Structure of an ant-myrmecophile-microbe community

Superorganismal ant colonies play host to a menagerie of symbiotic arthropods, termed myrmecophiles, which exhibit varying degrees of social integration into colony life. Such systems permit examination of how animal community interactions influence microbial assemblages. Here, we present an ecologically and phylogenetically comprehensive characterization of an ant-myrmecophile-microbe community in Southern California. Using 16S rRNA profiling, we find that microbiotas of the velvety tree ant (Liometopum occidentale) and its cohort of myrmecophiles are distinguished by species-specific characteristics but nevertheless bear signatures of their behavioral interactions. We found that the host ant microbiome was diverse at all taxonomic levels; that of a myrmecophilous cricket was moderately diverse, while microbiotas of three myrmecophilous rove beetles (Staphylinidae), which have convergently evolved symbiosis with Liometopum, were dominated by intracellular endosymbionts. Yet, despite these compositional differences, similarities between ant and myrmecophile microbiotas correlated with the nature and intimacy of their behavioral relationships. Physical interactions such as grooming and trophallaxis likely facilitate cross-species extracellular microbial sharing. Further, phylogenetic comparisons of microbiotas from myrmecophile rove beetles and outgroups revealed a lack of co-cladogenesis of beetles and intracellular endosymbionts, and limited evidence for convergence among the myrmecophiles' intracellular microbiotas. Comparative genomic analyses of the dominant Rickettsia endosymbiont of the most highly socially integrated myrmecophile imply possible functions unrelated to nutrient-provisioning in the host beetle's specialized lifestyle. Our findings indicate that myrmecophile microbiotas evolve largely independently of the constraints of deep evolutionary history, and that the transition to life inside colonies, including social interactions with hosts, plays a significant role in structuring bacterial assemblages of these symbiotic insects.

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An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi

Genetics ◽

10.1093/genetics/iyab066 ◽

2021 ◽

Author(s):

Matthew E Mead ◽

Jacob L Steenwyk ◽

Lilian P Silva ◽

Patrícia A de Castro ◽

Nauman Saeed ◽

...

Keyword(s):

Human Disease ◽

Evolutionary Rate ◽

Fungal Disease ◽

Comparative Genomic ◽

Genetic Elements ◽

Genomic Approach ◽

Evolutionary Genomic ◽

Repeated Evolution ◽

Species Specific ◽

Encoding Genes

Abstract Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus Aspergillus. Roughly 70% of infections are caused by Aspergillus fumigatus, with the rest stemming from approximately a dozen other Aspergillus species. Several of these pathogens are closely related to A. fumigatus and belong in the same taxonomic section, section Fumigati. Pathogenic species are frequently most closely related to non-pathogenic ones, suggesting Aspergillus pathogenicity evolved multiple times independently. To understand the repeated evolution of Aspergillus pathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in section Fumigati, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and non-pathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified over 1,700 genes whose evolutionary rate differed between pathogens and non-pathogens and dozens of genes whose rates differed between specific pathogens and the rest of the taxa. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and non-pathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity in Aspergillus involved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.

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Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content

BMC Genomics ◽

10.1186/1471-2164-10-358 ◽

2009 ◽

Vol 10 (1) ◽

pp. 358 ◽

Cited By ~ 52

Author(s):

Fumito Maruyama ◽

Mitsuhiko Kobata ◽

Ken Kurokawa ◽

Keishin Nishida ◽

Atsuo Sakurai ◽

...

Keyword(s):

Streptococcus Mutans ◽

Comparative Genomic ◽

Specific Content ◽

Genomic Analyses ◽

Species Specific

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The “good, the bad and the double-sword” effects of exposure to MPs and their organic additives on N2-fixing bacteria

10.1101/2020.07.21.210740 ◽

2020 ◽

Author(s):

Víctor Fernández-Juárez ◽

Xabier López-Alforja ◽

Aida Frank-Comas ◽

Pedro Echeveste ◽

Antoni Bennasar-Figueras ◽

...

Keyword(s):

Posidonia Oceanica ◽

Dioctyl Phthalate ◽

Benthic Organisms ◽

Protein Overexpression ◽

Organic Additives ◽

Physical Interactions ◽

High Concentrations ◽

Species Specific ◽

Micro Organisms ◽

First Time

AbstractThe accumulation of microplastics (MPs) pollution at depths suggests the susceptibility of benthic organisms (e.g. seagrasses and their associated macro- and micro-organisms) to the effects of these pollutants. Little is known about the direct effects of MPs and their organic additives on marine bacteria, e.g. in one of the most ecologically significant groups, the diazotrophs or N2-fixing bacteria. To fill this gap of knowledge, we exposed marine diazotrophs found in association with the endemic Mediterranean seagrass Posidonia oceanica to pure MPs which differ in physical properties (e.g. density, hydrophobicity and/or size), namely, polyethylene (PE), polypropylene (PP), polyvinyl chloride (PVC) and polystyrene (PS) and to their most abundant associated organic additives (e.g. fluoranthene, 1,2,5,6,9,10-hexabromocyclododecane [HBCD] and dioctyl-phthalate [DEHP]). Growth, protein overexpression, direct physical interactions between MPs and bacteria, phosphorus (P) acquisition mechanisms and N2-fixation rates were evaluated. Our results show species-specific responses of the autotrophic and heterotrophic N2-fixing bacteria tested and the responses were dependent on the type and concentration of MPs and additives. N2-fixing cyanobacteria were positively affected by environmental and high concentrations of MPs (e.g. PVC), as opposed to heterotrophic strains, that were only positively affected with high concentrations of ∼120 µm-size MPs (detecting the overexpression of proteins related to plastic degradation and C-transport), and negatively affected by 1 µm-size PS beads. Generally, the organic additives (e.g. fluoranthene) had a deleterious effect in both autotrophic and heterotrophic N2-fixing bacteria and the magnitude of the effect is suggested to be dependent on bacterial size. We did not find evidences that specific N2-fixation rates were significantly affected by exposure to MPs, albeit changes in bacterial abundance can affect the bulk N2-fixation rates. In summary, we reported for the first time, the beneficial (the “good”), deleterious (the “bad”) and/or both (the “double-sword”) effects of exposure to MPs and their organic additives on diazotrophs found in association with seagrasses.

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The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis

Nature Communications ◽

10.1038/s41467-019-12607-6 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 10

Author(s):

Lisong Hu ◽

Zhongping Xu ◽

Maojun Wang ◽

Rui Fan ◽

Daojun Yuan ◽

...

Keyword(s):

Reference Genome ◽

Gene Families ◽

Black Pepper ◽

Piper Nigrum ◽

Comparative Genomic ◽

Specific Gene ◽

Phylogenomic Analysis ◽

Genomic Analyses ◽

Species Specific ◽

Insight Into

Abstract Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis.

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Recovery and resiliency of skin microbial communities on the southern leopard frog (Lithobates sphenocephalus) following two biotic disturbances

Animal Microbiome ◽

10.1186/s42523-020-00053-5 ◽

2020 ◽

Vol 2 (1) ◽

Author(s):

Denita M. Weeks ◽

Matthew J. Parris ◽

Shawn P. Brown

Keyword(s):

Microbial Communities ◽

Fungal Pathogen ◽

Bacterial Species ◽

Leopard Frog ◽

Multiple Time ◽

Population Declines ◽

Community Interactions ◽

Amphibian Species ◽

Functional Relationships ◽

Species Specific

Abstract Background Microorganisms have intimate functional relationships with invertebrate and vertebrate taxa, with the potential to drastically impact health outcomes. Perturbations that affect microbial communities residing on animals can lead to dysbiosis, a change in the functional relationship, often associated with disease. Batrachochytrium dendrobatidis (Bd), a fungal pathogen of amphibians, has been responsible for catastrophic amphibian population declines around the globe. Amphibians harbor a diverse cutaneous microbiome, including some members which are known to be antagonistic to Bd (anti-Bd). Anti-Bd microorganisms facilitate the ability of some frog populations to persist in the presence of Bd, where other populations that lack anti-Bd microorganisms have declined. Research suggests disease-antagonistic properties of the microbiome may be a function of microbial community interactions, rather than individual bacterial species. Conservation efforts have identified amphibian-associated bacteria that exhibit anti-fungal properties for use as ‘probiotics’ on susceptible amphibian populations. Probiotic application, usually with a single bacterial species, may benefit from a greater understanding of amphibian species-specific microbiome responses to disturbances (e.g. dysbiosis vs. recovery). We assessed microbiome responses to two microbial disturbance events over multiple time points. Results Exposing Lithobates sphenocephalus (southern leopard frog) adults to the biopesticidal bacteria Bacillus thuringiensis, followed by exposure to the fungal pathogen Bd, did not have long term impacts on the microbiome. After initial shifts, microbial communities recovered and returned to a state that resembled pre-disturbance. Conclusions Our results indicate microbial communities on L. sphenocephalus are robust and resistant to permanent shifts from some disturbances. This resiliency of microbial communities may explain why L. sphenocephalus is not experiencing the population declines from Bd that impacts many other species. Conservation efforts may benefit from studies outlining amphibian species-specific microbiome responses to disturbances (e.g. dysbiosis vs. recovery). If microbial communities on a threatened amphibian species are unlikely to recover following a disturbance, additional measures may be implemented to ameliorate the impacts of physical and chemical stressors on host-associated microbial communities.

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Genome assembly of the tayra (Eira barbara, Mustelidae) and comparative genomic analysis reveal adaptive genetic variation in the subfamily Guloninae

10.1101/2021.09.27.461651 ◽

2021 ◽

Author(s):

Lorena Derežanin ◽

Asta Blažytė ◽

Pavel Dobrynin ◽

David A. Duchêne ◽

José H. Grau ◽

...

Keyword(s):

Body Condition ◽

De Novo ◽

Species Traits ◽

Ecological Niches ◽

Comparative Genomic ◽

Phenotypic Traits ◽

Adaptive Genetic Variation ◽

Eira Barbara ◽

Species Specific ◽

Candidate Loci

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes, as well as searching for species-specific structural variants (SVs). Among candidate loci that appear to be associated with phenotypic traits, we observed many genes related to diet, body condition and reproduction. For the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observe species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many specific changes in genes associated with diet and body condition. Despite restricting some of our analyses to single-copy orthologs present in all three study species, we observed many candidate loci that may be linked to species traits related to environment-specific challenges in their respective habitats.

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Genomic sequencing of Phyllosticta citriasiana provide insight into its conservation and diversification with closely related Phyllosticta species associated with citrus

10.1101/740852 ◽

2019 ◽

Author(s):

Mingshuang Wang ◽

Bei Liu ◽

Ruoxin Ruan ◽

Yibing Zeng ◽

Jinshui Luo ◽

...

Keyword(s):

Tan Spot ◽

Secreted Proteins ◽

Comparative Genomic ◽

Orphan Genes ◽

Core Set ◽

Genomic Analyses ◽

Genetic Mechanisms ◽

Or Gene ◽

Species Specific ◽

Insight Into

AbstractPhyllosticta citriasiana is the causal agent of the pomelo tan spot. Here, we presented the ~34Mb genome of P. citriasiana. The genome is organized in 92 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with other two Phyllosticta species (P. citricarpa and P. capitalensis) associated with citrus was conducted to understand their evolutionary conservation and diversification. Pairwise genome alignments revealed that these species are highly syntenic. All species encode similar numbers of CAZymes and secreted proteins. However, the molecular functions of the secretome showed that each species contains some enzymes with distinct activities. Three Phyllosticta species shared a core set of 7261 protein families. P. capitalensis had the largest set of orphan genes (2040), in complete contrast to that of P. citriasiana (371) and P. citricarpa (262). Most of the orphan genes were functionally unknown, but they contain a certain number of species-specific secreted proteins. A total of 23 secondary metabolites (SM) biosynthesis clusters were identified in the three Phyllosticta species, 21 of them are highly conserved among these species while the remaining 2 showed whole cluster gain and loss polymorphisms or gene content polymorphisms. Taken together, our study reveals insights into the genetic mechanisms of host adaptation of Phyllosticta species associated with citrus and paves the way to identify effectors that function in infection of citrus plants.

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Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

10.21203/rs.2.20588/v4 ◽

2020 ◽

Author(s):

Eiseul Kim ◽

Seung-Min Yang ◽

Bora Lim ◽

Si Hong Park ◽

Bryna Rackerby ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Genomic Analysis ◽

23S Rrna ◽

Lactobacillus Species ◽

Comparative Genomic ◽

Rrna Gene ◽

Gene Sequences ◽

23S Rrna Gene ◽

Species Specific

Abstract Background Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the simultaneous identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods. Results To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label. Conclusions The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus , and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

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An in silico comparative genomic report on transcription factors in three Arabidopsis species

Ciencia y Tecnología ◽

10.18779/cyt.v11i1.185 ◽

2018 ◽

Vol 11 (1) ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Seyed Mehdi Jazayeri ◽

Mahtab Pooralinaghi ◽

Ronald Oswaldo Villamar Torres

Keyword(s):

Transcription Factors ◽

Zinc Finger Protein ◽

Response Regulator ◽

Model Organism ◽

Gene Clusters ◽

Gene Copy ◽

Regulatory Function ◽

Comparative Genomic ◽

Species Specific ◽

Arabidopsis Species

Transcription factors (TF) are the elements, which regulate gene expression. Regulatory function of TFs play an important role in plant biological processes and mechanisms. They may interconnect with other transcription factors or functional genes to modulate their expression in response to an internal/external factor like life cycle stage, growth, development and stress. Arabidopsis is the well-known and the most used model organism. Transcription factors of three Arabidopsis species including A. halleri, A. lyrata and A. thaliana, were compared. basic/helix-loop-helix (bHLH) with 220 TFs was the most abundant family among three Arabidopsis species while MYB and MYB related families considering as a whole group were more than bHLH with 308 TFs. No STERILE APETALA (SAP) TF homolog was found for A.halleri. The common transcription factors among three species were 4,172 grouped in 1,212 clusters. The species-specific clustered TFs were 12, 30 and 58 for A. halleri, A. lyrata and A. thaliana respectively. Eight hundred ninety two single-copy gene clusters those have one gene copy from each species, i.e. 2,676 genes, were listed. Four hundred forty five TF singletons were not clustered and are unique among three species. For clustered TF belonging to each species, GO terms and SwissProt hits showed that A. halleri has two species-specific TFs involved in heavy metal response including Zinc finger protein AZF2 and two-component response regulator ARR11 while for A. lyrata specific TFs are involved in stress response and plant development. A. thaliana specific clustered TFs work on plant flower development and acclimation.

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