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Li J, Sauers L, Zhuang D, Ren H, Guo J, Wang L, Zhuang M, Guo Y, Zhang Z, Wu J, Yao J, Yang H, Huang J, Wang C, Lin Q, Zhang Z, Sadd BM. Divergence and convergence of gut microbiomes of wild insect pollinators. mBio 2023; 14:e0127023. [PMID: 37504575 PMCID: PMC10470603 DOI: 10.1128/mbio.01270-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/14/2023] [Indexed: 07/29/2023] Open
Abstract
Pollination services provided by wild insect pollinators are critical to natural ecosystems and crops around the world. There is an increasing appreciation that the gut microbiota of these insects influences their health and consequently their services. However, pollinator gut microbiota studies have focused on well-described social bees, but rarely include other, more phylogenetically divergent insect pollinators. To expand our understanding, we explored the insect pollinator microbiomes across three insect orders through two DNA sequencing approaches. First, in an exploratory 16S amplicon sequencing analysis of taxonomic community assemblages, we found lineage-specific divergences of dominant microbial genera and microbiota community composition across divergent insect pollinator genera. However, we found no evidence for a strong broad-scale phylogenetic signal, which we see for community relatedness at finer scales. Subsequently, we utilized metagenomic shotgun sequencing to obtain metagenome-assembled genomes and assess the functionality of the microbiota from pollinating flies and social wasps. We uncover a novel gut microbe from pollinating flies in the family Orbaceae that is closely related to Gilliamella spp. from social bees but with divergent functions. We propose this novel species be named Candidatus Gilliamella eristali. Further metagenomes of dominant fly and wasp microbiome members suggest that they are largely not host-insect adapted and instead may be environmentally derived. Overall, this study suggests selective processes involving ecology or physiology, or neutral processes determining microbe colonization may predominate in the turnover of lineages in insect pollinators broadly, while evolution with hosts may occur only under certain circumstances and on smaller phylogenetic scales. IMPORTANCE Wild insect pollinators provide many key ecosystem services, and the microbes associated with these insect pollinators may influence their health. Therefore, understanding the diversity in microbiota structure and function, along with the potential mechanisms shaping the microbiota across diverse insect pollinators, is critical. Our study expands beyond existing knowledge of well-studied social bees, like honey bees, including members from other bee, wasp, butterfly, and fly pollinators. We infer ecological and evolutionary factors that may influence microbiome structure across diverse insect pollinator hosts and the functions that microbiota members may play. We highlight significant differentiation of microbiomes among diverse pollinators. Closer analysis suggests that dominant members may show varying levels of host association and functions, even in a comparison of closely related microbes found in bees and flies. This work suggests varied importance of ecological, physiological, and non-evolutionary filters in determining structure and function across largely divergent wild insect pollinator microbiomes.
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Affiliation(s)
- Jilian Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China., Beijing, China
| | - Logan Sauers
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Daohua Zhuang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Haiqing Ren
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Liuhao Wang
- College of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Mingsheng Zhuang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China., Beijing, China
- Shanghai Suosheng Biotechnology Co., Ltd., Shanghai, China
| | - Yulong Guo
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China., Beijing, China
| | - Zhengyi Zhang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China., Beijing, China
| | - Jie Wu
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China., Beijing, China
| | - Jun Yao
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China., Beijing, China
| | - Huipeng Yang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China., Beijing, China
| | - Jiaxing Huang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China., Beijing, China
| | - Chengrui Wang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Qinghui Lin
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Zhigang Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary & Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ben M. Sadd
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
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Subhadra B, Cao D, Jensen R, Caswell C, Inzana TJ. Identification and initial characterization of Hfq-associated sRNAs in Histophilus somni strain 2336. PLoS One 2023; 18:e0286158. [PMID: 37220152 DOI: 10.1371/journal.pone.0286158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Small RNAs (sRNA), in association with the global chaperone regulator Hfq, positively or negatively regulate gene expression in bacteria. For this study, Histophilus somni sRNAs that bind to Hfq were identified and then partially characterized. The Hfq-associated sRNAs in H. somni were isolated and identified by co-immunoprecipitation using anti-Hfq antibody, followed by sRNA sequencing. Sequence analysis of the sRNA samples identified 100 putative sRNAs, out of which 16 were present in pathogenic strain 2336, but not in non-pathogenic strain 129Pt. Bioinformatic analyses suggested that the sRNAs HS9, HS79, and HS97 could bind to many genes putatively involved in virulence/biofilm formation. Furthermore, multi-sequence alignment of the sRNA regions in the genome revealed that HS9 and HS97 could interact with sigma 54, which is a transcription factor linked to important bacterial traits, including motility, virulence, and biofilm formation. Northern blotting was used to determine the approximate size, abundance and any processing events attributed to the sRNAs. Selected sRNA candidates were confirmed to bind Hfq, as determined by electrophoretic mobility shift assays using sRNAs synthesized by in vitro transcription and recombinant Hfq. The exact transcriptional start site of the sRNA candidates was determined by RNA ligase-mediated rapid amplification of cDNA ends, followed by cloning and sequencing. This is the first investigation of H. somni sRNAs that show they may have important regulatory roles in virulence and biofilm formation.
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Affiliation(s)
- Bindu Subhadra
- College of Veterinary Medicine, Long Island University, Brookville, New York, United States of America
| | - Dianjun Cao
- College of Veterinary Medicine, Long Island University, Brookville, New York, United States of America
| | - Roderick Jensen
- College of Science, Virginia Tech, Blacksburg, VA, United States of America
| | - Clayton Caswell
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States of America
| | - Thomas J Inzana
- College of Veterinary Medicine, Long Island University, Brookville, New York, United States of America
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States of America
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3
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Morawska LP, Kuipers OP. Cell-to-cell non-conjugative plasmid transfer between Bacillus subtilis and lactic acid bacteria. Microb Biotechnol 2023; 16:784-798. [PMID: 36547214 PMCID: PMC10034627 DOI: 10.1111/1751-7915.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/15/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can interact with a plethora of other microorganisms in its natural habitat. Due to the versatile interactions and its ability to form nanotubes, i.e., recently described membrane structures that trade cytoplasmic content between neighbouring cells, we investigated the potential of HGT from B. subtilis to industrially-relevant members of lactic acid bacteria (LAB). To explore the interspecies HGT events, we developed a co-culturing protocol and provided proof of transfer of a small high copy non-conjugative plasmid from B. subtilis to LABs. Interestingly, the plasmid transfer did not involve conjugation nor activation of the competent state by B. subtilis. Moreover, our study shows for the first time non-conjugative cell-to-cell intraspecies plasmid transfer for non-competent Lactococcus lactis sp. cremoris strains. Our study indicates that cell-to-cell transformation is a ubiquitous form of HGT and can be potentially utilized as an alternative tool for natural (non-GMO) strain improvement.
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Affiliation(s)
- Luiza P Morawska
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Farghaly M, Hynes MF, Nazari M, Checkley S, Liljebjelke K. Examination of the horizontal gene transfer dynamics of an integrative and conjugative element encoding multidrug resistance in Histophilus somni. Can J Microbiol 2023; 69:123-135. [PMID: 36495587 DOI: 10.1139/cjm-2021-0349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Integrative and conjugative elements (ICEs) are self-transferable mobile genetic elements that play a significant role in disseminating antimicrobial resistance between bacteria via horizontal gene transfer. A recently identified ICE in a clinical isolate of Histophilus somni (ICEHs02) is 72 914 base pairs in length and harbours seven predicted antimicrobial resistance genes conferring resistance to tetracycline (tetR-tet(H)), florfenicol (floR), sulfonamide (Sul2), aminoglycosides (APH(3″)-Ib, APH(6)-Id, APH(3')-Ia), and copper (mco). This study investigated ICEHs02 host range, assessed effects of antimicrobial stressors on transfer frequency, and examined effects of ICEHs02 acquisition on hosts. Conjugation assays examined transfer frequency of ICEHs02 to H. somni and Pasteurella multocida strains. Polymerase chain reaction assays confirmed the presence of a circular intermediate, ICE-associated core genes, and cargo genes in recipient strains. Susceptibility testing examined ICEHs02-associated resistance phenotypes in recipient strains. Tetracycline and ciprofloxacin induction significantly increased the transfer rates of ICEHs02 in vitro. The copy numbers of the circular intermediate of ICEHs02 per chromosome exhibited significant increases of ∼37-fold after tetracycline exposure and ∼4-fold after ciprofloxacin treatment. The acquisition of ICEHs02 reduced the relative fitness of H. somni transconjugants (TG) by 28% (w = 0.72 ± 0.04) and the relative fitness of P. multocida TG was decreased by 15% (w = 0.85 ± 0.01).
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Affiliation(s)
- Mai Farghaly
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael F Hynes
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Mohammad Nazari
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Sylvia Checkley
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Karen Liljebjelke
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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Yatsentyuk S, Pobolelova J, Gordeeva V, Timofeeva I. Whole-genome sequencing of Histophilus somni strains isolated in Russia. Vet World 2023; 16:272-280. [PMID: 37042002 PMCID: PMC10082713 DOI: 10.14202/vetworld.2023.272-280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/05/2023] [Indexed: 02/16/2023] Open
Abstract
Background and Aim: Histophilus somni is a Gram-negative bacterium belonging to the Pasteurellaceae family that can cause bovine histophilosis. Histophilus may act as a commensal or opportunistic bacterial cattle pathogen. Comparing genomes of the pathogenic strain 2336 with the non-pathogenic preputial 129Pt isolate revealed some putative virulence factors. The study of the complete genomes of H. somni strains circulating in Russia has never been conducted before. This study aimed to identify genetic features of the H. somni strains isolated in Russia and evaluate the possibility of using strains for vaccine development.
Materials and Methods: Three strains of H. somni were isolated from different sources. Strain 188-VIEV was isolated from a vaginal swab sample of cattle with endometritis. 532-VIEV and 551-VIEV were cultured from the cryopreserved bull semen samples imported from Canada. Histophilus somni strain ATCC 700025 provided by ATCC (American Type Culture Collection) was also used in the study. DNA extraction was performed using QIAamp DNA Mini Kit (QIAGEN, USA). The whole-genome sequencing of the four strains was performed using Illumina Miseq. The comparison of the resulting sequences with the complete genomes of H. somni 2336 and 129Pt, and detection of the resistance genes and virulence factors, was performed using the ResFinder and Virulence Factor Database web services.
Results: The genome size of the samples varied from 1.9 to 2.3 Mb. The number of coding sequences varied from 1795 to 2256. The average sequence density was 90%. The total guanine-cytosine (GC) content was 36.8%–37.2%, which coincided with data previously obtained for H. somni. Three out of four studied strains encoded putative virulence factors such as filamentous hemagglutinin homologs, lipooligosaccharide biosynthesis proteins, and proteins involved in iron transport and utilization. The Ser83Ile substitution was identified in the DNA topoisomerase II (gyrA) in H. somni strains 532-VIEV and 551-VIEV cultured from bull semen which led to resistance to fluoroquinolones. The gene (AAC-6-Ia + APH-2”) encoding a bifunctional aminoglycoside modification enzyme was detected in strain 551-VIEV.
Conclusion: Strains with virulence genes identified could be candidates for designing vaccines and potentially represent antigen sources. The results show that antibiotic-resistant H. somni can be spread with semen used for artificial insemination.
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Affiliation(s)
- Svetlana Yatsentyuk
- Department of Biotechnology, Russian State Center for Animal Feed and Drug Standardization and Quality, 5, Zvenigorodskoe Highway, Moscow, Russia
| | - Julia Pobolelova
- Department of Biotechnology, Russian State Center for Animal Feed and Drug Standardization and Quality, 5, Zvenigorodskoe Highway, Moscow, Russia
| | - Veronika Gordeeva
- Department of Biotechnology, Russian State Center for Animal Feed and Drug Standardization and Quality, 5, Zvenigorodskoe Highway, Moscow, Russia
| | - Irina Timofeeva
- Department of Biotechnology, Russian State Center for Animal Feed and Drug Standardization and Quality, 5, Zvenigorodskoe Highway, Moscow, Russia
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Antimicrobial susceptibility and genomic analysis of Histophilus somni isolated from cases of bovine respiratory disease in Autralian feedlot cattle. Vet Microbiol 2022; 270:109460. [DOI: 10.1016/j.vetmic.2022.109460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/01/2022] [Accepted: 05/09/2022] [Indexed: 11/19/2022]
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Siddaramappa S. Comparative genomics of the Pasteurella multocida toxin. Genome 2021; 64:679-692. [PMID: 33471631 DOI: 10.1139/gen-2020-0176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pasteurella multocida is a zoonotic pathogen whose genetic heterogeneity is well known. Five serogroups (A, B, D, E, and F) and 16 serotypes of P. multocida have been recognized thus far based on capsular polysaccharide typing and lipopolysaccharide typing, respectively. Progressive atrophic rhinitis in domestic pigs is caused by P. multocida strains containing toxA, which encodes a 146 kDa heat-labile toxin. Among the five serogroups, only some strains of serogroups A and D are toxigenic. In this study, by comparative analyses of the genomes of many strains, it has been shown that toxA is sparsely distributed in P. multocida. Furthermore, full-length homologs of P. multocida toxA were found only in two other bacterial species. It has also been shown that toxA is usually associated with a prophage, and that some strains contain an orthologous prophage but not toxA. Among the toxA-containing prophages that were compared, an operon putatively encoding a type II restriction-modification system was present only in strains LFB3, HN01, and HN06. These results indicate that the selection and maintenance of the heat-labile toxin and the type II restriction-modification system are evolutionarily less favorable among P. multocida strains. Phylogenetic analysis using the alignment- and parameter-free method CVTree3 showed that deduced proteome sequences can be used as effectively as whole/core genome single nucleotide polymorphisms to group P. multocida strains in relation to their serotypes and (or) genotypes. It remains to be determined if the toxA-containing prophages in strains HN01 and HN06 are inducible, and if they can be used for lysogenic transfer of toxA to other bacteria.
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Affiliation(s)
- Shivakumara Siddaramappa
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru, Karnataka 560100, India.,Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru, Karnataka 560100, India
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Liu YY, Liu XK, Cui XD, Chen M, Li SH, He DD, Liu JH, Yuan L, Hu GZ, Pan YS. Characterization of pTS14, an IncF2:A1:B1 Plasmid Carrying tet(M) in a Salmonella enterica Isolate. Front Microbiol 2020; 11:1523. [PMID: 32719670 PMCID: PMC7347964 DOI: 10.3389/fmicb.2020.01523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/12/2020] [Indexed: 11/21/2022] Open
Abstract
The objective of this study was to explore the genetic and biological features of the tet(M)-harboring plasmid pTS14 in Salmonella enterica strain S14 isolated from a chicken fecal sample. Plasmid pTS14 was identified by conjugation, S1-pulsed-field gel electrophoresis (PFGE), Southern hybridization, and plasmid sequencing. The biological characteristics of pTS14 were assessed via stability, growth kinetics, and starvation survival experiments. Strain S14, belonging to ST3007, harbored a 119-kb tet(M)-bearing IncF2:A1:B1 conjugative plasmid pTS14. The plasmid pTS14 contained a novel transposon Tn6709 with the genetic structure IS26-tnpA1-tnpA2-Δorf13-LP-tet(M)-tnpX-ΔtnpR-IS26, and the resistance genes tet(B), tet(D), strAB, sul2, and blaTEM–1b. In addition, pTS14 was found to be highly stable in the recipient strain E. coli J53. The transconjugant TS14 exhibited a higher survival ratio than E. coli J53 under permanent starvation-induced stress. The tet(M)-bearing IncF2 epidemic plasmid lineage may accelerate the dissemination of tet(M) and other genes by coselection, which could constitute a potentially serious threat to clinical treatment regimens.
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Affiliation(s)
- Ying-Ying Liu
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Xiao-Kang Liu
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Xiao-Die Cui
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Min Chen
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Shuai-Hua Li
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Dan-Dan He
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Jian-Hua Liu
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Li Yuan
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Gong-Zheng Hu
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Yu-Shan Pan
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
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Abstract
Metals and metalloids have been used alongside antibiotics in livestock production for a long time. The potential and acute negative impact on the environment and human health of these livestock feed supplements has prompted lawmakers to ban or discourage the use of some or all of these supplements. This article provides an overview of current use in the European Union and the United States, detected metal resistance determinants, and the proteins and mechanisms responsible for conferring copper and zinc resistance in bacteria. A detailed description of the most common copper and zinc metal resistance determinants is given to illustrate not only the potential danger of coselecting antibiotic resistance genes but also the potential to generate bacterial strains with an increased potential to be pathogenic to humans. For example, the presence of a 20-gene copper pathogenicity island is highlighted since bacteria containing this gene cluster could be readily isolated from copper-fed pigs, and many pathogenic strains, including Escherichia coli O104:H4, contain this potential virulence factor, suggesting a potential link between copper supplements in livestock and the evolution of pathogens.
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Bandara AB, Zuo Z, McCutcheon K, Ramachandran S, Heflin JR, Inzana TJ. Identification of Histophilus somni by a nanomaterial optical fiber biosensor assay. J Vet Diagn Invest 2018; 30:821-829. [PMID: 30264658 PMCID: PMC6505835 DOI: 10.1177/1040638718803665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Histophilus somni is an opportunistic pathogen responsible for respiratory and systemic diseases of cattle and sheep. Rapid and accurate detection of H. somni is essential to distinguish H. somni from other potential pathogens for proper control and treatment of infections. Nanomaterial optical fiber biosensors (NOFS) recognize analyte interactions, such as DNA hybridization, with high specificity and sensitivity, and were applied to detect H. somni DNA in culture and clinical samples. An ionic self-assembled multilayer (ISAM) film was fabricated on a long-period grating optical fiber, and a biotinylated, nucleotide probe complementary to the H. somni 16S rDNA gene was coupled to the ISAM film. Exposure of the ISAM::probe to ⩾100 killed cells of H. somni strain 2336 without DNA amplification resulted in attenuation of light transmission of ⩾9.4%. Exposure of the complexed fiber to Escherichia coli or non- H. somni species of Pasteurellaceae reduced light transmission by ⩽3.4%. Exposure of the ISAM::probe to blood, bronchoalveolar fluid, or spleen from mice or calves infected with H. somni resulted in ⩾24.3% transmission attenuation. The assay correctly detected all 6 strains of H. somni tested from culture, or tissues from 3 separate mice and calves tested in duplicate. Six heterologous strains (representing 6 genera) reacted at below the cutoff value of 4.87% attenuation of light transmission. NOFS detected at least 100 H. somni cells without DNA amplification within 45 min with high specificity. Although different fibers could vary in signal sensitivity, this did not affect the sensitivity or specificity of the assay.
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Affiliation(s)
| | | | | | | | | | - Thomas J. Inzana
- Thomas J. Inzana, College of Veterinary Medicine, Long Island University, Brookville, NY 11548.
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Ueno Y, Teratani C, Misumi W, Hoshinoo K, Takamatsu D, Tagawa Y, Katsuda K. A Predominant Clonal Thromboembolic Meningoencephalitis Group of Histophilus somni Assigned by Major Outer Membrane Protein Gene Sequencing and Pulsed-Field Gel Electrophoresis. Front Vet Sci 2018; 5:221. [PMID: 30283793 PMCID: PMC6156380 DOI: 10.3389/fvets.2018.00221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/24/2018] [Indexed: 11/13/2022] Open
Abstract
Histophilus somni, a member of the family Pasteurellaceae, causes a variety of diseases, including thromboembolic meningoencephalitis (TEME) and respiratory diseases, which result in considerable economic losses to the cattle and sheep industries. In this study, 132 chronologically diverse isolates from cattle in Japan and 68 isolates from other countries comprising 49 from cattle and 19 from sheep were characterized using major outer membrane protein (MOMP) gene sequence and pulsed-field gel electrophoresis (PFGE) analyses. The H. somni isolates formed nine MOMP genetic clades (clade Ia, Ib, and II-VIII) and 10 PFGE clusters (HS1-HS10). Except for two (1.0%), all isolates fell into one of the nine MOMP genetic clades, while 62 (31.0%) isolates belonged to no PFGE cluster. MOMP genetic clade Ia and PFGE cluster HS1 were the major groups, and all HS1 isolates possessed the clade Ia MOMP gene. Isolates from TEME cases were significantly associated with these major groups (chi-square test, p < 0.0001), as 88.2% of the TEME isolates belonged to MOMP genetic clade Ia and PFGE cluster HS1, which formed the most predominant clonal group. After an inactivated vaccine using an HS1 strain with the clade Ia MOMP gene was introduced in Japan in late 1989, the number of TEME cases and isolates assigned into the clonal group decreased simultaneously. However, the proportions of clade Ia and cluster HS1 isolates from TEME cases remained high after 1990. These results suggest a close association of TEME with PFGE cluster HS1 and MOMP genetic clade Ia, and imply the presence of factors or characteristics commonly possessed by those strains that contribute to the development of TEME.
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Affiliation(s)
- Yuichi Ueno
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Chie Teratani
- Hyogo Prefectural Asago Livestock Hygiene Service Center, Asago, Japan
| | - Wakako Misumi
- Kagoshima Prefectural Kagoshima Central Livestock Hygiene Service Center, Kagoshima, Japan
| | - Kaori Hoshinoo
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Daisuke Takamatsu
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Yuichi Tagawa
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Ken Katsuda
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
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Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease. G3-GENES GENOMES GENETICS 2017; 7:3059-3071. [PMID: 28739600 PMCID: PMC5592931 DOI: 10.1534/g3.117.1137] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole-genome sequencing offers a culture-independent alternative to current bacterial identification methods, but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic diversity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease–associated bacterial isolates (Histophilus somni, Mycoplasma bovis, Mannheimia haemolytica, and Pasteurella multocida) from dairy and beef cattle. One hundred genomically distinct assemblies were added to the NCBI database, doubling the available genomic sequences for these four species. Computer-based methods identified 11 predicted antimicrobial resistance genes in three species, with none being detected in M. bovis. While computer-based analysis can identify antibiotic resistance genes within whole-genome sequences (genotype), it may not predict the actual antimicrobial resistance observed in a living organism (phenotype). Antimicrobial susceptibility testing on 64 H. somni, M. haemolytica, and P. multocida isolates had an overall concordance rate between genotype and phenotypic resistance to the associated class of antimicrobials of 72.7% (P < 0.001), showing substantial discordance. Concordance rates varied greatly among different antimicrobial, antibiotic resistance gene, and bacterial species combinations. This suggests that antimicrobial susceptibility phenotypes are needed to complement genomically predicted antibiotic resistance gene genotypes to better understand how the presence of antibiotic resistance genes within a given bacterial species could potentially impact optimal bovine respiratory disease treatment and morbidity/mortality outcomes.
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Guérin J, Bigot S, Schneider R, Buchanan SK, Jacob-Dubuisson F. Two-Partner Secretion: Combining Efficiency and Simplicity in the Secretion of Large Proteins for Bacteria-Host and Bacteria-Bacteria Interactions. Front Cell Infect Microbiol 2017; 7:148. [PMID: 28536673 PMCID: PMC5422565 DOI: 10.3389/fcimb.2017.00148] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/10/2017] [Indexed: 12/31/2022] Open
Abstract
Initially identified in pathogenic Gram-negative bacteria, the two-partner secretion (TPS) pathway, also known as Type Vb secretion, mediates the translocation across the outer membrane of large effector proteins involved in interactions between these pathogens and their hosts. More recently, distinct TPS systems have been shown to secrete toxic effector domains that participate in inter-bacterial competition or cooperation. The effects of these systems are based on kin vs. non-kin molecular recognition mediated by specific immunity proteins. With these new toxin-antitoxin systems, the range of TPS effector functions has thus been extended from cytolysis, adhesion, and iron acquisition, to genome maintenance, inter-bacterial killing and inter-bacterial signaling. Basically, a TPS system is made up of two proteins, the secreted TpsA effector protein and its TpsB partner transporter, with possible additional factors such as immunity proteins for protection against cognate toxic effectors. Structural studies have indicated that TpsA proteins mainly form elongated β helices that may be followed by specific functional domains. TpsB proteins belong to the Omp85 superfamily. Open questions remain on the mechanism of protein secretion in the absence of ATP or an electrochemical gradient across the outer membrane. The remarkable dynamics of the TpsB transporters and the progressive folding of their TpsA partners at the bacterial surface in the course of translocation are thought to be key elements driving the secretion process.
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Affiliation(s)
- Jeremy Guérin
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry, Centre National de La Recherche Scientifique UMR 5086-Université Lyon 1, Institute of Biology and Chemistry of ProteinsLyon, France
| | - Robert Schneider
- NMR and Molecular Interactions, Université de Lille, Centre National de La Recherche Scientifique, UMR 8576-Unité de Glycobiologie Structurale et FonctionnelleLille, France
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Françoise Jacob-Dubuisson
- Université de Lille, Centre National de La Recherche Scientifique, Institut National de La Santé et de La Recherche Médicale, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-Centre d'Infection et d'Immunité de LilleLille, France
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Abstract
Histophilus somni is responsible for sporadic disease worldwide in cattle and, to a lesser extent, in small ruminants, bighorn sheep (Ovis canadensis), and North American bison (Bison bison). The importance of H. somni diseases can be attributed to improved clinical and laboratory recognition, combined with the growth in intensive management practices for cattle. Although outbreaks of bovine histophilosis can occur year-round, in northern and southern hemispheres, it is most frequent in late fall and early winter. Weather, stress, dietary changes, and comingling of cattle are likely to be major triggers for outbreaks. The most frequent clinical expressions of histophilosis include undifferentiated fever, fibrinosuppurative pneumonia, encephalitis-leptomeningitis, necrotizing myocarditis, and diffuse pleuritis. Neurological disease occurs either as thrombotic meningoencephalitis (TME) or as suppurative meningitis with ventriculitis. Acute myocarditis is characteristically necrotizing and generally involves one or both papillary muscles in the left ventricular myocardium. Biofilm-like aggregates of bacteria occur in capillaries and veins in myocardium, in the central nervous system, and on endocardial surfaces. H. somni is a component of bovine respiratory disease (BRD) complex. In our experience, it is most commonly diagnosed in subacute-to-chronic polymicrobial pulmonary infections in combination with Mannheimia haemolytica, Trueperella pyogenes, Pasteurella multocida, or Mycoplasma bovis. Other, less common forms of H. somni disease present as polyarthritis/tenosynovitis, abortion with placentitis and fetal septicemia, epididymitis-orchitis, and ocular infections. It is likely that H. somni is under-recognized clinically and diagnostically. Most state and provincial laboratories in North America rely on bacterial isolation to confirm infection. The use of more sensitive detection methods on field cases of histophilosis will help resolve the pathogenesis of H. somni in natural outbreaks, and whether the disease is as common elsewhere as it is in Canada.
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Ruhe ZC, Nguyen JY, Chen AJ, Leung NY, Hayes CS, Low DA. CDI Systems Are Stably Maintained by a Cell-Contact Mediated Surveillance Mechanism. PLoS Genet 2016; 12:e1006145. [PMID: 27355474 PMCID: PMC4927057 DOI: 10.1371/journal.pgen.1006145] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 06/07/2016] [Indexed: 11/17/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) systems are widespread amongst Gram-negative bacteria where they play important roles in inter-cellular competition and biofilm formation. CDI+ bacteria use cell-surface CdiA proteins to bind neighboring bacteria and deliver C-terminal toxin domains. CDI+ cells also express CdiI immunity proteins that specifically neutralize toxins delivered from adjacent siblings. Genomic analyses indicate that cdi loci are commonly found on plasmids and genomic islands, suggesting that these Type 5 secretion systems are spread through horizontal gene transfer. Here, we examine whether CDI toxin and immunity activities serve to stabilize mobile genetic elements using a minimal F plasmid that fails to partition properly during cell division. This F plasmid is lost from Escherichia coli populations within 50 cell generations, but is maintained in ~60% of the cells after 100 generations when the plasmid carries the cdi gene cluster from E. coli strain EC93. By contrast, the ccdAB "plasmid addiction" module normally found on F exerts only a modest stabilizing effect. cdi-dependent plasmid stabilization requires the BamA receptor for CdiA, suggesting that plasmid-free daughter cells are inhibited by siblings that retain the CDI+ plasmid. In support of this model, the CDI+ F plasmid is lost rapidly from cells that carry an additional cdiI immunity gene on a separate plasmid. These results indicate that plasmid stabilization occurs through elimination of non-immune cells arising in the population via plasmid loss. Thus, genetic stabilization reflects a strong selection for immunity to CDI. After long-term passage for more than 300 generations, CDI+ plasmids acquire mutations that increase copy number and result in 100% carriage in the population. Together, these results show that CDI stabilizes genetic elements through a toxin-mediated surveillance mechanism in which cells that lose the CDI system are detected and eliminated by their siblings.
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Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Josephine Y Nguyen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Annette J Chen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Nicole Y Leung
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, United States of America
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Madampage CA, Rawlyk N, Crockford G, Van Donkersgoed J, Dorin C, Potter A. Single nucleotide polymorphisms in the bovine Histophilus somni genome; a comparison of new and old isolates. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2015; 79:190-200. [PMID: 26130851 PMCID: PMC4445511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 01/02/2015] [Indexed: 06/04/2023]
Abstract
Histophilus somni, a causative agent of the bovine respiratory disease complex, can also cause a variety of systemic disorders, including bronchopneumonia, myocarditis, pericarditis, arthritis, pleuritis, and infectious thrombotic meningoencephalitis. The purpose of this study was to determine if currently circulating strains differ from those of the 1980s by identifying genomic changes. Single nucleotide polymorphisms (SNPs) and insertion and deletion (INDEL) sites were examined by whole-genome sequencing in 12 samples, 6 old and 6 new. The 31 028 SNP/INDELs recorded were compared against the reference genome sequence of the pathogenic H. somni strain 2336. The distribution of about 75% of these SNPs within a specified gene differed between old and new isolates and did not follow any particular pattern. The other 25% clustered into 2 groups containing the same SNPs in various genes: group I included 5 old isolates and 1 new isolate; group II included 5 new isolates and 1 old isolate. For putative virulence genes there were more SNPs in group I compared with strain 2336, itself an older isolate, than in group II. Although only 25% of all the SNPs formed 2 clusters, the results suggest some genetic difference in various genes between old and new strains.
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Affiliation(s)
- Claudia Avis Madampage
- Address all correspondence to Dr. Claudia Avis Madampage; telephone: 306-966-1516; fax: 306-966-7478; e-mail:
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The Many Facets of Lipooligosaccharide as a Virulence Factor for Histophilus somni. Curr Top Microbiol Immunol 2015; 396:131-48. [PMID: 26814887 DOI: 10.1007/82_2015_5020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The lipooligosaccharide (LOS) of Histophilus somni is a multifaceted molecule that provides critical protection to the bacterium against host defenses, may act as an adhesin, and like similar molecules of gram-negative bacteria, is an endotoxin that signals through toll-like receptor 4 and NF-κB to cause inflammation. The lipid A component is responsible for the endotoxic and apoptotic activity of the LOS. The H. somni LOS lacks O-side chains typically characteristic of gram-negative bacteria that have lipopolysaccharide, but has a complex, microheterogeneous outer core. The LOS of disease isolates is capable of undergoing structural and antigenic phase variation of its outer core due to slip-strand mispairing of glycosyltransferase genes that contain repetitive sequences of DNA base pairs. Such variation enables the bacteria to evade bactericidal antibodies made to oligosaccharide antigens. In addition, the LOS can be decorated with phase-variable phosphorylcholine (ChoP), which binds to platelet-activating factor receptor on host cells, thereby aiding in colonization of the upper respiratory tract. However, ChoP is likely not expressed when the bacteria are in systemic sites because ChoP also binds to C-reactive protein, resulting in activation of host complement and promoting bactericidal activity. The structure of some LOS outer core chains is identical to oligosaccharides on host glycosphingolipids of red blood cells, other cells, and merconium (lacto-N-neotetraose, lacto-N-biose, N-acetyllactosamine, etc.). Furthermore, terminal galactose residues on LOS and elsewhere are decorated with sialic acid, which blocks antibody binding, activation of complement, phagocytosis, and intracellular killing. Therefore, antigenic mimicry of host antigens is an important defense mechanism provided by the oligosaccharide component of the LOS to avoid innate and adaptive host defense mechanisms. However, some strains of H. somni isolated from the bovine genital tract, particularly the normal bovine prepuce, are incapable of LOS phase variation, sialylation of the LOS, and expression of ChoP. At least 1 such strain has been shown to be avirulent, underscoring the importance of the LOS as a virulence factor, although this strain is deficient in other factors as well. The structure and arrangement of the inner core glycoses (heptose and 3-deoxy-D-manno-2-octulosnic acid) is remarkably similar to the inner core oligosaccharide on some strains of Neisseria spp., and mutants that contain a truncated LOS oligosaccharide are considerably more serum-sensitive than the parent strain. Therefore, the LOS is a critical component that enables H. somni to resist host defenses and cause disease.
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19
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Abstract
Histophilus somni was proposed in 2003 as a common name for bacteria that earlier had been called "Haemophilus somni", "Haemophilus agni", "Haemophilus somnifer", and "Histophilus ovis". The species is clearly separated from other species and genera within the family Pasteurellaceae. The species is phenotypically variable, but highly uniform regarding the 16S rDNA sequence. Whole-genome sequencing has revealed distinct genetic differences between a commensal and a pathogenic strain, particularly in regard to putative virulence factors. However, broad generalizations regarding the genetics of H. somni cannot be applied to the entire species until the genomes of additional strains are sequenced.
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Affiliation(s)
- Øystein Angen
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway.
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Natural competence in Histophilus somni strain 2336. Vet Microbiol 2014; 173:371-8. [PMID: 25218867 DOI: 10.1016/j.vetmic.2014.07.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 07/09/2014] [Accepted: 07/26/2014] [Indexed: 01/03/2023]
Abstract
Histophilus somni is an etiologic agent of shipping fever pneumonia, myocarditis, and other systemic diseases of bovines. Virulence factors that have been identified in H. somni include biofilm formation, lipooligosaccharide phase variation, immunoglobulin binding proteins, survival in phagocytic cells, and many others. However, to identify the genes responsible for virulence, an efficient mutagenesis system is needed. Mutagenesis of H. somni using allelic exchange is difficult, likely due to its tight restriction modification system. Mutagenesis by natural transformation in Haemophilus influenzae is well established and shows a strong bias for fragments containing specific uptake signal sequences (USS) within the genome. We hypothesized that natural transformation may also be possible in H. somni strain 2336 because its genome is over-represented with H. influenzae USS (5'-AAGTGCGGT-3') and contains most of the genes necessary for competence. H. somni strain 2336 was successfully transformed and mutated with genomic linear DNA from an H. somni mutant (738Δlob2a), which contains a kanamycin-resistance (Kan(R)) gene and the USS within lob2A. Although most of the competence genes found in H. influenzae were present in H. somni, comD and the 5' portion of comE were absent, which may account for the low transformation efficiency. The transformation efficiency of strain 2336 was greatest during mid-log growth phase and when cyclic adenosine monophosphate was added to the transformation medium. However, mutants were not isolated when strain 2336 was transformed with genomic DNA containing the same Kan(R) gene from H. somni luxS or uspE mutants, which lack the USS in these specific genes. Shuttle vector pNS3K was also naturally transformed into strain 2336, though at a lower efficiency. However, natural transformation with either H. somni linear DNA (2336Δlob2A) or pNS3K was unsuccessful with H. somni commensal strain 129Pt and several other disease isolates.
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Genomic features of a bumble bee symbiont reflect its host environment. Appl Environ Microbiol 2014; 80:3793-803. [PMID: 24747890 DOI: 10.1128/aem.00322-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Here, we report the genome of one gammaproteobacterial member of the gut microbiota, for which we propose the name "Candidatus Schmidhempelia bombi," that was inadvertently sequenced alongside the genome of its host, the bumble bee, Bombus impatiens. This symbiont is a member of the recently described bacterial order Orbales, which has been collected from the guts of diverse insect species; however, "Ca. Schmidhempelia" has been identified exclusively with bumble bees. Metabolic reconstruction reveals that "Ca. Schmidhempelia" lacks many genes for a functioning NADH dehydrogenase I, all genes for the high-oxygen cytochrome o, and most genes in the tricarboxylic acid (TCA) cycle. "Ca. Schmidhempelia" has retained NADH dehydrogenase II, the low-oxygen specific cytochrome bd, anaerobic nitrate respiration, mixed-acid fermentation pathways, and citrate fermentation, which may be important for survival in low-oxygen or anaerobic environments found in the bee hindgut. Additionally, a type 6 secretion system, a Flp pilus, and many antibiotic/multidrug transporters suggest complex interactions with its host and other gut commensals or pathogens. This genome has signatures of reduction (2.0 megabase pairs) and rearrangement, as previously observed for genomes of host-associated bacteria. A survey of wild and laboratory B. impatiens revealed that "Ca. Schmidhempelia" is present in 90% of individuals and, therefore, may provide benefits to its host.
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