Genetics


Publications (271)

Complete Genome Sequence of “ <i>Candidatus</i> Hydrogeosomobacter endosymbioticus,” an Intracellular Bacterial Symbiont of the Anaerobic Ciliate Scuticociliate GW7

Citation
Shiohama et al. (2022). Microbiology Resource Announcements 11 (2)
Names
Ca. Hydrogenosomobacter endosymbioticus
Subjects
Genetics Immunology and Microbiology (miscellaneous) Molecular Biology
Abstract
The bacterium “ Candidatus Hydrogenosomobacter endosymbioticus” is an intracellular symbiont of anaerobic scuticociliate GW7, which is associated with hydrogenosome together with methanogenic archaea. Here, we report a complete genome sequence of the symbiont consisting of 827 kbp. Knowing this sequence would contribute to the understanding of the metabolic interactions and evolution of the tripartite symbiosis.

Complete Genome Sequence of Human Oral Saccharibacterium “ <i>Candidatus</i> Nanosynbacter sp. HMT352” Strain KC1

Citation
Cross et al. (2022). Microbiology Resource Announcements 11 (2)
Names
Ca. Nanosynbacter
Subjects
Genetics Immunology and Microbiology (miscellaneous) Molecular Biology
Abstract
“Cand. Nanosynbacter sp. HMT352” strain KC1 is an ectoparasitic saccharibacterium/TM7 that was co-isolated from a human saliva sample with its obligate bacterial host, Schaalia odontolytica . The genome of strain KC1 enables studies of the mechanisms and evolution of interspecies interactions and, for oral species, studies of their potential roles in health and disease.

Genome Sequence of a New “ <i>Candidatus</i> ” Phylum “Dependentiae” Isolate from Chiba, Japan

Citation
Takemura (2022). Microbiology Resource Announcements 11 (2)
Names
Ca. Dependentiae
Subjects
Genetics Immunology and Microbiology (miscellaneous) Molecular Biology
Abstract
Little is known about the bacterial phylum “ Candidatus Dependentiae,” because only three isolates have been reported. Here, I report the isolation and genome sequencing of a new member of this phylum, strain Noda2021. This is the fourth strain isolated from the phylum “ Candidatus Dependentiae.”

Candidatus Thiovulum sp. strain imperiosus: the largest free-living Epsilonproteobacteraeota Thiovulum strain lives in a marine mangrove environment

Citation
Sylvestre et al. (2022). Canadian Journal of Microbiology 68 (1)
Names
Ca. Thiovulum
Subjects
Applied Microbiology and Biotechnology General Medicine Genetics Immunology Microbiology Molecular Biology
Abstract
A large (47.75 ± 3.56 µm in diameter) Thiovulum bacterial strain forming white veils is described from a marine mangrove ecosystem. High sulfide concentrations (up to 8 mM of H2S) were measured on sunken organic matter (wood/bone debris) under laboratory conditions. This sulfur-oxidizing bacterium colonized the organic matter, forming a white veil. According to conventional scanning electron microscope (SEM) observations, bacterial cells are ovoid and slightly motile by numerous small flagella present on the cell surface. Large intracytoplasmic internal sulfur granules were observed, suggesting a sulfidic-based metabolism. Observations were confirmed by elemental sulfur distribution detected by energy-dispersive X-ray spectroscopy (EDXS) analysis using an environmental scanning electron microscope (ESEM) on non-dehydrated samples. Phylogenetic analysis of the partial sequence of 16S rDNA obtained from purified fractions of this Epsilonproteobacteraeota strain indicates that this bacterium belongs to the Thiovulaceae cluster and could be one of the largest Thiovulum ever described. We propose to name this species Candidatus Thiovulum sp. strain imperiosus.

Molecular signatures between citrus and Candidatus Liberibacter asiaticus

Citation
Hu et al. (2021). PLOS Pathogens 17 (12)
Names
Ca. Liberibacter asiaticus Liberibacter
Subjects
Genetics Immunology Microbiology Molecular Biology Parasitology Virology
Abstract
Citrus Huanglongbing (HLB), also known as citrus greening, is one of the most devastating citrus diseases worldwide. Candidatus Liberibacter asiaticus (CLas) is the most prevalent strain associated with HLB, which is yet to be cultured in vitro. None of the commercial citrus cultivars are resistant to HLB. The pathosystem of Ca. Liberibacter is complex and remains a mystery. In this review, we focus on the recent progress in genomic research on the pathogen, the interaction of host and CLas, and the influence of CLas infection on the transcripts, proteins, and metabolism of the host. We have also focused on the identification of candidate genes for CLas pathogenicity or the improvements of HLB tolerance in citrus. In the end, we propose potentially promising areas for mechanistic studies of CLas pathogenicity, defense regulators, and genetic improvement for HLB tolerance/resistance in the future.

Draft Genome Sequence of Schaalia odontolytica Strain ORNL0103, a Basibiont of “ Candidatus Saccharibacteria” HMT352

Citation
Podar et al. (2021). Microbiology Resource Announcements 10 (44)
Names
Ca. Saccharibacteria
Subjects
Genetics Immunology and Microbiology (miscellaneous) Molecular Biology
Abstract
Here, we report the draft, nearly complete genome sequence of the human oral actinobacterium Schaalia odontolytica strain ORNL0103, which was isolated in association with “ Candidatus Saccharibacteria” HMT352 strain ORNL0105. The genome was sequenced using a combination of Pacific Biosciences and Illumina platforms and encodes 1,948 proteins and 60 RNAs.

Metagenome Assembly and Metagenome-Assembled Genome of “ Candidatus Aramenus sulfurataquae” from Thermal Sediments from the Los Azufres Volcanic Complex

Citation
Marín-Paredes et al. (2021). Microbiology Resource Announcements 10 (39)
Names
Ca. Aramenus sulfurataquae
Subjects
Genetics Immunology and Microbiology (miscellaneous) Molecular Biology
Abstract
A plethora of hot springs are found at the Los Azufres volcanic complex in Mexico, and studies are needed to determine their microbial genomic diversity. Here, we report a metagenome of hot spring sediments and a metagenome-assembled genome of “ Candidatus Aramenus sulfurataquae.” This study reveals novel genomic sequences of Sulfolobales archaea.

The molecular interplay of the establishment of an infection – gene expression of Diaphorina citri gut and Candidatus Liberibacter asiaticus

Citation
Bento et al. (2021). BMC Genomics 22 (1)
Names
Ca. Liberibacter asiaticus
Subjects
Biotechnology Genetics
Abstract
Abstract Background Candidatus Liberibacter asiaticus (CLas) is one the causative agents of greening disease in citrus, an unccurable, devastating disease of citrus worldwide. CLas is vectored by Diaphorina citri, and the understanding of the molecular interplay between vector and pathogen will provide additional basis for the development and implementation of successful management strategies. We focused in the molecular interplay occurring in the gut of the vector, a major barrier for CLas invasion and colonization. Results We investigated the differential expression of vector and CLas genes by analyzing a de novo reference metatranscriptome of the gut of adult psyllids fed of CLas-infected and healthy citrus plants for 1-2, 3-4 and 5-6 days. CLas regulates the immune response of the vector affecting the production of reactive species of oxygen and nitrogen, and the production of antimicrobial peptides. Moreover, CLas overexpressed peroxiredoxin, probably in a protective manner. The major transcript involved in immune expression was related to melanization, a CLIP-domain serine protease we believe participates in the wounding of epithelial cells damaged during infection, which is supported by the down-regulation of pangolin. We also detected that CLas modulates the gut peristalsis of psyllids through the down-regulation of titin, reducing the elimination of CLas with faeces. The up-regulation of the neuromodulator arylalkylamine N-acetyltransferase implies CLas also interferes with the double brain-gut communication circuitry of the vector. CLas colonizes the gut by expressing two Type IVb pilin flp genes and several chaperones that can also function as adhesins. We hypothesized biofilm formation occurs by the expression of the cold shock protein of CLas. Conclusions The thorough detailed analysis of the transcritome of Ca. L. asiaticus and of D. citri at different time points of their interaction in the gut tissues of the host led to the identification of several host genes targeted for regulation by L. asiaticus, but also bacterial genes coding for potential effector proteins. The identified targets and effector proteins are potential targets for the development of new management strategies directed to interfere with the successful utilization of the psyllid vector by this pathogen.