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Rogers MB, Harner A, Buhay M, Firek B, Methé B, Morris A, Palmer OMP, Promes SB, Sherwin RL, Southerland L, Vieira AR, Yende S, Morowitz MJ, Huang DT. The salivary microbiota of patients with acute lower respiratory tract infection-A multicenter cohort study. PLoS One 2024; 19:e0290062. [PMID: 38206940 PMCID: PMC10783762 DOI: 10.1371/journal.pone.0290062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 08/01/2023] [Indexed: 01/13/2024] Open
Abstract
The human microbiome contributes to health and disease, but the oral microbiota is understudied relative to the gut microbiota. The salivary microbiota is easily accessible, underexplored, and may provide insight into response to infections. We sought to determine the composition, association with clinical features, and heterogeneity of the salivary microbiota in patients with acute lower respiratory tract infection (LRTI). We conducted a multicenter prospective cohort study of 147 adults with acute LRTI presenting to the emergency department of seven hospitals in three states (Pennsylvania, Michigan, and Ohio) between May 2017 and November 2018. Salivary samples were collected in the emergency department, at days 2-5 if hospitalized, and at day 30, as well as fecal samples if patients were willing. We compared salivary microbiota profiles from patients to those of healthy adult volunteers by sequencing and analyzing bacterial 16-rRNA. Compared to healthy volunteers, the salivary microbiota of patients with LRTI was highly distinct and strongly enriched with intestinal anaerobes such as Bacteroidaceae, Ruminococcaceae, and Lachnospiraceae (e.g., mean 10% relative abundance of Bacteroides vs < 1% in healthy volunteers). Within the LRTI population, COPD exacerbation was associated with altered salivary microbiota composition compared to other LRTI conditions. The largest determinant of microbiota variation within the LRTI population was geography (city in which the hospital was located).
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Affiliation(s)
- Matthew B. Rogers
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ashley Harner
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Megan Buhay
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Brian Firek
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Barbara Methé
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alison Morris
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Susan B. Promes
- Pennsylvania State University, State College, Pennsylvania, United States of America
| | | | - Lauren Southerland
- The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Alexandre R. Vieira
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sachin Yende
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael J. Morowitz
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - David T. Huang
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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Tansirichaiya S, Winje E, Wigand J, Al-Haroni M. Inverse PCR-based detection reveal novel mobile genetic elements and their associated genes in the human oral metagenome. BMC Oral Health 2022; 22:210. [PMID: 35624467 PMCID: PMC9137128 DOI: 10.1186/s12903-022-02209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
The human oral cavity is one of the hotspots harboring multiple mobile genetic elements (MGEs), which are segments of DNA that can move either within bacterial genomes or between bacterial cells that can facilitate the spreading of genetic materials, including antimicrobial resistance genes. It is, therefore, important to investigate genes associated with the MGEs as they have a high probability of dissemination within the bacterial population under selective pressure from human activities. As one-third of oral bacteria are not yet culturable in the laboratory condition, therefore, in this work, it is aimed to detect and identify the genetic contexts of MGEs in the oral cavity through an inverse PCR (IPCR)-based approach on the oral metagenomic. The human oral metagenome was extracted from saliva samples collected from healthy individuals in Tromsø, Norway. The extracted DNA was partially digested with the HindIII restriction enzyme and self-circularized by ligation. DNA primers targeting each MGE were designed to amplify outwards from the MGEs and used for the IPCR on the circularized DNA products. The IPCR amplicons were cloned into a pCR-XL-2-TOP vector, screened, and sequenced. Out of 40 IPCR amplicons, we confirmed and verified the genetic contexts of 11 samples amplified with primers targeting integron gene cassettes (GCs), IS431 composite transposons, and Tn916 conjugative transposons (tet(M) and xis-int). Novel integron GCs, MGEs, and variants of Tn916 conjugative transposons were identified, which is the first report using the IPCR technique to detect the genetic contexts of MGEs in the oral metagenomic DNA.
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Affiliation(s)
- Supathep Tansirichaiya
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
- Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway
| | - Endre Winje
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Johannes Wigand
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway.
- Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway.
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Integron gene cassettes harboring novel variants of D-alanine-D-alanine ligase confer high-level resistance to D-cycloserine. Sci Rep 2020; 10:20709. [PMID: 33244063 PMCID: PMC7691350 DOI: 10.1038/s41598-020-77377-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/10/2020] [Indexed: 11/08/2022] Open
Abstract
Antibiotic resistance poses an increasing threat to global health. To tackle this problem, the identification of principal reservoirs of antibiotic resistance genes (ARGs) plus an understanding of drivers for their evolutionary selection are important. During a PCR-based screen of ARGs associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding a d-alanine-d-alanine ligase (ddl6 and ddl7) located within gene cassettes in the first position of a reverse integron were identified. Treponema denticola was identified as the likely host of the ddl cassettes. Both ddl6 and ddl7 conferred high level resistance to d-cycloserine when expressed in Escherichia coli with ddl7 conferring four-fold higher resistance to D-cycloserine compared to ddl6. A SNP was found to be responsible for this difference in resistance phenotype between the two ddl variants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection of ddl containing integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP and d-cycloserine binding pockets of Ddl.
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Ali N, Lin Y, Qing Z, Xiao D, Ud Din A, Ali I, Lian T, Chen B, Wen R. The Role of Agriculture in the Dissemination of Class 1 Integrons, Antimicrobial Resistance, and Diversity of Their Gene Cassettes in Southern China. Genes (Basel) 2020; 11:genes11091014. [PMID: 32872161 PMCID: PMC7564866 DOI: 10.3390/genes11091014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
Integrons are hot spots for acquiring gene cassettes from the environment and play a major role in the bacterial evolution and dissemination of antimicrobial resistance (AMR), thus posing a serious threat. There are currently studies on integrons and antibiotic resistance genes; however, the presence and association of integrons in different agricultural crops and their subsequent dissemination and role in AMR have not been reported previously. This study examines the abundance of integrons, their gene cassette diversity in various crop soils, and their role in the dissemination of AMR in the southern region of China. Samples from different agri-crop soil, such as rice (R.S), sugarcane (S.S), citrus (C.S), banana (B.S), agricultural runoff (the point where the runoff of all sites meet (R.O)), and wild (non-agricultural) soil (W.S), were collected. Quantitative PCR was used to determine the abundance of integrons, and clone libraries were constructed to examine the gene cassette arrays. All the tested samples were found positive for Class-I (CL1) integrons and revealed a higher concentration and higher relative abundance of R.S than the others, with the least found at the W.S site. The W.S CL1 cassette arrays were found empty, and no putative conserved domains were found. The R.O was found to contain a high number of gene cassettes with various functions, while the smallest number of gene cassettes was found in the S.S among the crop soils. Most of the gene cassettes presented by the R.O were primarily shared with other sites, and the antibiotic-resistant genes were consistently observed to be dominant. The constructed clone libraries represented a diverse gene cassette array with 16% novel gene cassettes that play a vital role in pathogenesis, transportation, biosynthesis, and AMR. Most resistance-related gene cassettes were associated with the genes encoding resistance to quaternary ammonium compound (QAC) and aminoglycosides. This study highlights the significant differences in the abundance of integrons among various agricultural soils and offers deep insight into the pools of gene cassettes that play a key role in the dissemination of integrons and AMR.
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Affiliation(s)
- Niyaz Ali
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
| | - Yinfu Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
| | - Zhen Qing
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
| | - Dan Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
| | - Ahmad Ud Din
- Drug Discovery Research Center, South West Medical University, Luzhou 646000, China;
| | - Izhar Ali
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
| | - Tengxiang Lian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, South China Agricultural University, Guangzhou 510642, China;
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
- Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ronghui Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
- Correspondence: ; Tel.: +86-13669614062
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5
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Buongermino Pereira M, Österlund T, Eriksson KM, Backhaus T, Axelson-Fisk M, Kristiansson E. A comprehensive survey of integron-associated genes present in metagenomes. BMC Genomics 2020; 21:495. [PMID: 32689930 PMCID: PMC7370490 DOI: 10.1186/s12864-020-06830-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 06/15/2020] [Indexed: 12/19/2022] Open
Abstract
Background Integrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging. Results Here, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants. Conclusions Our results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes.
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Affiliation(s)
- Mariana Buongermino Pereira
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - K Martin Eriksson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Centre for Sustainable Development, Chalmers University of Technology, Gothenburg, Sweden
| | - Thomas Backhaus
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Marina Axelson-Fisk
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden. .,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.
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Berglund F, Österlund T, Boulund F, Marathe NP, Larsson DGJ, Kristiansson E. Identification and reconstruction of novel antibiotic resistance genes from metagenomes. MICROBIOME 2019; 7:52. [PMID: 30935407 PMCID: PMC6444489 DOI: 10.1186/s40168-019-0670-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 03/21/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Environmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables cultivation-independent characterization of bacterial communities but the resulting data is noisy and highly fragmented, severely hampering the identification of previously undescribed ARGs. We have therefore developed fARGene, a method for identification and reconstruction of ARGs directly from shotgun metagenomic data. RESULTS fARGene uses optimized gene models and can therefore with high accuracy identify previously uncharacterized resistance genes, even if their sequence similarity to known ARGs is low. By performing the analysis directly on the metagenomic fragments, fARGene also circumvents the need for a high-quality assembly. To demonstrate the applicability of fARGene, we reconstructed β-lactamases from five billion metagenomic reads, resulting in 221 ARGs, of which 58 were previously not reported. Based on 38 ARGs reconstructed by fARGene, experimental verification showed that 81% provided a resistance phenotype in Escherichia coli. Compared to other methods for detecting ARGs in metagenomic data, fARGene has superior sensitivity and the ability to reconstruct previously unknown genes directly from the sequence reads. CONCLUSIONS We conclude that fARGene provides an efficient and reliable way to explore the unknown resistome in bacterial communities. The method is applicable to any type of ARGs and is freely available via GitHub under the MIT license.
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Affiliation(s)
- Fanny Berglund
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Boulund
- Center for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Nachiket P Marathe
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Institute of Marine Research (IMR), Bergen, Norway
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
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7
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The oral microbiome. Emerg Top Life Sci 2017; 1:287-296. [DOI: 10.1042/etls20170040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 11/17/2022]
Abstract
The human microbiome is receiving a great deal of attention as its role in health and disease becomes ever more apparent. The oral microbiome, perhaps due to the ease with which we can obtain samples, is arguably the most well-studied human microbiome to date. It is obvious, however, that we have only just begun to scratch the surface of the complex bacterial and bacterial–host interactions within this complex community. Here, we describe the factors which are known to influence the development of the seemingly globally conserved, core, oral microbiome and those which are likely to be responsible for the observed differences at the individual level. We discuss the paradoxical situation of maintaining a stable core microbiome which is at the same time incredibly resilient and adaptable to many different stresses encountered in the open environment of the oral cavity. Finally, we explore the interactions of the oral microbiome with the host and discuss the interactions underlying human health and disease.
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8
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Pereira MB, Wallroth M, Kristiansson E, Axelson-Fisk M. HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models. J Comput Biol 2016; 23:891-902. [PMID: 27428829 DOI: 10.1089/cmb.2016.0024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Integrons are genetic elements that facilitate the horizontal gene transfer in bacteria and are known to harbor genes associated with antibiotic resistance. The gene mobility in the integrons is governed by the presence of attC sites, which are 55 to 141-nucleotide-long imperfect inverted repeats. Here we present HattCI, a new method for fast and accurate identification of attC sites in large DNA data sets. The method is based on a generalized hidden Markov model that describes each core component of an attC site individually. Using twofold cross-validation experiments on a manually curated reference data set of 231 attC sites from class 1 and 2 integrons, HattCI showed high sensitivities of up to 91.9% while maintaining satisfactory false-positive rates. When applied to a metagenomic data set of 35 microbial communities from different environments, HattCI found a substantially higher number of attC sites in the samples that are known to contain more horizontally transferred elements. HattCI will significantly increase the ability to identify attC sites and thus integron-mediated genes in genomic and metagenomic data. HattCI is implemented in C and is freely available at http://bioinformatics.math.chalmers.se/HattCI .
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Affiliation(s)
- Mariana Buongermino Pereira
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden .,2 Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Mikael Wallroth
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden
| | - Erik Kristiansson
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden .,2 Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Marina Axelson-Fisk
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden
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9
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Detection of Novel Integrons in the Metagenome of Human Saliva. PLoS One 2016; 11:e0157605. [PMID: 27304457 PMCID: PMC4909258 DOI: 10.1371/journal.pone.0157605] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/01/2016] [Indexed: 01/08/2023] Open
Abstract
Integrons are genetic elements capable of capturing and expressing open reading frames (ORFs) embedded within gene cassettes. They are involved in the dissemination of antibiotic resistance genes (ARGs) in clinically important pathogens. Although the ARGs are common in the oral cavity the association of integrons and antibiotic resistance has not been reported there. In this work, a PCR-based approach was used to investigate the presence of integrons and associated gene cassettes in human oral metagenomic DNA obtained from both the UK and Bangladesh. We identified a diverse array of gene cassettes containing ORFs predicted to confer antimicrobial resistance and other adaptive traits. The predicted proteins include a putative streptogramin A O-acetyltransferase, a bleomycin binding protein, cof-like hydrolase, competence and motility related proteins. This is the first study detecting integron gene cassettes directly from oral metagenomic DNA samples. The predicted proteins are likely to carry out a multitude of functions; however, the function of the majority is yet unknown.
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10
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Nimkulrat S, Lee H, Doak TG, Ye Y. Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola. Front Microbiol 2016; 7:852. [PMID: 27375574 PMCID: PMC4891356 DOI: 10.3389/fmicb.2016.00852] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/23/2016] [Indexed: 12/11/2022] Open
Abstract
Diversity-generating retroelements (DGRs) are genetic cassettes that can produce massive protein sequence variation in prokaryotes. Presumably DGRs confer selective advantages to their hosts (bacteria or viruses) by generating variants of target genes—typically resulting in target proteins with altered ligand-binding specificity—through a specialized error-prone reverse transcription process. The only extensively studied DGR system is from the Bordetella phage BPP-1, although DGRs are predicted to exist in other species. Using bioinformatics analysis, we discovered that the DGR system associated with the Treponema denticola species (a human oral-associated periopathogen) is dynamic (with gains/losses of the system found in the isolates) and diverse (with multiple types found in isolated genomes and the human microbiota). The T. denticola DGR is found in only nine of the 17 sequenced T. denticola strains. Analysis of the DGR-associated template regions and reverse transcriptase gene sequences revealed two types of DGR systems in T. denticola: the ATCC35405-type shared by seven isolates including ATCC35405; and the SP32-type shared by two isolates (SP32 and SP33), suggesting multiple DGR acquisitions. We detected additional variants of the T. denticola DGR systems in the human microbiomes, and found that the SP32-type DGR is more abundant than the ATCC35405-type in the healthy human oral microbiome, although the latter is found in more sequenced isolates. This is the first comprehensive study to characterize the DGRs associated with T. denticola in individual genomes as well as human microbiomes, demonstrating the importance of utilizing both individual genomes and metagenomes for characterizing the elements, and for analyzing their diversity and distribution in human populations.
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Affiliation(s)
- Sutichot Nimkulrat
- School of Informatics and Computing, Indiana University, Bloomington IN, USA
| | - Heewook Lee
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh PA, USA
| | - Thomas G Doak
- Department of Biology, Indiana University, BloomingtonIN, USA; National Center for Genome Analysis Support, Indiana University, BloomingtonIN, USA
| | - Yuzhen Ye
- School of Informatics and Computing, Indiana University, Bloomington IN, USA
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11
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Ye Y, Tang H. Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. Bioinformatics 2015; 32:1001-8. [PMID: 26319390 PMCID: PMC4896364 DOI: 10.1093/bioinformatics/btv510] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 08/24/2015] [Indexed: 11/26/2022] Open
Abstract
Motivation: Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture of microbial species) and other meta-omics approaches hold even greater promise for providing additional insights into functional and regulatory characteristics of the microbial communities. Current metatranscriptomics projects are often carried out without matched metagenomic datasets (of the same microbial communities). For the projects that produce both metatranscriptomic and metagenomic datasets, their analyses are often not integrated. Metagenome assemblies are far from perfect, partially explaining why metagenome assemblies are not used for the analysis of metatranscriptomic datasets. Results: Here, we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We developed an application of this mapping algorithm: a reference-based approach to metatranscriptome assembly using graphs of metagenome assembly as the reference. Our results show that this new approach (called TAG) helps to assemble substantially more transcripts that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome. Availability and implementation: TAG was implemented in C++ and has been tested extensively on the Linux platform. It is available for download as open source at http://omics.informatics.indiana.edu/TAG. Contact:yye@indiana.edu
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Affiliation(s)
- Yuzhen Ye
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
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12
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Abstract
Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.
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Dupin C, Tamanai-Shacoori Z, Ehrmann E, Dupont A, Barloy-Hubler F, Bousarghin L, Bonnaure-Mallet M, Jolivet-Gougeon A. Oral Gram-negative anaerobic bacilli as a reservoir of β-lactam resistance genes facilitating infections with multiresistant bacteria. Int J Antimicrob Agents 2015; 45:99-105. [DOI: 10.1016/j.ijantimicag.2014.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 10/15/2014] [Indexed: 11/15/2022]
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Cardenas PA, Cookson WO. The Microbiome at Other Mucosal Sites. Mucosal Immunol 2015. [DOI: 10.1016/b978-0-12-415847-4.00006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Culligan EP, Sleator RD, Marchesi JR, Hill C. Metagenomics and novel gene discovery: promise and potential for novel therapeutics. Virulence 2014; 5:399-412. [PMID: 24317337 PMCID: PMC3979868 DOI: 10.4161/viru.27208] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/21/2013] [Accepted: 11/14/2013] [Indexed: 02/06/2023] Open
Abstract
Metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. Herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of each type of approach, as well as potential solutions. Furthermore, we discuss the potential for metagenomic biotherapeutic discovery, with a particular focus on the human gut microbiome and finally, we outline how the discovery of novel genes may be used to create bioengineered probiotics.
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Affiliation(s)
- Eamonn P Culligan
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- School of Microbiology; University College Cork; Cork, Ireland
| | - Roy D Sleator
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland
| | - Julian R Marchesi
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- Cardiff School of Biosciences; Cardiff University; Cardiff, UK
- Department of Hepatology and Gastroenterology; Imperial College London; London, UK
| | - Colin Hill
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- School of Microbiology; University College Cork; Cork, Ireland
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Multiple Pathways of Genome Plasticity Leading to Development of Antibiotic Resistance. Antibiotics (Basel) 2013; 2:288-315. [PMID: 27029305 PMCID: PMC4790341 DOI: 10.3390/antibiotics2020288] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/21/2013] [Accepted: 05/23/2013] [Indexed: 02/05/2023] Open
Abstract
The emergence of multi-resistant bacterial strains is a major source of concern and has been correlated with the widespread use of antibiotics. The origins of resistance are intensively studied and many mechanisms involved in resistance have been identified, such as exogenous gene acquisition by horizontal gene transfer (HGT), mutations in the targeted functions, and more recently, antibiotic tolerance through persistence. In this review, we focus on factors leading to integron rearrangements and gene capture facilitating antibiotic resistance acquisition, maintenance and spread. The role of stress responses, such as the SOS response, is discussed.
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Wu YW, Doak TG, Ye Y. The gain and loss of chromosomal integron systems in the Treponema species. BMC Evol Biol 2013; 13:16. [PMID: 23339550 PMCID: PMC3607928 DOI: 10.1186/1471-2148-13-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 01/11/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Integron systems are now recognized as important agents of bacterial evolution and are prevalent in most environments. One of the human pathogens known to harbor chromosomal integrons, the Treponema spirochetes are the only clade among spirochete species found to carry integrons. With the recent release of many new Treponema genomes, we were able to study the distribution of chromosomal integrons in this genus. RESULTS We find that the Treponema spirochetes implicated in human periodontal diseases and those isolated from cow and swine intestines contain chromosomal integrons, but not the Treponema species isolated from termite guts. By examining the species tree of selected spirochetes (based on 31 phylogenetic marker genes) and the phylogenetic tree of predicted integron integrases, and assisted by our analysis of predicted integron recombination sites, we found that all integron systems identified in Treponema spirochetes are likely to have evolved from a common ancestor--a horizontal gain into the clade. Subsequent to this event, the integron system was lost in the branch leading to the speciation of T. pallidum and T. phagedenis (the Treponema sps. implicated in sexually transmitted diseases). We also find that the lengths of the integron attC sites shortened through Treponema speciation, and that the integron gene cassettes of T. denticola are highly strain specific. CONCLUSIONS This is the first comprehensive study to characterize the chromosomal integron systems in Treponema species. By characterizing integron distribution and cassette contents in the Treponema sps., we link the integrons to the speciation of the various species, especially to the pathogens T. pallidum and T. phagedenis.
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Affiliation(s)
- Yu-Wei Wu
- School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA
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