scholarly journals An introduction to phylosymbiosis

2019 ◽  
Author(s):  
Shen Jean Lim ◽  
Seth R Bordenstein
Keyword(s):  
Host Species ◽  
Genetic Relationships ◽  
Relevant Literature ◽  
Positive Association ◽  
Evolutionary Modeling ◽  
Host Phylogeny ◽  
Host Genetic ◽  
Cross System ◽  
Transplant Experiments

Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as “microbial community relationships that recapitulate the phylogeny of their host”, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modeling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual, and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigations from a diversity of disciplines.

scholarly journals An introduction to phylosymbiosis

2019 ◽  
Author(s):  
Shen Jean Lim ◽  
Seth R Bordenstein
Keyword(s):  
Host Species ◽  
Genetic Relationships ◽  
Relevant Literature ◽  
Positive Association ◽  
Evolutionary Modeling ◽  
Host Phylogeny ◽  
Host Genetic ◽  
Cross System ◽  
Transplant Experiments

Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as “microbial community relationships that recapitulate the phylogeny of their host”, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modeling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual, and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigations from a diversity of disciplines.

scholarly journals An introduction to phylosymbiosis

2020 ◽  
Vol 287 (1922) ◽  
pp. 20192900 ◽  
Author(s):  
Shen Jean Lim ◽  
Seth R. Bordenstein
Keyword(s):  
Host Species ◽  
Bacterial Communities ◽  
Genetic Relationships ◽  
Relevant Literature ◽  
Positive Association ◽  
Host Phylogeny ◽  
Host Genetic ◽  
Cross System ◽  
Transplant Experiments

Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as ‘microbial community relationships that recapitulate the phylogeny of their host’, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host–microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host–microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modelling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigation from a diversity of disciplines.

scholarly journals An introduction to phylosymbiosis

2019 ◽  
Author(s):  
Shen Jean Lim ◽  
Seth R Bordenstein
Keyword(s):  
Conservation Biology ◽  
Evolutionary Biology ◽  
Genetic Relationships ◽  
Relevant Literature ◽  
Positive Association ◽  
Host Phylogeny ◽  
Host Genetic ◽  
Regular Patterns ◽  
Transplant Experiments

Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of an emerging trend in host-associated microbiomes. Defining phylosymbiosis as “microbial community relationships that recapitulate the phylogeny of their host”, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in the analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating the distinguishability of microbiomes between hosts, topological congruency between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent in gut and surface microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection underpinning phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host-microbiome mismatches. The pervasiveness of phylosymbiosis carries several important implications for analyses of host-microbiome interactions, evolutionary biology, personalized microbiology, and conservation biology. Important future steps will be to apply evolutionary modelling for an increasingly sophisticated understanding of phylosymbiosis and to unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual, and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigations from a diversity of disciplines, scholars, and students.

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 Molecular characterization of some selected persimmon genotypes and cultivars by srap and ssr markers

Genetika ◽  
2017 ◽  
Vol 49 (2) ◽  
pp. 693-704
Author(s):  
Hasan Pinar ◽  
Ercan Yildiz ◽  
Mustafa Kaplankiran ◽  
Celil Toplu ◽  
Mustafa Unlu ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Clonal Propagation ◽  
Genetic Relationships ◽  
The Other ◽  
Diospyros Kaki ◽  
Ssr Primers ◽  
Similarity Ratio ◽  
Polymorphic Bands ◽  
Dna Primers

In this study, SRAP and SSR markers were employed to determine genetic relationships among 42 persimmon genotypes (Diospyros kaki Thunb) obtained from Hatay province and 3 persimmon cultivars, 2 of which belong to Diospyros kaki Thunb and one belongs to Diospyros oleifera Cheng. Genetic relationships were determined by using a total of 29 molecular DNA primers (SRAP and SSR). Of these primers, 21 SRAP primer combinations produced a total of 107 bands and 77.6% of them were polymorphic; 8 SSR primers produced 26 polymorphic bands with an average polymorphism ratio of 84.6%. The SRAP and SSR markers produced 4.6 bands as average and the number of bands produced per marker was calculated as 3.6. The lowest similarity was observed between MK-113 (Diospyros oleifera Cheng) and the other genotypes all belongs to Diospyros kaki Thunb (with similarity ratios of 0.41-0.69 for SRAP primers, between 0.25-0.67 for SSR primers). The genotypes/cultivars belongs to Diospyros kaki had similarity ratio between 0.98-1.00 according to SRAP and SSR markers. This synonym or similarity could be results of clonal propagation rather than autogamy.

Morphology and description of infraciliary bands pattern in four Metadinium Awerinzew & Mutafowa, 1914 species (Ciliophora, Entodiniomorphida, Ophryoscolecidae) with taxonomic notes on the genus

Zootaxa ◽  
2018 ◽  
Vol 4500 (4) ◽  
pp. 574 ◽  
Author(s):  
FRANCIANE CEDROLA ◽  
MARIANA FONSECA ROSSI ◽  
ISABEL MARTINELE ◽  
MARTA D’AGOSTO ◽  
ROBERTO JÚNIO PEDROSO DIAS
Keyword(s):  
Host Species ◽  
Morphological Similarity ◽  
Type Pattern ◽  
Anterior Body ◽  
Contractile Vacuoles ◽  
Geographical Locations

The genus Metadinium includes ophryoscolecid ciliates, with two retractile ciliary zones in the anterior body portion, two broad skeletal plates, a lobed macronucleus and two contractile vacuoles. Species belonging to this genus were recorded in several geographical locations and in different host species. However, they were mostly described based on a single ciliatological technique, and until now, there is only one description of the infraciliary pattern in Metadinium ciliates (Metadinium medium). The present study performs the morphological and infraciliature characterization of four species belonging to Metadinium: M. esalqum, M. minorum, M. rotundatum and M. ypsilon; and presents taxonomic notes on the genus. The oral infraciliature in these four Metadinium species corresponds to the Diplodinium-type, pattern shared with genera Diplodinium, Diploplastron, Eudiplodinium, Eremoplastron and Polyplastron. A brief review conducted highlights the difficulty of delimiting Metadinium species due to the morphological similarity among them. 

scholarly journals Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis

2020 ◽  
Author(s):  
Qiulong Yan ◽  
Yu Wang ◽  
Xiuli Chen ◽  
Hao Jin ◽  
Guangyang Wang ◽  
...  
Keyword(s):  
Ethnic Origin ◽  
Chinese Adults ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Dna And Rna ◽  
Bacterial Microbiome ◽  
Chinese Cohort ◽  
Host Genetic

AbstractBackgroundTrillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remain unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, e.g. ethnic origin, on the gut virome is rarely investigated.Methods and ResultsHere, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing 24 healthy adults and 6 children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals’ gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were inherited from the that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between virus and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (p<0.001), and they both influenced the holistic bacterial composition and vice versa.ConclusionsThis study provides an overview of gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.

scholarly journals Biogeography and Independent Diversification in the Protist Symbiont Community of Heterotermes tenuis

2021 ◽  
Vol 9 ◽  
Author(s):  
Francesca De Martini ◽  
Nicole L. Coots ◽  
Daniel E. Jasso-Selles ◽  
Jordyn Shevat ◽  
Alison Ravenscraft ◽  
...  
Keyword(s):  
Regional Differences ◽  
Amplicon Sequencing ◽  
Genetic Distances ◽  
Species Level ◽  
Mantel Tests ◽  
Geographical Distances ◽  
Host Phylogeny ◽  
Single Cell Isolation ◽  
Host Genetic ◽  
Protist Species

The eukaryotic microbiome of “lower” termites is highly stable and host-specific. This is due to the mutually obligate nature of the symbiosis and the direct inheritance of protists by proctodeal trophallaxis. However, vertical transmission is occasionally imperfect, resulting in daughter colonies that lack one or more of the expected protist species. This phenomenon could conceivably lead to regional differences in protist community composition within a host species. Here, we have characterized the protist symbiont community of Heterotermes tenuis (Hagen) (Blattodea: Rhinotermitidae) from samples spanning South and Central America. Using light microscopy, single cell isolation, and amplicon sequencing, we report eight species-level protist phylotypes belonging to four genera in the phylum Parabasalia. The diversity and distribution of each phylotype’s 18S rRNA amplicon sequence variants (ASVs) mostly did not correlate with geographical or host genetic distances according to Mantel tests, consistent with the lack of correlation we observed between host genetic and geographical distances. However, the ASV distances of Holomastigotoides Ht3 were significantly correlated with geography while those of Holomastigotoides Ht1 were significantly correlated with host phylogeny. These results suggest mechanisms by which termite-associated protist species may diversify independently of each other and of their hosts, shedding light on the coevolutionary dynamics of this important symbiosis.

Characterization of Fasciola samples from different host species and geographical localities in Spain by sequences of internal transcribed spacers of rDNA

2007 ◽  
Vol 101 (5) ◽  
pp. 1245-1250 ◽  
Author(s):  
S. Alasaad ◽  
C. Q. Huang ◽  
Q. Y. Li ◽  
J. E. Granados ◽  
C. García-Romero ◽  
...  
Keyword(s):  
Host Species ◽  
Internal Transcribed Spacers

Care to Share?

2015 ◽  
pp. 222-244
Author(s):  
Paolo Santi ◽  
Carlo Ratti
Keyword(s):  
Urban Environment ◽  
Methodological Approach ◽  
Relevant Literature ◽  
Taxi Driver ◽  
Data Sets ◽  
Exciting Field ◽  
Ride Sharing ◽  
Gps Devices ◽  
The Impact

GPS technology has been extensively used to optimize operation of taxi systems since the first appearance of commercial GPS devices. Owing to this, data sets generated by taxi fleets are amongst the first and most representative examples of massive GPS data that have been systematically collected. The analysis of these data sets has recently generated a rich literature aimed at, among other things, identifying optimal taxi driver strategies, predicting taxi demand or location of vacant taxis, etc. This chapter focuses on what is a new, exciting field of investigation of GPS taxi data analysis, namely, evaluating the impact of a shared taxi system on the urban environment. After introducing the notion of (taxi) ride sharing, the chapter presents the relevant literature, describing in greater details a methodological approach called “shareability network” that allows formal characterization of taxi sharing opportunities in an urban environment.

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