevalent family of prophages in Streptococcus, designated SMphages, which harbor twenty-five ARGs that collectively confer resistance to ten antimicrobial classes, including vanG-type vancomycin resistance locus and oxazolidinone resistance gene optrA. SMphages integrate into four chromosome attachment sites by utilizing three types of integration modules and undergo excision in response to phage induction. Moreover, we characterize four subtypes of Alp-related surface proteins within SMphages, the lethal effects of which are extensively validated in cell and animal models. SMphages transfer via high-frequency conjugation that is facilitated by integrative and conjugative elements from either donors or recipients. Our findings explain the widespread of SMphages and the rapid dissemination of ARGs observed in members of the Streptococcus genus.
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Affiliation(s)
- Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingyang Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yijun Tang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanqiu Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peizhao Han
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaqi Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangjin Liu
- Key Lab of Animal Bacteriology, Ministry of Agriculture, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, 99164, USA
| | - Jinxin Liu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
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29
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van Dijk B, Buffard P, Farr AD, Giersdorf F, Meijer J, Dutilh BE, Rainey PB. Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome. ISME Commun 2023; 3:90. [PMID: 37640834 PMCID: PMC10462680 DOI: 10.1038/s43705-023-00294-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.
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Affiliation(s)
- Bram van Dijk
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
| | - Pauline Buffard
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Andrew D Farr
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Franz Giersdorf
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL CNRS, Paris, France.
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30
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Liao J, Shenhav L, Urban JA, Serrano M, Zhu B, Buck GA, Korem T. Microdiversity of the vaginal microbiome is associated with preterm birth. Nat Commun 2023; 14:4997. [PMID: 37591872 PMCID: PMC10435516 DOI: 10.1038/s41467-023-40719-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield insights into these associations. Here, we analyze metagenomic data from 705 vaginal samples collected during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative. We find that the vaginal microbiome of pregnancies that ended preterm exhibited unique genetic profiles. It was more genetically diverse at the species level, a result which we validate in an additional cohort, and harbored a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species drove this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. underwent more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our population genetics analyses reveal associations between the vaginal microbiome and PTB and suggest that evolutionary processes acting on vaginal microbes may play a role in adverse pregnancy outcomes such as PTB.
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Affiliation(s)
- Jingqiu Liao
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA.
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA
| | - Julia A Urban
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Myrna Serrano
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Bin Zhu
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Gregory A Buck
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA.
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, ON, Canada.
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31
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Dwiyanto J, Huët MAL, Hussain MH, Su TT, Tan JBL, Toh KY, Lee JWJ, Rahman S, Chong CW. Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia. NPJ Biofilms Microbiomes 2023; 9:55. [PMID: 37573460 PMCID: PMC10423249 DOI: 10.1038/s41522-023-00425-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 08/03/2023] [Indexed: 08/14/2023] Open
Abstract
The prevalence of antibiotic-resistant bacteria in Southeast Asia is a significant concern, yet there is limited research on the gut resistome and its correlation with lifestyle and environmental factors in the region. This study aimed to profile the gut resistome of 200 individuals in Malaysia using shotgun metagenomic sequencing and investigate its association with questionnaire data comprising demographic and lifestyle variables. A total of 1038 antibiotic resistance genes from 26 classes were detected with a mean carriage rate of 1.74 ± 1.18 gene copies per cell per person. Correlation analysis identified 14 environmental factors, including hygiene habits, health parameters, and intestinal colonization, that were significantly associated with the resistome (adjusted multivariate PERMANOVA, p < 0.05). Notably, individuals with positive yeast cultures exhibited a reduced copy number of 15 antibiotic resistance genes. Network analysis highlighted Escherichia coli as a major resistome network hub, with a positive correlation to 36 antibiotic-resistance genes. Our findings suggest that E. coli may play a pivotal role in shaping the resistome dynamics in Segamat, Malaysia, and its abundance is strongly associated with the community's health and lifestyle habits. Furthermore, the presence of yeast appears to be associated with the suppression of antibiotic-resistance genes.
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Affiliation(s)
- J Dwiyanto
- AMILI, Singapore, 118261, Singapore.
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - M A L Huët
- Faculty of Science, University of Mauritius, Reduit, 80837, Mauritius
| | - M H Hussain
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
| | - T T Su
- South East Asia Community Observatory, Segamat, 85000, Malaysia
| | - J B L Tan
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
| | - K Y Toh
- AMILI, Singapore, 118261, Singapore
| | - J W J Lee
- AMILI, Singapore, 118261, Singapore
- Department of Medicine, National University Hospital, Singapore, 119228, Singapore
| | - S Rahman
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
- Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
| | - C W Chong
- AMILI, Singapore, 118261, Singapore.
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Malaysia.
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32
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Zahedi Bialvaei A, Eslami P, Ganji L, Dolatyar Dehkharghani A, Asgari F, Koupahi H, Barzegarian Pashacolaei HR, Rahbar M. Prevalence and epidemiological investigation of mgrB-dependent colistin resistance in extensively drug resistant Klebsiella pneumoniae in Iran. Sci Rep 2023; 13:10680. [PMID: 37393362 PMCID: PMC10314893 DOI: 10.1038/s41598-023-37845-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/28/2023] [Indexed: 07/03/2023] Open
Abstract
Carbapenemases-producing K. pneumoniae are challenging antimicrobial therapy of hospitalised patients, which is further complicated by colistin resistance. The aim of this study was to investigate the molecular epidemiological insights into carbapenemases-producing and colistin-resistant clinical K. pneumoniaeA total of 162 colistin resistant clinical strains of K. pneumoniae were collected during 2017-2019. Antimicrobial susceptibility and the colistin minimum inhibitory concentration were determined. Using PCR assay, the prevalence of resistance-associated genes including blaKPC, blaIMP, blaVIM, blaOXA-48, blaNDM-1 and mcr-1 to -9 was examined. Additionally, a PCR assay was used to examine the mgrB gene in colistin-resistant bacteria. 94.4% of the tested strains were resistant to imipenem and 96.3% were resistant to meropenem. Colistin resistance (MIC > 4 µg/L) was observed in 161 isolates (99.4%) by Colistin Broth Disk Elution method. The KPC enzyme was the most common carbapenemase and was identified in 95 strains (58.6%), followed by the IMP, VIM and OXA-48 detected in 47 (29%), 23 (14.2%) and 12 (7.4%) isolates, respectively. However, no NDM-1 gene was detected. Additionally, none of the studied isolates harbored mcr variants, while mgrB gene was observed in 152 (92.6%) isolates. Colistin resistance of K. pneumoniae isolates may be associated with mgrB gene mutation. To stop the spread of resistant K. pneumoniae, surveillance must be improved, infection prevention protocols must be followed, and antibiotic stewardship must be practised.
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Affiliation(s)
- Abed Zahedi Bialvaei
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Parisa Eslami
- Department of Microbiology, Milad Hospital, Tehran, Iran
| | - Leila Ganji
- Department of Microbiology, Ministry of Health & Medical Education, Iranian Reference Health Laboratories Research Center, Tehran, Iran
| | - Alireza Dolatyar Dehkharghani
- Department of Microbiology, Ministry of Health & Medical Education, Iranian Reference Health Laboratories Research Center, Tehran, Iran
| | - Farhad Asgari
- Department of Microbiology, Ministry of Health & Medical Education, Iranian Reference Health Laboratories Research Center, Tehran, Iran
| | - Hossein Koupahi
- Department of Microbiology, Islamic Azad University, Varamin-Pishva Branch, Varamin, Iran
| | | | - Mohammad Rahbar
- Department of Microbiology, Ministry of Health & Medical Education, Iranian Reference Health Laboratories Research Center, Tehran, Iran.
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33
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Abel SM, Hong Z, Williams D, Ireri S, Brown MQ, Su T, Hung KY, Henke JA, Barton JP, Le Roch KG. Small RNA sequencing of field Culex mosquitoes identifies patterns of viral infection and the mosquito immune response. Sci Rep 2023; 13:10598. [PMID: 37391513 PMCID: PMC10313667 DOI: 10.1038/s41598-023-37571-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023] Open
Abstract
Mosquito-borne disease remains a significant burden on global health. In the United States, the major threat posed by mosquitoes is transmission of arboviruses, including West Nile virus by mosquitoes of the Culex genus. Virus metagenomic analysis of mosquito small RNA using deep sequencing and advanced bioinformatic tools enables the rapid detection of viruses and other infecting organisms, both pathogenic and non-pathogenic to humans, without any precedent knowledge. In this study, we sequenced small RNA samples from over 60 pools of Culex mosquitoes from two major areas of Southern California from 2017 to 2019 to elucidate the virome and immune responses of Culex. Our results demonstrated that small RNAs not only allowed the detection of viruses but also revealed distinct patterns of viral infection based on location, Culex species, and time. We also identified miRNAs that are most likely involved in Culex immune responses to viruses and Wolbachia bacteria, and show the utility of using small RNA to detect antiviral immune pathways including piRNAs against some pathogens. Collectively, these findings show that deep sequencing of small RNA can be used for virus discovery and surveillance. One could also conceive that such work could be accomplished in various locations across the world and over time to better understand patterns of mosquito infection and immune response to many vector-borne diseases in field samples.
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Affiliation(s)
- Steven M Abel
- Department of Molecular, Cell and Systems Biology, Center for Infection Disease and Vector Research, University of California, Riverside, CA, 92521, USA
| | - Zhenchen Hong
- Department of Physics and Astronomy, University of California, Riverside, CA, 92521, USA
| | - Desiree Williams
- Department of Molecular, Cell and Systems Biology, Center for Infection Disease and Vector Research, University of California, Riverside, CA, 92521, USA
| | - Sally Ireri
- Department of Molecular, Cell and Systems Biology, Center for Infection Disease and Vector Research, University of California, Riverside, CA, 92521, USA
| | - Michelle Q Brown
- West Valley Mosquito & Vector Control District, Ontario, CA, 91761, USA
| | - Tianyun Su
- West Valley Mosquito & Vector Control District, Ontario, CA, 91761, USA
| | - Kim Y Hung
- Coachella Valley Mosquito & Vector Control District, Indio, CA, 92201, USA
| | - Jennifer A Henke
- Coachella Valley Mosquito & Vector Control District, Indio, CA, 92201, USA
| | - John P Barton
- Department of Physics and Astronomy, University of California, Riverside, CA, 92521, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, Center for Infection Disease and Vector Research, University of California, Riverside, CA, 92521, USA.
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34
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Azizimoghaddam Y, Kermanpour S, Mirzaei N, Houri H, Nabavi-Rad A, Asadzadeh Aghdaei H, Yadegar A, Zali MR. Genetic diversity of Helicobacter pylori type IV secretion system cagI and cagN genes and their association with clinical diseases. Sci Rep 2023; 13:10264. [PMID: 37355714 PMCID: PMC10290643 DOI: 10.1038/s41598-023-37392-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023] Open
Abstract
A number of cagPAI genes in the Helicobacter pylori genome are considered the most evolved genes under a diversifying selection and evolutionary pressure. Among them, cagI and cagN are described as a part of the two different-operon of cagPAI that are involved in the T4SS machinery, but the definite association of these factors with clinical manifestations is still unclear. A total of 70 H. pylori isolates were obtained from different gastroduodenal patients. All isolates were examined for the presence of primary H. pylori virulence genes by PCR analysis. Direct DNA sequence analysis was performed for the cagI and cagN genes. The results were compared with the reference strain. The cagI, cagN, cagA, cagL, vacA s1m1, vacA s1m2, vacA s2m2, babA2, sabA, and dupA genotypes were detected in 80, 91.4, 84, 91.4, 32.8, 42.8, 24.4, 97.1, 84.3, and 84.3% of the total isolates, respectively. The most variable codon usage in cagI was observed at residues 20-25, 55-60, 94, 181-199, 213-221, 241-268, and 319-320, while the most variable codon usage in CagN hypervariable motif (CagNHM) was observed at residues 53 to 63. Sequencing data analysis of cagN revealed a hypothetical hexapeptide motif (EAKDEN/K) in residues of 278-283 among six H. pylori isolates, which needs further studies to evaluate its putative function. The present study demonstrated a high prevalence of cagI and cagN genes among Iranian H. pylori isolates with gastroduodenal diseases. Furthermore, no significant correlation between cagI and cagN variants and clinical diseases was observed in the present study. However, all patients had a high prevalence of cagPAI genes including cagI, cagN, cagA, and cagL, which indicates more potential role of these genes in disease outcome.
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Affiliation(s)
- Yasaman Azizimoghaddam
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sadaf Kermanpour
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nasrin Mirzaei
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Houri
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Krzyżanowska DM, Jabłońska M, Kaczyński Z, Czerwicka-Pach M, Macur K, Jafra S. Host-adaptive traits in the plant-colonizing Pseudomonas donghuensis P482 revealed by transcriptomic responses to exudates of tomato and maize. Sci Rep 2023; 13:9445. [PMID: 37296159 PMCID: PMC10256816 DOI: 10.1038/s41598-023-36494-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
Pseudomonads are metabolically flexible and can thrive on different plant hosts. However, the metabolic adaptations required for host promiscuity are unknown. Here, we addressed this knowledge gap by employing RNAseq and comparing transcriptomic responses of Pseudomonas donghuensis P482 to root exudates of two plant hosts: tomato and maize. Our main goal was to identify the differences and the common points between these two responses. Pathways upregulated only by tomato exudates included nitric oxide detoxification, repair of iron-sulfur clusters, respiration through the cyanide-insensitive cytochrome bd, and catabolism of amino and/or fatty acids. The first two indicate the presence of NO donors in the exudates of the test plants. Maize specifically induced the activity of MexE RND-type efflux pump and copper tolerance. Genes associated with motility were induced by maize but repressed by tomato. The shared response to exudates seemed to be affected both by compounds originating from the plants and those from their growth environment: arsenic resistance and bacterioferritin synthesis were upregulated, while sulfur assimilation, sensing of ferric citrate and/or other iron carriers, heme acquisition, and transport of polar amino acids were downregulated. Our results provide directions to explore mechanisms of host adaptation in plant-associated microorganisms.
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Affiliation(s)
- Dorota M Krzyżanowska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland
| | - Magdalena Jabłońska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland
| | - Zbigniew Kaczyński
- Laboratory of Structural Biochemistry, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Małgorzata Czerwicka-Pach
- Laboratory of Structural Biochemistry, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Katarzyna Macur
- Laboratory of Mass Spectrometry, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdańsk, ul. A. Abrahama 58, 80-307, Gdańsk, Poland.
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36
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Lin L, Du R, Wu Q, Xu Y. Metabolic cooperation between conspecific genotypic groups contributes to bacterial fitness. ISME Commun 2023; 3:41. [PMID: 37117489 PMCID: PMC10147913 DOI: 10.1038/s43705-023-00250-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023]
Abstract
Microbial interactions are important for the survival of species and the stability of the microbial ecosystem. Although bacteria have diverse conspecific genotypes in the natural microbial ecosystem, little is known about whether wild-type strains within species would interact with each other and how the intraspecific interaction influences the growth of the species. In this work, using Lactobacillus acetotolerans, a dominant species with diverse conspecific genotypes in natural food fermentation ecosystems as a case, we studied the interactions between different genotypic groups of this species. In interspecific and intraspecific pairwise cocultures, the growth of L. acetotolerans decreased, but the increase of the phylogenetic similarity would reduce this negative effect, indicating a potential intraspecific interaction of this species. Meanwhile, the strain classification method affected the analysis of intraspecific interactions, which can be efficiently demonstrated using 99.5% average nucleotide identity (ANI) as the strain-level classification method. Using this ANI classification method, we revealed the population fitness significantly increased in cocultures of different genotypic groups. Facilitation involving 11 amino acids was identified between different ANI genotypic groups, which was beneficial for increasing population fitness. This work revealed that wild-type conspecific strains could interact with each other via cooperative metabolic changes and benefit each other to increase fitness. It shed new light on the survival and stability of species in natural microbial ecosystems.
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Affiliation(s)
- Lin Lin
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Rubing Du
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Qun Wu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
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Gatt YE, Savion D, Bamberger T, Margalit H. Convergent Within-Host Adaptation of Pseudomonas aeruginosa through the Transcriptional Regulatory Network. mSystems 2023; 8:e0002423. [PMID: 36975785 PMCID: PMC10134825 DOI: 10.1128/msystems.00024-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Bacteria adapt to their host by mutating specific genes and by reprogramming their gene expression. Different strains of a bacterial species often mutate the same genes during infection, demonstrating convergent genetic adaptation. However, there is limited evidence for convergent adaptation at the transcriptional level. To this end, we utilize genomic data of 114 Pseudomonas aeruginosa strains, derived from patients with chronic pulmonary infection, and the P. aeruginosa transcriptional regulatory network. Relying on loss-of-function mutations in genes encoding transcriptional regulators and predicting their effects through the network, we demonstrate predicted expression changes of the same genes in different strains through different paths in the network, implying convergent transcriptional adaptation. Furthermore, through the transcription lens we associate yet-unknown processes, such as ethanol oxidation and glycine betaine catabolism, with P. aeruginosa host adaptation. We also find that known adaptive phenotypes, including antibiotic resistance, which were identified before as achieved by specific mutations, are achieved also through transcriptional changes. Our study has revealed novel interplay between the genetic and transcriptional levels in host adaptation, demonstrating the versatility of the adaptive arsenal of bacterial pathogens and their ability to adapt to the host conditions in a myriad of ways. IMPORTANCE Pseudomonas aeruginosa causes significant morbidity and mortality. The pathogen's remarkable ability to establish chronic infections greatly depends on its adaptation to the host environment. Here, we use the transcriptional regulatory network to predict expression changes during adaptation. We expand the processes and functions known to be involved in host adaptation. We show that the pathogen modulates the activity of genes during adaptation, including genes implicated in antibiotic resistance, both directly via genomic mutations and indirectly via mutations in transcriptional regulators. Furthermore, we detect a subgroup of genes whose predicted changes in expression are associated with mucoid strains, a major adaptive phenotype in chronic infections. We propose that these genes constitute the transcriptional arm of the mucoid adaptive strategy. Identification of different adaptive strategies utilized by pathogens during chronic infection has major promise in the treatment of persistent infections and opens the door to personalized tailored antibiotic treatment in the future.
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Affiliation(s)
- Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Savion
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tal Bamberger
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Kaval KG, Chimalapati S, Siegel SD, Garcia N, Jaishankar J, Dalia AB, Orth K. Membrane-localized expression, production and assembly of Vibrio parahaemolyticus T3SS2 provides evidence for transertion. Nat Commun 2023; 14:1178. [PMID: 36859532 PMCID: PMC9977878 DOI: 10.1038/s41467-023-36762-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
It has been proposed that bacterial membrane proteins may be synthesized and inserted into the membrane by a process known as transertion, which involves membrane association of their encoding genes, followed by coupled transcription, translation and membrane insertion. Here, we provide evidence supporting that the pathogen Vibrio parahaemolyticus uses transertion to assemble its type III secretion system (T3SS2), to inject virulence factors into host cells. We propose a two-step transertion process where the membrane-bound co-component receptor (VtrA/VtrC) is first activated by bile acids, leading to membrane association and expression of its target gene, vtrB, located in the T3SS2 pathogenicity island. VtrB, the transmembrane transcriptional activator of T3SS2, then induces the localized expression and membrane assembly of the T3SS2 structural components and its effectors. We hypothesize that the proposed transertion process may be used by other enteric bacteria for efficient assembly of membrane-bound molecular complexes in response to extracellular signals.
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Affiliation(s)
- Karan Gautam Kaval
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Sara D Siegel
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27606, USA
| | - Nalleli Garcia
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Jananee Jaishankar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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Średnicka P, Roszko MŁ, Popowski D, Kowalczyk M, Wójcicki M, Emanowicz P, Szczepańska M, Kotyrba D, Juszczuk-Kubiak E. Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach. Sci Rep 2023; 13:3026. [PMID: 36810418 DOI: 10.1038/s41598-023-29637-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/08/2023] [Indexed: 02/23/2023] Open
Abstract
Gut microbiota (GM) plays many key functions and helps maintain the host's health. Consequently, the development of GM cultivation under in vitro stimulating physiological conditions has gained extreme interest in different fields. In this study, we evaluated the impact of four culture media: Gut Microbiota Medium (GMM), Schaedler Broth (SM), Fermentation Medium (FM), and Carbohydrate Free Basal Medium (CFBM) on preserving the biodiversity and metabolic activity of human GM in batch in vitro cultures using PMA treatment coupled with 16S rDNA sequencing (PMA-seq) and LC-HR-MS/MS untargeted metabolomics supplemented with GC-MS SCFA profiling. Before the experiments, we determined the possibility of using the pooled faecal samples (MIX) from healthy donors (n = 15) as inoculum to reduce the number of variables and ensure the reproducibility of in vitro cultivation tests. Results showed the suitability of pooling faecal samples for in vitro cultivation study. Non-cultured MIX inoculum was characterized by higher α-diversity (Shannon effective count, and Effective microbial richness) compared to inocula from individual donors. After 24 h of cultivation, a significant effect of culture media composition on GM taxonomic and metabolomic profiles was observed. The SM and GMM had the highest α-diversity (Shannon effective count). The highest number of core ASVs (125) shared with non-cultured MIX inoculum and total SCFAs production was observed in the SM. These results might contribute to the development of standardized protocols for human GM in vitro cultivation by preventing methodological bias in the data.
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40
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Sabin S, Jones S, Patel D, Subramaniam G, Kelley J, Aidoo M, Talundzic E. Portable and cost-effective genetic detection and characterization of Plasmodium falciparum hrp2 using the MinION sequencer. Sci Rep 2023; 13:2893. [PMID: 36801925 PMCID: PMC9938884 DOI: 10.1038/s41598-022-26935-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/22/2022] [Indexed: 02/20/2023] Open
Abstract
The prevalence of Plasmodium falciparum hrp2 (pfhrp2)-deleted parasites threatens the efficacy of the most used and sensitive malaria rapid diagnostic tests and highlights the need for continued surveillance for this gene deletion. While PCR methods are adequate for determining pfhrp2 presence or absence, they offer a limited view of its genetic diversity. Here, we present a portable sequencing method using the MinION. Pfhrp2 amplicons were generated from individual samples, barcoded, and pooled for sequencing. To overcome potential crosstalk between barcodes, we implemented a coverage-based threshold for pfhrp2 deletion confirmation. Amino acid repeat types were then counted and visualized with custom Python scripts following de novo assembly. We evaluated this assay using well-characterized reference strains and 152 field isolates with and without pfhrp2 deletions, of which 38 were also sequenced on the PacBio platform to provide a standard for comparison. Of 152 field samples, 93 surpassed the positivity threshold, and of those samples, 62/93 had a dominant pfhrp2 repeat type. PacBio-sequenced samples with a dominant repeat-type profile from the MinION sequencing data matched the PacBio profile. This field-deployable assay can be used alone for surveilling pfhrp2 diversity or as a sequencing-based addition to the World Health Organization's existing deletion surveillance protocol.
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Affiliation(s)
- Susanna Sabin
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA. .,Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.
| | - Sophie Jones
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA ,Williams Consulting, Catonsville, MD USA
| | - Dhruviben Patel
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA ,Williams Consulting, Catonsville, MD USA
| | - Gireesh Subramaniam
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA ,grid.410547.30000 0001 1013 9784Oak Ridge Institute for Science and Education, Oak Ridge, TN USA
| | - Julia Kelley
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Michael Aidoo
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Eldin Talundzic
- grid.416738.f0000 0001 2163 0069Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
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Fanelli G, Pasqua M, Prosseda G, Grossi M, Colonna B. AcrAB efflux pump impacts on the survival of adherent-invasive Escherichia coli strain LF82 inside macrophages. Sci Rep 2023; 13:2692. [PMID: 36792672 PMCID: PMC9931695 DOI: 10.1038/s41598-023-29817-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The tripartite complex AcrAB-TolC is the major RND pump in Escherichia coli and other Enterobacteriaceae. It consists of the AcrB transporter, which is embedded in the inner membrane, the AcrA adapter located in the periplasm, and the channel protein TolC responsible for the transport of substrates towards the extracellular environment. Besides conferring resistance to many classes of antibiotics, AcrAB plays a role in the pathogenesis and virulence of several bacterial pathogens. Here we report that the AcrAB pump heavily affects the infection process of the LF82 strain, the prototype of Adherent-Invasive Escherichia coli (AIEC) which are highly abundant in the ileal mucosa of Chron disease patients. We found that the deletion of genes encoding AcrA and/or AcrB leads to decreased survival of LF82 within macrophages. Ectopic AcrAB expression in a acrAB defective mutant restores the wild type condition. Furthermore, we demonstrate that inhibition of AcrB and replacement of the transporter with an unfunctional AcrB also interfere with bacterial viability inside macrophages. Overall, these data suggest a pivotal role of the AcrAB efflux pump in bacteria-host cell interactions also in AIEC.
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Affiliation(s)
- Giulia Fanelli
- grid.7841.aDepartment of Biology and Biotechnology “C. Darwin”, Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | - Martina Pasqua
- grid.7841.aDepartment of Biology and Biotechnology “C. Darwin”, Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | - Gianni Prosseda
- grid.7841.aDepartment of Biology and Biotechnology “C. Darwin”, Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | - Milena Grossi
- Department of Biology and Biotechnology "C. Darwin", Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy.
| | - Bianca Colonna
- Department of Biology and Biotechnology "C. Darwin", Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy.
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Seo H, Kang S, Lee D, Yun CW. Regulation of pseurotin A biosynthesis by GliZ and zinc in Aspergillus fumigatus. Sci Rep 2023; 13:2431. [PMID: 36765124 PMCID: PMC9918513 DOI: 10.1038/s41598-023-29753-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/09/2023] [Indexed: 02/12/2023] Open
Abstract
Recently, we reported that zinc regulates gliotoxin biosynthesis via ZafA, which is a zinc-responsive transcriptional activator. From an HPLC analysis of culture media of Aspergillus fumigatus, we found a trend of decreasing gliotoxin production but increasing pseurotin A and fumagillin production in proportion to the zinc concentration. The expression of the genes involved in pseurotin A biosynthesis was upregulated under high zinc concentrations. Furthermore, upregulated expression of pseurotin A biosynthetic genes and higher production of pseurotin A were observed in the zafA deletion strain. Interestingly, the deletion of gliZ, a transcriptional activator of gliotoxin biosynthesis genes, resulted in upregulated expression of pseurotin A biosynthetic genes and increased production of pseurotin A. We detected upregulation of fumR expression in the gliZ and zafA deletion mutants. The overexpression of gliZ observed in the zafA deletion mutant resulted in the failure of the mutant to increase pseurotin A production, which is a phenotype of the zafA deletion mutant. These results suggest that ZafA sequentially regulates pseurotin A biosynthesis through GliZ. Finally, we found through a murine virulence test that the gliZ and fumR double-deletion mutants showed a delayed death rate compared with the single-deletion mutants of either gliZ or fumR. Taken together, these results suggested that the biosynthesis of gliotoxin and pseurotin A are regulated in opposite ways by zinc utilization and that each secondary metabolite is synthesized when the synthesis of another secondary metabolite fails to protect it against the defense system of the host.
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Affiliation(s)
- Hyewon Seo
- School of Life Sciences and Biotechnology, Korea University, Anam-Dong, Sungbuk-Gu, Seoul, Republic of Korea
| | - Suzie Kang
- School of Life Sciences and Biotechnology, Korea University, Anam-Dong, Sungbuk-Gu, Seoul, Republic of Korea
| | - Dongho Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Cheol-Won Yun
- School of Life Sciences and Biotechnology, Korea University, Anam-Dong, Sungbuk-Gu, Seoul, Republic of Korea.
- NeuroEsgel Co., Anam-Dong, Sungbuk-Gu, Seoul, Republic of Korea.
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Kreth J, Merritt J. Illuminating the oral microbiome and its host interactions: tools and approaches for molecular ecological studies. FEMS Microbiol Rev 2023; 47:fuac052. [PMID: 36564013 PMCID: PMC9936263 DOI: 10.1093/femsre/fuac052] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022] Open
Abstract
A more comprehensive understanding of oral diseases like caries and periodontitis is dependent on an intimate understanding of the microbial ecological processes that are responsible for disease development. With this review, we provide a comprehensive overview of relevant molecular ecology techniques that have played critical roles in the current understanding of human oral biofilm development, interspecies interactions, and microbiome biogeography. The primary focus is on relevant technologies and examples available in the oral microbiology literature. However, most, if not all, of the described technologies should be readily adaptable for studies of microbiomes from other mucosal sites in the body. Therefore, this review is intended to serve as a reference guide used by microbiome researchers as they inevitably transition into molecular mechanistic studies of the many significant phenotypes observed clinically.
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Affiliation(s)
- Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, MRB433, 3181 SW Sam Jackson Park Rd., #L595, Portland, OR 97239, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, MRB433, 3181 SW Sam Jackson Park Rd., #L595, Portland, OR 97239, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States
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Napier G, Campino S, Phelan JE, Clark TG. Large-scale genomic analysis of Mycobacterium tuberculosis reveals extent of target and compensatory mutations linked to multi-drug resistant tuberculosis. Sci Rep 2023; 13:623. [PMID: 36635309 DOI: 10.1038/s41598-023-27516-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
Resistance to isoniazid (INH) and rifampicin (RIF) first-line drugs in Mycobacterium tuberculosis (Mtb), together called multi-drug resistance, threatens tuberculosis control. Resistance mutations in katG (for INH) and rpoB (RIF) genes often come with fitness costs. To overcome these costs, Mtb compensatory mutations have arisen in rpoC/rpoA (RIF) and ahpC (INH) loci. By leveraging the presence of known compensatory mutations, we aimed to detect novel resistance mutations occurring in INH and RIF target genes. Across ~ 32 k Mtb isolates with whole genome sequencing (WGS) data, there were 6262 (35.7%) with INH and 5435 (30.7%) with RIF phenotypic resistance. Known mutations in katG and rpoB explained ~ 99% of resistance. However, 188 (0.6%) isolates had ahpC compensatory mutations with no known resistance mutations in katG, leading to the identification of 31 putative resistance mutations in katG, each observed in at least 3 isolates. These putative katG mutations can co-occur with other INH variants (e.g., katG-Ser315Thr, fabG1 mutations). For RIF, there were no isolates with rpoC/rpoA compensatory mutations and unknown resistance mutations. Overall, using WGS data we identified putative resistance markers for INH that could be used for genotypic drug-resistance profiling. Establishing the complete repertoire of Mtb resistance mutations will assist the clinical management of tuberculosis.
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Shrode RL, Knobbe JE, Cady N, Yadav M, Hoang J, Cherwin C, Curry M, Garje R, Vikas P, Sugg S, Phadke S, Filardo E, Mangalam AK. Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria. Sci Rep 2023; 13:526. [PMID: 36631533 PMCID: PMC9834383 DOI: 10.1038/s41598-023-27436-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
As geographical location can impact the gut microbiome, it is important to study region-specific microbiome signatures of various diseases. Therefore, we profiled the gut microbiome of breast cancer (BC) patients of the Midwestern region of the United States. The bacterial component of the gut microbiome was profiled utilizing 16S ribosomal RNA sequencing. Additionally, a gene pathway analysis was performed to assess the functional capabilities of the bacterial microbiome. Alpha diversity was not significantly different between BC and healthy controls (HC), however beta diversity revealed distinct clustering between the two groups at the species and genera level. Wilcoxon Rank Sum test revealed modulation of several gut bacteria in BC specifically reduced abundance of those linked with beneficial effects such as Faecalibacterium prausnitzii. Machine learning analysis confirmed the significance of several of the modulated bacteria found by the univariate analysis. The functional analysis showed a decreased abundance of SCFA (propionate) production in BC compared to HC. In conclusion, we observed gut dysbiosis in BC with the depletion of SCFA-producing gut bacteria suggesting their role in the pathobiology of breast cancer. Mechanistic understanding of gut bacterial dysbiosis in breast cancer could lead to refined prevention and treatment.
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Affiliation(s)
- Rachel L. Shrode
- grid.214572.70000 0004 1936 8294Department of Informatics, University of Iowa, Iowa City, IA 52242 USA
| | - Jessica E. Knobbe
- grid.214572.70000 0004 1936 8294Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242 USA ,grid.214572.70000 0004 1936 8294Stead Family Department of Pediatrics, University of Iowa, Iowa City, IA 52242 USA ,grid.214572.70000 0004 1936 8294Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA
| | - Nicole Cady
- grid.214572.70000 0004 1936 8294Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA ,grid.214458.e0000000086837370Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Meeta Yadav
- grid.214572.70000 0004 1936 8294Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA ,grid.214572.70000 0004 1936 8294College of Dentistry, University of Iowa, Iowa City, IA 52242 USA
| | - Jemmie Hoang
- grid.214572.70000 0004 1936 8294College of Nursing, University of Iowa, Iowa City, IA 52242 USA
| | - Catherine Cherwin
- grid.214572.70000 0004 1936 8294College of Nursing, University of Iowa, Iowa City, IA 52242 USA
| | - Melissa Curry
- grid.412584.e0000 0004 0434 9816Holden Comprehensive Cancer Center, University of Iowa Hospital and Clinics, Iowa City, IA 52242 USA
| | - Rohan Garje
- grid.214572.70000 0004 1936 8294Department of Internal Medicine, University of Iowa, Iowa City, IA 52242 USA
| | - Praveen Vikas
- grid.214572.70000 0004 1936 8294Department of Internal Medicine, University of Iowa, Iowa City, IA 52242 USA
| | - Sonia Sugg
- grid.214572.70000 0004 1936 8294Department of Surgery, University of Iowa, Iowa City, IA 52242 USA
| | - Sneha Phadke
- grid.214572.70000 0004 1936 8294Division of Hematology, Oncology, and Blood and Marrow Transplantation, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242 USA
| | | | - Ashutosh K. Mangalam
- grid.214572.70000 0004 1936 8294Department of Informatics, University of Iowa, Iowa City, IA 52242 USA ,grid.214572.70000 0004 1936 8294Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242 USA ,grid.214572.70000 0004 1936 8294Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA ,grid.214572.70000 0004 1936 8294College of Dentistry, University of Iowa, Iowa City, IA 52242 USA ,grid.214572.70000 0004 1936 8294University of Iowa, 25 S Grand Ave, 1080-ML, Iowa City, IA 52246 USA
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Wu HY, Mortensen UH, Chang FR, Tsai H. Whole genome sequence characterization of Aspergillus terreus ATCC 20541 and genome comparison of the fungi A. terreus. Sci Rep 2023; 13:194. [PMID: 36604572 DOI: 10.1038/s41598-022-27311-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Aspergillus terreus is well-known for lovastatin and itaconic acid production with biomedical and commercial importance. The mechanisms of metabolite formation have been extensively studied to improve their yield through genetic engineering. However, the combined repertoire of carbohydrate-active enzymes (CAZymes), cytochrome P450s (CYP) enzymes, and secondary metabolites (SMs) in the different A. terreus strains has not been well studied yet, especially with respect to the presence of biosynthetic gene clusters (BGCs). Here we present a 30 Mb whole genome sequence of A. terreus ATCC 20541 in which we predicted 10,410 protein-coding genes. We compared the CAZymes, CYPs enzyme, and SMs across eleven A. terreus strains, and the results indicate that all strains have rich pectin degradation enzyme and CYP52 families. The lovastatin BGC of lovI was linked with lovF in A. terreus ATCC 20541, and the phenomenon was not found in the other strains. A. terreus ATCC 20541 lacked a non-ribosomal peptide synthetase (AnaPS) participating in acetylaszonalenin production, which was a conserved protein in the ten other strains. Our results present a comprehensive analysis of CAZymes, CYPs enzyme, and SM diversities in A. terreus strains and will facilitate further research in the function of BGCs associated with valuable SMs.
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Chaouni B, Idrissi Azami A, Raoui S, Amzazi S, Nejjari C, Bakkali F, Zaid EH, Hamamouch N, Amaral-Zettler L, Ghazal H. Spatio-temporal patterns of Synechococcus oligotypes in Moroccan lagoonal environments. Sci Rep 2023; 13:110. [PMID: 36596878 DOI: 10.1038/s41598-022-27263-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Synechococcus are unicellular cyanobacteria susceptible to environmental fluctuations and can be used as bioindicators of eutrophication in marine ecosystems. We examined their distribution in two Moroccan lagoons, Marchica on the Mediterranean coast and Oualidia on the Atlantic, in the summers of 2014 and 2015 using 16S rRNA amplicon oligotyping. Synechococcus representatives recruited a higher number of reads from the 16S rRNA in Marchica in comparison to Oualidia. We identified 31 Synechococcus oligotypes that clustered into 10 clades with different distribution patterns. The Synechococcus community was mainly represented by oligotype 1 (clade III) in Marchica. Cooccurring clades IV and I had an important relative abundance in Marchica in the summer of 2014, which is unusual, as these clades are widespread in cold waters. Moreover, Clades VII and subcluster "5.3" formed a sizeable percentage of the Synechococcus community in Marchica. Notably, we found low Synechococcus sequence counts in the Atlantic Lagoon. These results showed that the relative abundance of Synechococcus reads is not constant over space and time and that rare members of the Synechococcus community did not follow a consistent pattern. Further studies are required to decipher Synechococcus dynamics and the impact of environmental parameters on their spatial and temporal distributions.
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Wilson CN, Musicha P, Beale MA. Genomic epidemiology on the move. Nat Rev Microbiol 2023; 21:69. [PMID: 36536144 DOI: 10.1038/s41579-022-00836-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This Genome Watch article explores how portable sequencing technology is re-shaping the field of genomic epidemiology.
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Sit B, Srisuknimit V, Bueno E, Zingl FG, Hullahalli K, Cava F, Waldor MK. Undecaprenyl phosphate translocases confer conditional microbial fitness. Nature 2023; 613:721-728. [PMID: 36450355 PMCID: PMC9876793 DOI: 10.1038/s41586-022-05569-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022]
Abstract
The microbial cell wall is essential for maintenance of cell shape and resistance to external stressors1. The primary structural component of the cell wall is peptidoglycan, a glycopolymer with peptide crosslinks located outside of the cell membrane1. Peptidoglycan biosynthesis and structure are responsive to shifting environmental conditions such as pH and salinity2-6, but the mechanisms underlying such adaptations are incompletely understood. Precursors of peptidoglycan and other cell surface glycopolymers are synthesized in the cytoplasm and then delivered across the cell membrane bound to the recyclable lipid carrier undecaprenyl phosphate7 (C55-P, also known as UndP). Here we identify the DUF368-containing and DedA transmembrane protein families as candidate C55-P translocases, filling a critical gap in knowledge of the proteins required for the biogenesis of microbial cell surface polymers. Gram-negative and Gram-positive bacteria lacking their cognate DUF368-containing protein exhibited alkaline-dependent cell wall and viability defects, along with increased cell surface C55-P levels. pH-dependent synthetic genetic interactions between DUF368-containing proteins and DedA family members suggest that C55-P transporter usage is dynamic and modulated by environmental inputs. C55-P transporter activity was required by the cholera pathogen for growth and cell shape maintenance in the intestine. We propose that conditional transporter reliance provides resilience in lipid carrier recycling, bolstering microbial fitness both inside and outside the host.
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Affiliation(s)
- Brandon Sit
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Veerasak Srisuknimit
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Emilio Bueno
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Franz G Zingl
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Karthik Hullahalli
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA. .,Department of Microbiology, Harvard Medical School, Boston, MA, USA. .,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Howard Hughes Medical Institute, Bethesda, MD, USA.
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Han AX, Toporowski A, Sacks JA, Perkins MD, Briand S, van Kerkhove M, Hannay E, Carmona S, Rodriguez B, Parker E, Nichols BE, Russell CA. SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs. Nat Genet 2023; 55:26-33. [PMID: 36624344 DOI: 10.1038/s41588-022-01267-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/11/2022] [Indexed: 01/11/2023]
Abstract
The first step in SARS-CoV-2 genomic surveillance is testing to identify people who are infected. However, global testing rates are falling as we emerge from the acute health emergency and remain low in many low- and middle-income countries (mean = 27 tests per 100,000 people per day). We simulated COVID-19 epidemics in a prototypical low- and middle-income country to investigate how testing rates, sampling strategies and sequencing proportions jointly impact surveillance outcomes, and showed that low testing rates and spatiotemporal biases delay time to detection of new variants by weeks to months and can lead to unreliable estimates of variant prevalence, even when the proportion of samples sequenced is increased. Accordingly, investments in wider access to diagnostics to support testing rates of approximately 100 tests per 100,000 people per day could enable more timely detection of new variants and reliable estimates of variant prevalence. The performance of global SARS-CoV-2 genomic surveillance programs is fundamentally limited by access to diagnostic testing.
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