The hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria

AbstractSulfur-oxidizing Thioglobaceae, often referred to as SUP05 and Arctic96BD clades, are widespread and common to hydrothermal vents and oxygen minimum zones. They impact global biogeochemical cycles and exhibit a variety of host-associated and free-living lifestyles. The evolutionary driving forces that led to the versatility, adoption of multiple lifestyles and global success of this family are largely unknown. Here, we perform an in-depth comparative genomic analysis using all available and newly generated Thioglobaceae genomes. Gene content variation was common, throughout taxonomic ranks and lifestyles. We uncovered a pool of variable genes within most Thioglobaceae populations in single environmental samples and we referred to this as the ‘hidden pangenome’. The ‘hidden pangenome’ is often overlooked in comparative genomic studies and our results indicate a much higher intra-specific diversity within environmental bacterial populations than previously thought. Our results show that core-community functions are different from species core genomes suggesting that core functions across populations are divided among the intra-specific members within a population. Defense mechanisms against foreign DNA and phages were enriched in symbiotic lineages, indicating an increased exchange of genetic material in symbioses. Our study suggests that genomic plasticity and frequent exchange of genetic material drives the global success of this family by increasing its evolvability in a heterogeneous environment.

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Diversity matters: Deep-sea mussels harbor multiple symbiont strains

10.1101/531459 ◽

2019 ◽

Cited By ~ 3

Author(s):

Rebecca Ansorge ◽

Stefano Romano ◽

Lizbeth Sayavedra ◽

Anne Kupczok ◽

Halina E. Tegetmeyer ◽

...

Keyword(s):

Deep Sea ◽

Defense Mechanisms ◽

Hydrothermal Vents ◽

Low Cost ◽

Intracellular Bacteria ◽

Adaptive Potential ◽

Free Living ◽

Nutrient Sources ◽

Metabolic Functions ◽

Sulfur Oxidizing

AbstractGenetic diversity of closely-related free-living microbes is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Indeed, symbiont strain diversity has long assumed to be restricted in intracellular bacteria associated with animals. Here, we sequenced the metagenomes and metatranscriptomes of 18 Bathymodiolus mussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individual Bathymodiolus mussels. Co-occurring symbiont strains differed extensively in key metabolic functions, such as the use of energy and nutrient sources, electron acceptors and viral defense mechanisms. Most strain-specific genes were expressed, highlighting their adaptive potential. We show that fine-scale diversity is pervasive in Bathymodiolus symbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, not the host, feeds the symbionts.

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Multiple origins of obligate nematode and insect symbionts by a clade of bacteria closely related to plant pathogens

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2000860117 ◽

2020 ◽

Vol 117 (50) ◽

pp. 31979-31986

Author(s):

Vincent G. Martinson ◽

Ryan M. R. Gawryluk ◽

Brent E. Gowen ◽

Caitlin I. Curtis ◽

John Jaenike ◽

...

Keyword(s):

Hydrothermal Vents ◽

Pathogenic Bacteria ◽

Plant Pathogens ◽

Genomic Analysis ◽

Comparative Genomic ◽

Intracellular Bacteria ◽

Multiple Origins ◽

Severe Reduction ◽

Insect Symbionts ◽

Erosion Characteristic

Obligate symbioses involving intracellular bacteria have transformed eukaryotic life, from providing aerobic respiration and photosynthesis to enabling colonization of previously inaccessible niches, such as feeding on xylem and phloem, and surviving in deep-sea hydrothermal vents. A major challenge in the study of obligate symbioses is to understand how they arise. Because the best studied obligate symbioses are ancient, it is especially challenging to identify early or intermediate stages. Here we report the discovery of a nascent obligate symbiosis in Howardula aoronymphium, a well-studied nematode parasite of Drosophila flies. We have found that H. aoronymphium and its sister species harbor a maternally inherited intracellular bacterial symbiont. We never find the symbiont in nematode-free flies, and virtually all nematodes in the field and the laboratory are infected. Treating nematodes with antibiotics causes a severe reduction in fly infection success. The association is recent, as more distantly related insect-parasitic tylenchid nematodes do not host these endosymbionts. We also report that the Howardula nematode symbiont is a member of a widespread monophyletic group of invertebrate host-associated microbes that has independently given rise to at least four obligate symbioses, one in nematodes and three in insects, and that is sister to Pectobacterium, a lineage of plant pathogenic bacteria. Comparative genomic analysis of this group, which we name Candidatus Symbiopectobacterium, shows signatures of genome erosion characteristic of early stages of symbiosis, with the Howardula symbiont’s genome containing over a thousand predicted pseudogenes, comprising a third of its genome.

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Comparative Genomic Analysis of Bifidobacterium Catenulatum Reveal the Genetic Divergence of its Two Subspecies from Infant and Adult Gut

10.21203/rs.3.rs-957925/v1 ◽

2021 ◽

Author(s):

Jiaqi Liu ◽

Weicheng Li ◽

Caiqing Yao ◽

Jie Yu ◽

Heping Zhang

Keyword(s):

Genetic Divergence ◽

Gc Content ◽

Genomic Analysis ◽

Glycoside Hydrolases ◽

Comparative Genomic ◽

Carbohydrate Binding ◽

Functional Difference ◽

Carbohydrate Utilization ◽

Carbohydrate Binding Modules ◽

Genomic Studies

Abstract Background: Bifidobacterium catenulatum, which includes two subspecies that B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum are usually from infant and adult gut respectively, while the genomic studies of functional difference and genetic divergence in them have been rarely reported. In this study, we analyzed 16 B. catenulatum strains through comparative genomics, including two novel sequenced strains. Results: A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated and confirmed their colonizing bias in infants and adults. Comparison of general genomic characteristics revealed that the two subspecies had significantly different genomic sizes but similar GC content. Functional annotations found that they peculiarly differ in utilization of carbohydrates and amino acid. Among them, we found that carbohydrate metabolism seems to play an important role in the divergence because of their carbohydrate-active enzymes (CAZyme) present two different clustering patterns. B. catenulatum subsp. kashiwanohense have functional genes that specifically adapted to the infant gut for glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51), which specifically participated in the metabolism of Human Milk Oligosaccharides (HMOs), and specific genes fuc that related to HMOs were also detected. While B. catenulatum subsp. catenulatum rich in GH3 and glycosyltransferases 4 (GT4) tended to metabolize plant-derived glycan that may help it metabolize more complex carbohydrates (eg. xylan) in the adult intestine. Conclusions: Our findings revealed genomic evidence of carbohydrate utilization bias which may be a key leading to the genetic divergence of two subspecies of B. catenulatum.

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Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae

10.1101/2021.08.06.455448 ◽

2021 ◽

Author(s):

Claudio Montenegro ◽

Livia Martins ◽

Fernanda de Oliveira Bustamante ◽

Ana Christina Brasileiro-Vidal ◽

Andrea Pedrosa-Harand

Keyword(s):

Genomic Analysis ◽

In Silico Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Orthologous Genes ◽

Genomic Analyses ◽

Genomic Studies ◽

Macroptilium Atropurpureum ◽

Evolutionary New Centromeres ◽

Silico Analysis

The tribe Phaseoleae (Leguminosae; Papilionoideae) includes several legume crops with assembled genomes. Comparative genomic studies indicated the preservation of large genomic blocks in legumes. However, the chromosome dynamics along its evolution was not investigated in the tribe. We conducted a comparative genomic analysis using CoGe Synmap platform to define a useful genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We defined the GBs based on orthologous genes between Phaseolus vulgaris and Vigna unguiculata genomes (n = 11), then searched for these GBs in different genome species belonging to the Phaseolinae (P. lunatus, n = 11) and Glycininae (Amphicarpaea edgeworthii, n = 11 and Spatholobus suberectus, n = 9) subtribes, and in the outgroup (Medicago truncaluta, n = 8). To support our in silico analysis, we used oligo-FISH probes of P. vulgaris chromosomes 2 and 3 to paint the orthologous chromosomes of the non-sequenced Phaseolinae species (Macroptilium atropurpureum and Lablab purpureusi, n = 11). We inferred the APK with n = 11, 22 GBs (A to V) and 60 sub-GBs. We hypothesized that the main rearrangements within Phaseolinae involved nine APK chromosomes, with extensive centromere repositioning resulting from evolutionary new centromeres (ENC) in the Phaseolus lineage. We demonstrated that the A. edgeworthii genome is more reshuffled than the dysploid S. suberectus genome, in which we could reconstructed the main events responsible for the chromosome number reduction. The development of the GB system and the proposed APK provide useful tools for future comparative genomic analyses of legume species.

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Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

International Journal of Genomics ◽

10.1155/2019/8987436 ◽

2019 ◽

Vol 2019 ◽

pp. 1-14

Author(s):

Jianchao Ying ◽

Jun Ye ◽

Teng Xu ◽

Qian Wang ◽

Qiyu Bao ◽

...

Keyword(s):

Core Genome ◽

Genomic Analysis ◽

Rhodococcus Equi ◽

Comparative Genomic Analysis ◽

Genomic Islands ◽

Genomic Diversity ◽

Comparative Genomic ◽

Niche Adaptation ◽

Genomic Studies ◽

Insight Into

Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.

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Origins of the current seventh cholera pandemic

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1608732113 ◽

2016 ◽

Vol 113 (48) ◽

pp. E7730-E7739 ◽

Cited By ~ 58

Author(s):

Dalong Hu ◽

Bin Liu ◽

Lu Feng ◽

Peng Ding ◽

Xi Guo ◽

...

Keyword(s):

Middle East ◽

Driving Forces ◽

Genomic Analysis ◽

Comparative Genomic ◽

Bacterial Strains ◽

Pandemic Strain ◽

Nonpathogenic Strain ◽

Rapid Diversification ◽

El Tor ◽

Key Events

Vibrio choleraehas caused seven cholera pandemics since 1817, imposing terror on much of the world, but bacterial strains are currently only available for the sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in Indonesia, but did not originate directly from the classical biotype sixth-pandemic strain. Previous studies focused mainly on the spread of the seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin, evolution, and transition to pandemicity of the seventh-pandemic strain. We used high-resolution comparative genomic analysis of strains collected from 1930 to 1964, covering the evolution from the first available El Tor biotype strain to the start of the seventh pandemic. We define six stages leading to the pandemic strain and reveal all key events. The seventh pandemic originated from a nonpathogenic strain in the Middle East, first observed in 1897. It subsequently underwent explosive diversification, including the spawning of the pandemic lineage. This rapid diversification suggests that, when first observed, the strain had only recently arrived in the Middle East, possibly from the Asian homeland of cholera. The lineage migrated to Makassar, Indonesia, where it gained the important virulence-associated elementsVibrioseventh pandemic island I (VSP-I), VSP-II, and El Tor type cholera toxin prophage by 1954, and it then became pandemic in 1961 after only 12 additional mutations. Our data indicate that specific niches in the Middle East and Makassar were important in generating the pandemic strain by providing gene sources and the driving forces for genetic events.

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NeisseriaBase: a specialisedNeisseriagenomic resource and analysis platform

PeerJ ◽

10.7717/peerj.1698 ◽

2016 ◽

Vol 4 ◽

pp. e1698

Author(s):

Wenning Zheng ◽

Naresh V.R. Mutha ◽

Hamed Heydari ◽

Avirup Dutta ◽

Cheuk Chuen Siow ◽

...

Keyword(s):

Web Application ◽

Genetic Material ◽

Gc Content ◽

Genomic Analysis ◽

Genome Comparison ◽

Comparative Genomic ◽

Trna Genes ◽

Diverse Range ◽

Web Interfaces ◽

The Web

Background.The gram-negativeNeisseriais associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for theNeisseriagenomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genusNeisseriaencompassing the complete and draft genomes of 15 pathogenic and commensalNeisseriaspecies.Methods.The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages.Results.Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227Neisseriagenomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing ofNeisseriagenomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis ofNeisseriastrains.Discussion.This user-friendly database not only provides access to a host of genomic resources onNeisseriabut also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested inNeisseriaresearch. This database is freely available athttp://neisseria.um.edu.my.

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Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains

10.1101/2020.12.09.418327 ◽

2020 ◽

Author(s):

Inês Silvestre ◽

Alexandra Nunes ◽

Vítor Borges ◽

Joana Isidro ◽

Catarina Silva ◽

...

Keyword(s):

Amino Acid ◽

Streptococcus Agalactiae ◽

Defense Mechanisms ◽

Amino Acid Change ◽

Genomic Analysis ◽

Dnase Activity ◽

Neonatal Meningitis ◽

Comparative Genomic ◽

Genetic Traits ◽

Predicted Signal Peptide

AbstractStreptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis. We performed a comparative genomic analysis between ST17 and ST19 human strains with different cell tropism and distinct DNase production phenotypes. All S. agalactiae ST17 strains, with the exception of 2211-04, were found to display DNase activity, while the opposite scenario was observed for ST19, where 1203-05 was the only DNase(+) strain. The analysis of the genetic variability of the seven genes putatively encoding secreted DNases in S. agalactiae revealed an exclusive amino acid change in the predicted signal peptide of GBS0661 (NucA) of the ST17 DNase(-), and an exclusive amino acid change alteration in GBS0609 of the ST19 DNase(+) strain. Further core-genome analysis identified some specificities (SNVs or indels) differentiating the DNase(-) ST17 2211-04 and the DNase(+) ST19 1203-05 from the remaining strains of each ST. The pan-genomic analysis evidenced an intact phage without homology in S. agalactiae and a transposon homologous to TnGBS2.3 in ST17 DNase(-) 2211-04; the transposon was also found in one ST17 DNase(+) strain, yet with a different site of insertion. A group of nine accessory genes were identified among all ST17 DNase(+) strains, including the Eco47II family restriction endonuclease and the C-5 cytosine-specific DNA methylase. None of these loci was found in any DNase(-) strain, which may suggest that these proteins might contribute to the lack of DNase activity. In summary, we provide novel insights on the genetic diversity between DNase(+) and DNase(-) strains, and identified genetic traits, namely specific mutations affecting predicted DNases (NucA and GBS0609) and differences in the accessory genome, that need further investigation as they may justify distinct DNase-related virulence phenotypes in S. agalactiae.

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Biosynthetic gene cluster profiling predicts the positive association between antagonism and phylogeny in Bacillus

10.1101/2021.08.29.457868 ◽

2021 ◽

Author(s):

Liming Xia ◽

Youzhi Miao ◽

A'li Cao ◽

Yan Liu ◽

Zihao Liu ◽

...

Keyword(s):

Driving Forces ◽

Interference Competition ◽

Genomic Analysis ◽

Positive Association ◽

Gene Clusters ◽

Microbial Interactions ◽

Comparative Genomic ◽

Phylogenetic Distance ◽

Biosynthetic Gene ◽

Exploitation Competition

Understanding the driving forces and intrinsic mechanisms of microbial competition is a fundamental question in microbial ecology. Despite the well-established negative correlation between exploitation competition and phylogenetic distance, the process of interference competition that is exemplified by antagonism remains controversial. Here, we studied the genus Bacillus, a commonly recognized producer of multifarious antibiotics, to explore the role of phylogenetic patterns of biosynthetic gene clusters (BGCs) in mediating the relationship between antagonism and phylogeny. Comparative genomic analysis revealed a positive association between BGC distance and phylogenetic distance. Antagonistic tests demonstrated that the inhibition phenotype positively correlated with both phylogenetic and predicted BGC distance, especially for antagonistic strains possessing abundant BGCs. Mutant-based verification showed that the antagonism was dependent on the BGCs that specifically harbored by the antagonistic strain. These findings highlight that BGC-phylogeny coherence regulates the positive correlation between congeneric antagonism and phylogenetic distance, which deepens our understanding of the driving force and intrinsic mechanism of microbial interactions.

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Comparative Genomic Analysis ofLactobacillus plantarum: An Overview

International Journal of Genomics ◽

10.1155/2019/4973214 ◽

2019 ◽

Vol 2019 ◽

pp. 1-11 ◽

Cited By ~ 7

Author(s):

Eliane Evanovich ◽

Patricia Jeanne de Souza Mendonça Mattos ◽

João Farias Guerreiro

Keyword(s):

Antibiotic Resistance ◽

Genetic Material ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

High Rate ◽

Comparative Genomic ◽

Fermented Foods ◽

Protein Coding ◽

Potential Applications ◽

Arsenic Detoxification

Background.Lactobacillus plantarumis widely used in the manufacture of dairy products, fermented foods, and bacteriocins. The genomes of the strains contain multiple genes which may have been acquired by horizontal gene transfer. Many of these genes are important for the regulation, metabolism, and transport of various sugars; however, other genes may carry and spread virulence and antibiotic resistance determinants. In this way, monitoring these genomes is essential to the manufacture of food. In this study, we aim to provide an overview of the genomic properties ofL. plantarumbased on approaches of comparative genomics.Results. The finding of the current study indicates that the core genome ofL. plantarumpresents 1425 protein-coding genes and is mostly related to the metabolic process. The accessory genome has on average 1320 genes that encodes protein involved in processes as the formation of bacteriocins, degradation of halogen, arsenic detoxification, and nisin resistance. Most of the strains show an ancestral synteny, similar to the one described in the genomes ofL. pentosusKCA1 andL. plantarumWCFS1. The lifestyle island analyses did not show a pattern of arrangement or gene content according to habitat.Conclusions. Our results suggest that there is a high rate of transfer of genetic material between the strains. We did not identify any virulence factors and antibiotic resistance genes on the genomes. Thus, the strains may be useful for the biotechnology, bioremediation, and production of bacteriocins. The potential applications are, however, restricted to particular strains.

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