scholarly journals Genomes of Gut Bacteria from Nasonia Wasps Shed Light on Phylosymbiosis and Microbe-Assisted Hybrid Breakdown

mSystems ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Karissa L. Cross ◽  
Brittany A. Leigh ◽  
E. Anne Hatmaker ◽  
Aram Mikaelyan ◽  
Asia K. Miller ◽  
...  
Keyword(s):  
Proteus Mirabilis ◽  
Host Species ◽  
Parental Species ◽  
Parasitoid Wasp ◽  
Gut Bacteria ◽  
Hybrid Breakdown ◽  
Bacterial Genomes ◽  
Providencia Rettgeri ◽  
Content Type ◽  
Host Phylogeny

ABSTRACT Phylosymbiosis is a cross-system trend whereby microbial community relationships recapitulate the host phylogeny. In Nasonia parasitoid wasps, phylosymbiosis occurs throughout development, is distinguishable between sexes, and benefits host development and survival. Moreover, the microbiome shifts in hybrids as a rare Proteus bacterium in the microbiome becomes dominant. The larval hybrids then catastrophically succumb to bacterium-assisted lethality and reproductive isolation between the species. Two important questions for understanding phylosymbiosis and bacterium-assisted lethality in hybrids are (i) do the Nasonia bacterial genomes differ from other animal isolates and (ii) are the hybrid bacterial genomes the same as those in the parental species? Here, we report the cultivation, whole-genome sequencing, and comparative analyses of the most abundant gut bacteria in Nasonia larvae, Providencia rettgeri and Proteus mirabilis. Characterization of new isolates shows Proteus mirabilis forms a more robust biofilm than Providencia rettgeri and that, when grown in coculture, Proteus mirabilis significantly outcompetes Providencia rettgeri. Providencia rettgeri genomes from Nasonia are similar to each other and more divergent from pathogenic, human associates. Proteus mirabilis from Nasonia vitripennis, Nasonia giraulti, and their hybrid offspring are nearly identical and relatively distinct from human isolates. These results indicate that members of the larval gut microbiome within Nasonia are most similar to each other, and the strain of the dominant Proteus mirabilis in hybrids is resident in parental species. Holobiont interactions between shared, resident members of the wasp microbiome and the host underpin phylosymbiosis and hybrid breakdown. IMPORTANCE Animal and plant hosts often establish intimate relationships with their microbiomes. In varied environments, closely related host species share more similar microbiomes, a pattern termed phylosymbiosis. When phylosymbiosis is functionally significant and beneficial, microbial transplants between host species and host hybridization can have detrimental consequences on host biology. In the Nasonia parasitoid wasp genus, which contains a phylosymbiotic gut community, both effects occur and provide evidence for selective pressures on the holobiont. Here, we show that bacterial genomes in Nasonia differ from other environments and harbor genes with unique functions that may regulate phylosymbiotic relationships. Furthermore, the bacteria in hybrids are identical to those in parental species, thus supporting a hologenomic tenet that the same members of the microbiome and the host genome impact phylosymbiosis, hybrid breakdown, and speciation.

scholarly journals Genomes of gut bacteria from Nasonia wasps shed light on phylosymbiosis and microbe-assisted hybrid breakdown

2021 ◽  
Author(s):  
Karissa L. Cross ◽  
Brittany A. Leigh ◽  
E. Anne Hatmaker ◽  
Aram Mikaelyan ◽  
Asia K. Miller ◽  
...  
Keyword(s):  
Proteus Mirabilis ◽  
Host Species ◽  
Parental Species ◽  
Parasitoid Wasp ◽  
Gut Bacteria ◽  
Hybrid Breakdown ◽  
Bacterial Genomes ◽  
Providencia Rettgeri ◽  
Host Phylogeny

ABSTRACTPhylosymbiosis is a cross-system trend whereby microbial community relationships recapitulate the host phylogeny. In Nasonia parasitoid wasps, phylosymbiosis occurs throughout development, is distinguishable between sexes, and benefits host development and survival. Moreover, the microbiome shifts in hybrids as a rare Proteus bacteria in the microbiome becomes dominant. The larval hybrids then catastrophically succumb to bacterial-assisted lethality and reproductive isolation between the species. Two important questions for understanding phylosymbiosis and bacterial-assisted lethality in hybrids are: (i) Do the Nasonia bacterial genomes differ from other animal isolates and (ii) Are the hybrid bacterial genomes the same as those in the parental species? Here we report the cultivation, whole genome sequencing, and comparative analyses of the most abundant gut bacteria in Nasonia larvae, Providencia rettgeri and Proteus mirabilis. Characterization of new isolates shows Proteus mirabilis forms a more robust biofilm than Providencia rettgeri and when grown in co-culture, Proteus mirabilis significantly outcompetes Providencia rettgeri. Providencia rettgeri genomes from Nasonia are similar to each other and more divergent to pathogenic, human-associates strains. Proteus mirabilis from N. vitripennis, N. giraulti, and their hybrid offspring are nearly identical and relatively distinct from human isolates. These results indicate that members of the larval gut microbiome within Nasonia are most similar to each other, and the strain of the dominant Proteus mirabilis in hybrids is resident in parental species. Holobiont interactions between shared, resident members of the wasp microbiome and the host underpin phylosymbiosis and hybrid breakdown.IMPORTANCEAnimal and plant hosts often establish intimate relationships with their microbiomes. In varied environments, closely-related host species share more similar microbiomes, a pattern termed phylosymbiosis. When phylosymbiosis is functionally significant and beneficial, microbial transplants between host species or host hybridization can have detrimental consequences on host biology. In the Nasonia parasitoid wasp genus that contains a phylosymbiotic gut community, both effects occur and provide evidence for selective pressures on the holobiont. Here, we show that bacterial genomes in Nasonia differ from other environments and harbor genes with unique functions that may regulate phylosymbiotic relationships. Furthermore, the bacteria in hybrids are identical to parental species, thus supporting a hologenomic tenet that the same members of the microbiome and the host genome impact phylosymbiosis, hybrid breakdown, and speciation.

scholarly journals Captivity and the co-diversification of great ape microbiomes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alex H. Nishida ◽  
Howard Ochman
Keyword(s):  
Host Species ◽  
Great Apes ◽  
Host Shift ◽  
Gut Bacteria ◽  
Evolutionary Relationships ◽  
Great Ape ◽  
Bacterial Strains ◽  
Host Phylogeny ◽  
Geographic Separation ◽  
Insight Into

AbstractWild great apes harbor clades of gut bacteria that are restricted to each host species. Previous research shows the evolutionary relationships among several host-restricted clades mirror those of great-ape species. However, processes such as geographic separation, host-shift speciation, and host-filtering based on diet or gut physiology can generate host-restricted bacterial clades and mimic patterns of co-diversification across host species. To gain insight into the distribution of host-restricted taxa, we examine captive great apes living under conditions where sharing of bacterial strains is readily possible. Here, we show that increased sampling of wild and captive apes identifies additional host-restricted lineages whose relationships are not concordant with the host phylogeny. Moreover, the gut microbiomes of captive apes converge through the displacement of strains that are restricted to their wild conspecifics by human-restricted strains. We demonstrate that host-restricted and co-diversifying bacterial strains in wild apes lack persistence and fidelity in captive environments.

scholarly journals Complete Sequences of Two Plasmids Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain

2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Fabrício S. Campos ◽  
Fernando B. Cerqueira ◽  
Gil R. Santos ◽  
Eliseu J. G. Pereira ◽  
Roberto F. T. Corrêia ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Crucial Role ◽  
Bacterial Genomes ◽  
Content Type ◽  
Complete Sequences

Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. In this work, we sequenced two plasmids found in a Brazilian Bacillus thuringiensis serovar israelensis strain which showed 100% nucleotide identities with Bacillus thuringiensis serovar kurstaki plasmids.

scholarly journals New Aspects of RpoE in Uropathogenic Proteus mirabilis

2014 ◽  
Vol 83 (3) ◽  
pp. 966-977 ◽  
Author(s):  
Ming-Che Liu ◽  
Kuan-Ting Kuo ◽  
Hsiung-Fei Chien ◽  
Yi-Lin Tsai ◽  
Shwu-Jen Liaw
Keyword(s):  
Urinary Tract ◽  
Virulence Factors ◽  
Stress Responses ◽  
Proteus Mirabilis ◽  
Immune Cell ◽  
Polymyxin B ◽  
Urothelial Cells ◽  
Cationic Antimicrobial Peptide ◽  
Content Type ◽  
Tract Infections

Proteus mirabilisis a common human pathogen causing recurrent or persistent urinary tract infections (UTIs). The underlying mechanisms forP. mirabilisto establish UTIs are not fully elucidated. In this study, we showed that loss of the sigma factor E (RpoE), mediating extracytoplasmic stress responses, decreased fimbria expression, survival in macrophages, cell invasion, and colonization in mice but increased the interleukin-8 (IL-8) expression of urothelial cells and swarming motility. This is the first study to demonstrate that RpoE modulated expression of MR/P fimbriae by regulatingmrpI, a gene encoding a recombinase controlling the orientation of MR/P fimbria promoter. By real-time reverse transcription-PCR, we found that the IL-8 mRNA amount of urothelial cells was induced significantly by lipopolysaccharides extracted fromrpoEmutant but not from the wild type. These RpoE-associated virulence factors should be coordinately expressed to enhance the fitness ofP. mirabilisin the host, including the avoidance of immune attacks. Accordingly,rpoEmutant-infected mice displayed more immune cell infiltration in bladders and kidneys during early stages of infection, and therpoEmutant had a dramatically impaired ability of colonization. Moreover, it is noteworthy that urea (the major component in urine) and polymyxin B (a cationic antimicrobial peptide) can induce expression ofrpoEby the reporter assay, suggesting that RpoE might be activated in the urinary tract. Altogether, our results indicate that RpoE is important in sensing environmental cues of the urinary tract and subsequently triggering the expression of virulence factors, which are associated with the fitness ofP. mirabilis, to build up a UTI.

scholarly journals Microfluidic PCR Combined with Pyrosequencing for Identification of Allelic Variants with Phenotypic Associations among Targeted Salmonella Genes

2012 ◽  
Vol 78 (20) ◽  
pp. 7480-7482 ◽  
Author(s):  
Min Yue ◽  
Robert Schmieder ◽  
Robert A. Edwards ◽  
Shelley C. Rankin ◽  
Dieter M. Schifferli
Keyword(s):  
Genetic Variation ◽  
Antimicrobial Resistance ◽  
Host Species ◽  
Massive Parallel Sequencing ◽  
Allelic Variants ◽  
Parallel Sequencing ◽  
Content Type ◽  
Potential Applications ◽  
Fimbrial Adhesins ◽  
Diagnostic Microbiology

ABSTRACTA novel targeted massive parallel sequencing approach identified genetic variation in eight known or predicted fimbrial adhesins for 46Salmonellastrains. The results highlight associations between specific adhesin alleles, host species, and antimicrobial resistance. The differentiation of allelic variants has potential applications for diagnostic microbiology and epidemiological investigations.

scholarly journals Estudo etiológico da infecção do trato urinário em cães

1995 ◽  
Vol 32 (1) ◽  
pp. 31 ◽  
Author(s):  
Marcia Mery Kogika ◽  
Vera Assunta Batistini Fortunato ◽  
Elsa Masae Mamizuka ◽  
Mitika Kuribayashi Hagiwara ◽  
Maria de Fatima Borges Pavan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Proteus Mirabilis ◽  
Enterobacter Cloacae ◽  
Citrobacter Freundii ◽  
Providencia Rettgeri ◽  
Cocker Spaniel

Foram estudados 51 casos de infecção urinária, em cães, considerando-se diversos fatores, tais como: agente etiológico, localização da infecção, fatores predisponentes, sexo, idade e raça. O diagnóstico da infecção do trato urinário (ITU) foi baseado no exame bacteriológico, sendo considerado positivo quando a amostra de urina, colhida com auxílio de cateter, apresentava acima de 105 bactérias/ml. Dos animais examinados, quatro cães apresentaram infecção mista, totalizando 55 microorganismos isolados. Escherichia coli foi a mais freqüentemente isolada (35,3%), seguida de Staphylococcus sp (23,5%), Proteus mirabilis (15,7%), Streptococcus sp (13,7%), Klebsiella sp (9,8%), Pseudomonas aeruginosa (3,9%), Enterobacter cloacae (2.0%), Citrobacter freundii (2.0%) e Providencia rettgeri (2,0%). Quanto à sensibilidade dos germes isolados frente a diversos agentes antimicrobianos, a norfloxacina e a gentamicina mostraram-se eficazes no tratamento de microorganismos Gram-negativos, enquanto a cefalotina e a nitrofurantoina foram mais eficazes contra bactérias Gram-positivas. Os animais que apresentaram maior frequência de ITU pertenciam às raças Cocker Spaniel e Pastor Alemão, envolvendo mais machos do que fêmeas com predominância de pielonefrites. Embora as infecções urinárias tivessem sido observadas em todas as idades, houve um predomínio nos cães de média idade. Observou-se ainda que a urolitíase foi um fator pré-disponente ou adjacente de ITU, envolvendo germes como Staphylococcus sp. e Proteus mirabilis naqueles casos com pH urinário alcalino.

scholarly journals Analysis of the diversity of the glycoside hydrolase family 130 in mammal gut microbiomes reveals a novel mannoside-phosphorylase function

2020 ◽  
Vol 6 (10) ◽  
Author(s):  
Ao Li ◽  
Elisabeth Laville ◽  
Laurence Tarquis ◽  
Vincent Lombard ◽  
David Ropartz ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Sequence Similarity ◽  
Gut Bacteria ◽  
Glycoside Hydrolase Family ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Content Type ◽  
Multiple Sequence Alignments ◽  
Hydrolase Family

Mannoside phosphorylases are involved in the intracellular metabolization of mannooligosaccharides, and are also useful enzymes for the in vitro synthesis of oligosaccharides. They are found in glycoside hydrolase family GH130. Here we report on an analysis of 6308 GH130 sequences, including 4714 from the human, bovine, porcine and murine microbiomes. Using sequence similarity networks, we divided the diversity of sequences into 15 mostly isofunctional meta-nodes; of these, 9 contained no experimentally characterized member. By examining the multiple sequence alignments in each meta-node, we predicted the determinants of the phosphorolytic mechanism and linkage specificity. We thus hypothesized that eight uncharacterized meta-nodes would be phosphorylases. These sequences are characterized by the absence of signal peptides and of the catalytic base. Those sequences with the conserved E/K, E/R and Y/R pairs of residues involved in substrate binding would target β-1,2-, β-1,3- and β-1,4-linked mannosyl residues, respectively. These predictions were tested by characterizing members of three of the uncharacterized meta-nodes from gut bacteria. We discovered the first known β-1,4-mannosyl-glucuronic acid phosphorylase, which targets a motif of the Shigella lipopolysaccharide O-antigen. This work uncovers a reliable strategy for the discovery of novel mannoside-phosphorylases, reveals possible interactions between gut bacteria, and identifies a biotechnological tool for the synthesis of antigenic oligosaccharides.

scholarly journals Roles of Host Species, Geographic Separation, and Isolation in the Seroprevalence of Jamestown Canyon and Snowshoe Hare Viruses in Newfoundland

2012 ◽  
Vol 78 (18) ◽  
pp. 6734-6740 ◽  
Author(s):  
Gregory Goff ◽  
Hugh Whitney ◽  
Michael A. Drebot
Keyword(s):  
Host Species ◽  
Neutralization Assay ◽  
Snowshoe Hare ◽  
Large Mammals ◽  
Content Type ◽  
Neuroinvasive Disease ◽  
Snowshoe Hares ◽  
Jamestown Canyon Virus ◽  
Geographic Separation ◽  
California Serogroup

ABSTRACTCalifornia serogroup viruses, including Jamestown Canyon virus (JCV) and snowshoe hare virus (SSHV), are mosquito-borne members of theBunyaviridaefamily and are endemic across North America. These arboviruses are potential pathogens which occasionally cause neuroinvasive disease in humans and livestock. A neutralization assay was used to document JCV and SSHV seroprevalence using blood collected from a variety of domestic and wildlife host species. These species were sampled in an island setting, Newfoundland, which contains diverse ecoregions, ecological landscapes, and habitats. Seroprevalence rates for each virus differed significantly among host species and within certain species across different geographic areas. JCV was significantly associated with large mammals, and SSHV was significantly associated with snowshoe hares. Seroprevalence rates in the 5 species of animals tested for prior exposure to JCV ranged from 0% in snowshoe hares to 64% in horses. Seroprevalence rates for SSHV ranged from less than 1% in bovines to 55% in all snowshoe hares. The seroprevalence of SSHV differed significantly (P< 0.05) among hares occupying the discrete habitats of watersheds separated by 14 to 35 km. Cattle on farms in boreal forest landscapes displayed significantly higher JCV seroprevalence (P< 0.001) than those on farms located in seacoast landscapes. Lifelong geographic isolation of cattle to insular Newfoundland was associated with significantly lower JCV seroprevalence (P< 0.01) than that for cattle which had lived off-island.

scholarly journals Cotesia congregata Bracovirus Circles Encoding PTP and Ankyrin Genes Integrate into the DNA of Parasitized Manduca sexta Hemocytes

2018 ◽  
Vol 92 (15) ◽  
Author(s):  
Germain Chevignon ◽  
Georges Periquet ◽  
Gabor Gyapay ◽  
Nathalie Vega-Czarny ◽  
Karine Musset ◽  
...  
Keyword(s):  
Manduca Sexta ◽  
High Throughput Sequencing ◽  
Particle Production ◽  
Parasitoid Wasp ◽  
Gene Families ◽  
Parasitoid Wasps ◽  
Content Type ◽  
Virulence Proteins ◽  
Cotesia Congregata ◽  
Dividing Cells

ABSTRACT Polydnaviruses (PDVs) are essential for the parasitism success of tens of thousands of species of parasitoid wasps. PDVs are present in wasp genomes as proviruses, which serve as the template for the production of double-stranded circular viral DNA carrying virulence genes that are injected into lepidopteran hosts. PDV circles do not contain genes coding for particle production, thereby impeding viral replication in caterpillar hosts during parasitism. Here, we investigated the fate of PDV circles of Cotesia congregata bracovirus during parasitism of the tobacco hornworm, Manduca sexta, by the wasp Cotesia congregata. Sequences sharing similarities with host integration motifs (HIMs) of Microplitis demolitor bracovirus (MdBV) circles involved in integration into DNA could be identified in 12 CcBV circles, which encode PTP and VANK gene families involved in host immune disruption. A PCR approach performed on a subset of these circles indicated that they persisted in parasitized M. sexta hemocytes as linear forms, possibly integrated in host DNA. Furthermore, by using a primer extension capture method based on these HIMs and high-throughput sequencing, we could show that 8 out of 9 circles tested were integrated in M. sexta hemocyte genomic DNA and that integration had occurred specifically using the HIM, indicating that an HIM-mediated specific mechanism was involved in their integration. Investigation of BV circle insertion sites at the genome scale revealed that certain genomic regions appeared to be enriched in BV insertions, but no specific M. sexta target site could be identified. IMPORTANCE The identification of a specific and efficient integration mechanism shared by several bracovirus species opens the question of its role in braconid parasitoid wasp parasitism success. Indeed, results obtained here show massive integration of bracovirus DNA in somatic immune cells at each parasitism event of a caterpillar host. Given that bracoviruses do not replicate in infected cells, integration of viral sequences in host DNA might allow the production of PTP and VANK virulence proteins within newly dividing cells of caterpillar hosts that continue to develop during parasitism. Furthermore, this integration process could serve as a basis to understand how PDVs mediate the recently identified gene flux between parasitoid wasps and Lepidoptera and the frequency of these horizontal transfer events in nature.

scholarly journals Modulating Pathogenesis with Mobile-CRISPRi

2019 ◽  
Vol 201 (22) ◽  
Author(s):  
Jiuxin Qu ◽  
Neha K. Prasad ◽  
Michelle A. Yu ◽  
Shuyan Chen ◽  
Amy Lyden ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Effector Proteins ◽  
Infection Model ◽  
Secretion Systems ◽  
Bacterial Genomes ◽  
Gene Encoding ◽  
Content Type ◽  
Animal Infection

ABSTRACT Conditionally essential (CE) genes are required by pathogenic bacteria to establish and maintain infections. CE genes encode virulence factors, such as secretion systems and effector proteins, as well as biosynthetic enzymes that produce metabolites not found in the host environment. Due to their outsized importance in pathogenesis, CE gene products are attractive targets for the next generation of antimicrobials. However, the precise manipulation of CE gene expression in the context of infection is technically challenging, limiting our ability to understand the roles of CE genes in pathogenesis and accordingly design effective inhibitors. We previously developed a suite of CRISPR interference-based gene knockdown tools that are transferred by conjugation and stably integrate into bacterial genomes that we call Mobile-CRISPRi. Here, we show the efficacy of Mobile-CRISPRi in controlling CE gene expression in an animal infection model. We optimize Mobile-CRISPRi in Pseudomonas aeruginosa for use in a murine model of pneumonia by tuning the expression of CRISPRi components to avoid nonspecific toxicity. As a proof of principle, we demonstrate that knock down of a CE gene encoding the type III secretion system (T3SS) activator ExsA blocks effector protein secretion in culture and attenuates virulence in mice. We anticipate that Mobile-CRISPRi will be a valuable tool to probe the function of CE genes across many bacterial species and pathogenesis models. IMPORTANCE Antibiotic resistance is a growing threat to global health. To optimize the use of our existing antibiotics and identify new targets for future inhibitors, understanding the fundamental drivers of bacterial growth in the context of the host immune response is paramount. Historically, these genetic drivers have been difficult to manipulate precisely, as they are requisite for pathogen survival. Here, we provide the first application of Mobile-CRISPRi to study conditionally essential virulence genes in mouse models of lung infection through partial gene perturbation. We envision the use of Mobile-CRISPRi in future pathogenesis models and antibiotic target discovery efforts.

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