The Diversity and Evolutionary Relationships of Ticks and Tick-borne Bacteria in China

Abstract Background Ticks (order Ixodida) are ectoparasites of vertebrates that transmit diverse pathogens to humans and domestic animals. However, information on the genomic diversity of ticks in China is currently limited to a small number of common species, leaving substantial knowledge gap in the evolution of both ticks and their associated bacterial. Results We collected more than 20,000 contemporary and historical (up to 60 years of preservation) tick samples representing a wide range of tick biodiversity across diverse geographic regions in China, including 18 common species, nine rare species, and two undetermined species. Metagenomic sequencing was performed on individual ticks to obtain the complete or near-complete mitochondrial (mt) genome sequences from 46 tick species, among which 30 species were revealed for the first time. These new mt genomes data greatly expanded the diversity of many tick groups and revealed five cryptic species. Utilizing the same metagenomic sequence data we identified divergent and abundant bacteria in Haemaphysalis, Ixodes, Dermacentor and Carios ticks, including nine species of pathogenetic bacteria and potentially new species within the genus Borrelia. We also used these data to explore the evolutionary relationship between ticks and their associated bacteria, revealing a pattern of long-term co-divergence relationship between ticks and Rickettsia and Coxiella bacteria. Conclusions In sum, our study provides important new information on the prevalence of tick-borne pathogens in China and sheds new light on the long-term evolutionary and ecological relationships between ticks and their associated bacteria.

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Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria

Microbiome ◽

10.1186/s40168-021-01140-8 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Olga M. Pérez-Carrascal ◽

Nicolas Tromas ◽

Yves Terrat ◽

Elisa Moreno ◽

Alessandra Giani ◽

...

Keyword(s):

Genetic Diversity ◽

Heterotrophic Bacteria ◽

Bacterial Species ◽

Colony Growth ◽

Genomic Diversity ◽

Gene Copy ◽

Metagenomic Sequencing ◽

Associated Bacteria ◽

Microbiome Composition

Abstract Background Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria—their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies—including cyanobacteria and associated bacterial genomes—isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil. Results We identified 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in only two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter. These phylogenetically associated genera could enrich the metabolic repertoire of Microcystis, for example by encoding the biosynthesis of complementary carotenoid molecules. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting. Conclusions We have introduced a method for culture-free isolation of single colonies from nature followed by metagenomic sequencing, which could be applied to other types of microbes. Together, our results expand the known genetic diversity of both Microcystis and its microbiome in natural settings, and support their long-term, specific, and potentially beneficial associations.

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MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

F1000Research ◽

10.12688/f1000research.18866.2 ◽

2019 ◽

Vol 8 ◽

pp. 726

Author(s):

Mike W.C. Thang ◽

Xin-Yi Chua ◽

Gareth Price ◽

Dominique Gorse ◽

Matt A. Field

Keyword(s):

Microbial Communities ◽

Sequence Data ◽

Metagenomic Data ◽

Marker Genes ◽

Metagenomic Sequencing ◽

Differential Analysis ◽

Biomedical Sciences ◽

Metagenomic Sequence ◽

Differential Abundance ◽

Differential Abundance Analysis

Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences. While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs. Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics. MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.

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Patterns of genomic diversification reflect differences in life history and reproductive biology between figs (Ficus) and the stone oaks (Lithocarpus)

Genome ◽

10.1139/gen-2016-0188 ◽

2017 ◽

Vol 60 (9) ◽

pp. 756-761 ◽

Cited By ~ 3

Author(s):

Chai-Shian Kua ◽

Charles H. Cannon

Keyword(s):

Life History ◽

Evolutionary Relationship ◽

Genomic Diversity ◽

Evolutionary Strategies ◽

Life History Strategies ◽

Wide Range ◽

Genomic Divergence ◽

History Of ◽

Background History ◽

Diverse Groups

One of the remarkable aspects of the tremendous biodiversity found in tropical forests is the wide range of evolutionary strategies that have produced this diversity, indicating many paths to diversification. We compare two diverse groups of trees with profoundly different biologies to discover whether these differences are reflected in their genomes. Ficus (Moraceae), with its complex co-evolutionary relationship with obligate pollinating wasps, produces copious tiny seeds that are widely dispersed. Lithocarpus (Fagaceae), with generalized insect pollination, produces large seeds that are poorly dispersed. We hypothesize that these different reproductive biologies and life history strategies should have a profound impact on the basic properties of genomic divergence within each genus. Using shallow whole genome sequencing for six species of Ficus, seven species of Lithocarpus, and three outgroups, we examined overall genomic diversity, how it is shared among the species within each genus, and the fraction of this shared diversity that agrees with the major phylogenetic pattern. A substantially larger fraction of the genome is shared among species of Lithocarpus, a considerable amount of this shared diversity was incongruent with the general background history of the genomes, and each fig species possessed a substantially larger fraction of unique diversity than Lithocarpus.

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Occurrence and genetic diversity of CRESS DNA viruses in wild birds: a Hungarian study

Scientific Reports ◽

10.1038/s41598-020-63795-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Eszter Kaszab ◽

György Lengyel ◽

Szilvia Marton ◽

Ádám Dán ◽

Krisztián Bányai ◽

...

Keyword(s):

Sequence Data ◽

Bird Species ◽

Cloacal Swab ◽

Genomic Diversity ◽

Virus Species ◽

Dna Viruses ◽

Specific Pcr ◽

New Information ◽

Protein Encoding ◽

Conserved Gene

AbstractCircoviruses, cycloviruses and other circular, replication-associated protein-encoding single stranded (CRESS) DNA viruses have been detected in a variety of animal taxa. In this study, cloacal swab samples (n = 90) were examined for CRESS DNA viruses from 31 wild bird species living at various aquatic sites in Hungary to identify possible reservoirs of viruses pathogenic to domestic poultry. A total of 30 (33.3%) specimens tested positive with pan-CRESS DNA virus specific PCR. Goose circovirus (GoCV), Duck associated cyclovirus 1 (DuACyV-1) and Garrulus glandarius associated circular virus 1 (GgaCV-1) were detected in nine, three and two different bird species, respectively. Selected specimens were subjected to whole genome sequencing. The obtained sequence data revealed conserved gene structure within the identified virus species and detected homologous (within GoCV) and possible heterologous recombination (within DuACyV-1) events. Results presented here provide new information on the genomic diversity and evolution of selected CRESS DNA viruses.

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Fast functional annotation of metagenomic shotgun data by DNA alignment to a microbial gene catalog

10.1101/120402 ◽

2017 ◽

Author(s):

Stuart M. Brown ◽

Yuhan Hao ◽

Hao Chen ◽

Bobby P. Laungani ◽

Thahmina A. Ali ◽

...

Keyword(s):

Functional Annotation ◽

Sequence Data ◽

Human Microbiome ◽

Metagenomic Data ◽

Metagenomic Sequencing ◽

Alternative Analysis ◽

Metagenomic Sequence ◽

Shotgun Metagenomics ◽

Gene Functions ◽

Dna Alignment

AbstractBackgroundMetagenomic shotgun sequencing is becoming increasingly popular to study microbes associated with the human body and in environmental samples. A key goal of shotgun metagenomic sequencing is to identify gene functions and metabolic pathways that differ between samples or conditions. However, current methods to identify function in the large number of reads in a high-throughput sequence data file rely on the computationally intensive and low stringency approach of mapping each read to a generic database of proteins or reference microbial genomes.ResultsWe have developed an alternative analysis approach for shotgun metagenomic sequence data utilizing Bowtie2 DNA-DNA alignment of the reads to a database of well annotated genes compiled from human microbiome data. This method is rapid, and provides high stringency matches (>90% DNA sequence identity) of shotgun metagenomics reads to genes with annotated functions. We demonstrate the use of this method with synthetic data, Human Microbiome Project shotgun metagenomic data sets, and data from a study of liver disease. Differentially abundant KEGG gene functions can be detected in these experiments.ConclusionsFunctional annotation of metagenomic shotgun sequence reads can be accomplished by rapid DNA-DNA matching to a custom database of microbial sequences using the Bowtie2 sequence alignment tool. This method can be used for a variety of microbiome studies and allows functional analysis which is otherwise computationally demanding. This rapid annotation method is freely available as a Galaxy workflow within a Docker image.

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Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics

10.1101/180406 ◽

2017 ◽

Cited By ~ 13

Author(s):

Richard M. Leggett ◽

Cristina Alcon-Giner ◽

Darren Heavens ◽

Shabhonam Caim ◽

Thomas C. Brook ◽

...

Keyword(s):

Gut Microbiota ◽

Real Time ◽

Time Course ◽

Sequence Data ◽

Clinical Samples ◽

Metagenomic Sequencing ◽

Time Analysis ◽

Metagenomic Sequence ◽

Real Time Analysis ◽

Increased Risk

ABSTRACTThe Oxford Nanopore MinION sequencing platform offers near real time analysis of DNA reads as they are generated, which makes the device attractive for in-field or clinical deployment, e.g. rapid diagnostics. We used the MinION platform for shotgun metagenomic sequencing and analysis of gut-associated microbial communities; firstly, we used a 20-species human microbiota mock community to demonstrate how Nanopore metagenomic sequence data can be reliably and rapidly classified. Secondly, we profiled faecal microbiomes from preterm infants at increased risk of necrotising enterocolitis and sepsis. In single patient time course, we captured the diversity of the immature gut microbiota and observed how its complexity changes over time in response to interventions, i.e. probiotic, antibiotics and episodes of suspected sepsis. Finally, we performed ‘real-time’ runs from sample to analysis using faecal samples of critically ill infants and of healthy infants receiving probiotic supplementation. Real-time analysis was facilitated by our new NanoOK RT software package which analysed sequences as they were generated. We reliably identified potentially pathogenic taxa (i.e. Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance (AMR) gene profiles within as little as one hour of sequencing. Antibiotic treatment decisions may be rapidly modified in response to these AMR profiles, which we validated using pathogen isolation, whole genome sequencing and antibiotic susceptibility testing. Our results demonstrate that our pipeline can process clinical samples to a rich dataset able to inform tailored patient antimicrobial treatment in less than 5 hours.

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MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

F1000Research ◽

10.12688/f1000research.18866.1 ◽

2019 ◽

Vol 8 ◽

pp. 726 ◽

Cited By ~ 1

Author(s):

Mike W.C. Thang ◽

Xin-Yi Chua ◽

Gareth Price ◽

Dominique Gorse ◽

Matt A. Field

Keyword(s):

Microbial Communities ◽

Sequence Data ◽

Metagenomic Data ◽

Marker Genes ◽

Metagenomic Sequencing ◽

Differential Analysis ◽

Biomedical Sciences ◽

Metagenomic Sequence ◽

Differential Abundance ◽

Differential Abundance Analysis

Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences yet analysis workflows remain immature relative to other field such as DNASeq and RNASeq analysis pipelines. While software for detailing the composition of microbial communities using 16S rRNA marker genes is constantly improving, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs. Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics. MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.

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Metagenomic Analysis of Regularly Microwave-Treated and Untreated Domestic Kitchen Sponges

Microorganisms ◽

10.3390/microorganisms8050736 ◽

2020 ◽

Vol 8 (5) ◽

pp. 736 ◽

Cited By ~ 3

Author(s):

Susanne Jacksch ◽

Jyothi Thota ◽

Sudarshan Shetty ◽

Hauke Smidt ◽

Sylvia Schnell ◽

...

Keyword(s):

Microbial Communities ◽

Sequence Data ◽

Well Being ◽

Long Term Effects ◽

Pathogenic Potential ◽

Metagenomic Sequence ◽

Metabolic Properties ◽

Cleaning And Disinfection ◽

Kitchen Sponges

Kitchen sponges massively absorb and spread microorganisms, leading to contamination of kitchen appliances, surfaces, and food. Microwaving as an effective and widespread technique can rapidly reduce the microbial load of kitchen sponges. However, long-term effects of such treatments are largely unknown. Notably, it has been speculated that regularly applied domestic cleaning and disinfection may select for microbial communities with a higher pathogenic potential and/or malodorous properties. In this study, we distributed newly purchased polyurethane kitchen sponges to 20 participants, with the instruction to use them under normal household conditions for four weeks. Ten of the participants sanitized their sponges regularly by a standardized microwaving protocol, while the remaining ten sponges remained untreated. Metagenomic sequence data evaluation indicated that, in addition to bacteria, viruses, eukaryotes, and archaea were also part of the kitchen sponge microbiome. Comparisons of sanitized and untreated kitchen sponges indicated a trend towards a reduced structural microbial diversity while functional diversity increased. Microwave sanitization appeared to alter composition and metabolic properties of the microbial communities. Follow-up studies will have to show whether these changes are more positive or negative in terms of domestic hygiene, human health, and well-being.

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Tough, armed and omnivorous: Hermodice carunculata (Annelida: Amphinomidae) is prepared for ecological challenges

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315417000091 ◽

2017 ◽

Vol 97 (5) ◽

pp. 1075-1080 ◽

Cited By ~ 11

Author(s):

Anja Schulze ◽

Candace J. Grimes ◽

Tiffany E. Rudek

Keyword(s):

Feeding Habits ◽

Common Species ◽

Defence Mechanisms ◽

Defensive Strategies ◽

Hermodice Carunculata ◽

Wide Range ◽

Nuisance Species ◽

Reef Decline

The bearded fireworm, Hermodice carunculata, is a common species in the marine annelid taxon Amphinomidae. It has a widespread distribution throughout the Atlantic, Gulf of Mexico, the Caribbean, Mediterranean and Red Seas. We review its environmental tolerances, defence mechanisms and feeding habits to evaluate its potential to survive in changing ocean conditions, to increasingly emerge as a nuisance species and to invade new geographic areas. Hermodice carunculata tolerates a wide range of environmental conditions, including temperature, salinity, oxygen saturation and various types of pollution. It has few natural predators because it is protected by its sharp chaetae and probably by toxins. Hermodice carunculata is best known for consuming live cnidarians, and has been implicated in transmitting coral pathogens, but it also feeds non-selectively on detritus. In the short term, we predict that H. carunculata will be able to withstand many future ecological challenges and possibly contribute to coral reef decline. In the long term, ocean acidification may negatively impact its defence mechanisms and survival. Its invasive potential may be significant. We highlight the gaps in our knowledge about the reproduction and development of this species, the nature and origin of its toxins and role of microbes in their feeding behaviour and defensive strategies.

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Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

10.1101/112235 ◽

2017 ◽

Cited By ~ 1

Author(s):

Henry Richard Johnston ◽

Yi-Juan Hu ◽

Jingjing Gao ◽

Timoty D. O’Connor ◽

Goncalo Abecasis ◽

...

Keyword(s):

Genetic Variation ◽

African Diaspora ◽

Large Scale ◽

Sequence Data ◽

African Ancestry ◽

Genomic Diversity ◽

Whole Genome Sequence ◽

Genotyping Array ◽

Wide Range ◽

Novel Variation

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an ‘African Diaspora Power Chip’ (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30x depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study1 cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

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