Computer Science Applications


Publications
35

Refinement of the “ Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration

Citation
Stewart et al. (2024). mSystems 9 (3)
Names
“Accumulibacter”
Abstract
ABSTRACT Members of the “ Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 “ Ca . Accumulibacter” species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (

A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide

Citation
Petriglieri et al. (2023). mSystems 8 (6)
Names
“Epilinea brevis” “Epilinea” “Leptofilum” “Epilineaceae” “Epilineales” “Avedoeria danica” “Avedoeria” “Brachythrix odensensis” “Brachythrix” “Defluviilinea gracilis” “Defluviilinea” “Defluviilinea proxima” “Villigracilis vicinus” “Villigracilis adiacens” “Villigracilis propinquus” “Villigracilis” “Villigracilis affinis” “Villigracilis proximus” “Villigracilis saccharophilus” “Villigracilaceae” “Hadersleviella danica” “Hadersleviella” “Trichofilum aggregatum” “Trichofilum” “Promineofilum glycogenicum” “Leptofilum gracile” “Leptofilum proximum” “Leptovillus gracilis” “Leptovillus affinis” “Leptovillus” “Flexicrinis affinis” “Flexicrinis proximus” “Flexicrinis” “Flexifilum breve” “Flexifilum affine” “Flexifilum” “Flexifilaceae” “Amarolinea dominans” “Fredericiella danica” “Fredericiella” “Caldilinea saccharophila” “Ribeiella danica” “Ribeiella” “Kouleothrix ribensis” “Amarobacter glycogenicus” “Amarobacter” “Amarobacillus elongatus” “Amarobacillus”
Abstract
ABSTRACT Filamentous Chloroflexota are abundant in activated sludge wastewater treatment plants (WWTPs) worldwide and are occasionally associated with poor solid-liquid separation or foaming, but most of the abundant lineages remain undescribed. Here, we present a comprehensive overview of Chloroflexota abundant in WWTPs worldwide, using high-quality metagenome-assembled genomes (MAGs) and 16S rRNA amplicon data from 740 Danish and global WWTPs. Many novel taxa were descri

Metagenomics Revealed a New Genus ‘Candidatus Thiocaldithrix dubininis’ gen. nov., sp. nov. and a New Species ‘Candidatus Thiothrix putei’ sp. nov. in the Family Thiotrichaceae, Some Members of Which Have Traits of Both Na+- and H+-Motive Energetics

Citation
Ravin et al. (2023). International Journal of Molecular Sciences 24 (18)
Names
Ca. Thiocaldithrix dubininis Ca. Thiothrix putei
Abstract
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1–55.6%).

Effects of Candidatus Liberibacter asiaticus infection on metagenome of Diaphorina citri gut endosymbiont

Citation
Pan et al. (2023). Scientific Data 10 (1)
Names
Ca. Liberibacter asiaticus
Abstract
AbstractAsian citrus psyllid (Diaphorina citri, D. citri) is the important vector of “Candidatus Liberibacter asiaticus” (CLas), associated with Huanglongbing, the most devastating citrus disease worldwide. CLas can affect endosymbiont abundance of D. citri. Here, we generated the high-quality gut endosymbiont metagenomes of Diaphorina citri on the condition of CLas infected and uninfected. The dataset comprised 6616.74 M and 6586.04 M raw reads, on overage, from CLas uninfected and infected psy

Diversity Analysis and Function Prediction of Bacterial Communities in the Different Colored Pericarp of Citrus reticulata cv. ‘Shatangju’ Due to ‘Candidatus Liberibacter asiaticus’ Infection

Citation
Wang et al. (2023). International Journal of Molecular Sciences 24 (14)
Names
Liberibacter Ca. Liberibacter asiaticus
Abstract
Huanglongbing (HLB), caused by the Candidatus Liberibacter spp., is the most devastating disease in the citrus industry. HLB significantly affects and alters the microbial community structure or potential function of the microbial community of leaves and roots. However, it is unknown how the microbial community structure of the pericarp with different pigments is affected by Candidatus Liberibacter asiaticus (CLas). This study identified the enriched taxa of the microbial community in the citrus

Distribution, abundance, and ecogenomics of the Palauibacterales , a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum

Citation
Aldeguer-Riquelme et al. (2023). mSystems
Names
Palauibacteraceae Palauibacterales Palauibacter Benthicola Humimonas Caribbeanibacter Carthagonibacter Indicimonas Kutchimonas Humimonas hydrogenitrophica Ts Caribbeanibacter nitroreducens Ts Benthicola marisminoris Ts Indicimonas acetifermentans Ts Benthicola azotiphorus Palauibacter soopunensis Ts Palauibacter scopulicola Palauibacter rhopaloidicola Palauibacter poriticola Palauibacter australiensis Palauibacter irciniicola Palauibacter denitrificans Carthagonibacter metallireducens Ts Kutchimonas denitrificans Ts Palauibacter polyketidifaciens Palauibacter ramosifaciens
Abstract
ABSTRACT The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or me

Spatial Distribution and Temporal Dynamics of Candidatus Liberibacter Asiaticus in Different Stages of Embryos, Nymphs and Adults of Diaphorina citri

Citation
Nian et al. (2023). International Journal of Molecular Sciences 24 (10)
Names
Liberibacter Ca. Liberibacter asiaticus
Abstract
Huanglongbing, a globally devastating citrus disease, is associated with Candidatus Liberibacter asiaticus (CLas) and is mainly transmitted by Diaphorina citri. Verification of the distribution and dynamics of CLas in D. citri is critical to understanding CLas transmitted by vectors in nature. Here, the distribution and titers of CLas in different sexes and tissues of D. citri adults were investigated by fluorescence in-situ hybridization (FISH) and quantitative real-time PCR (qRT-PCR). Results

Metagenomic Discovery of “ Candidatus Parvarchaeales”-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments

Citation
Rao et al. (2023). mSystems 8 (2)
Names
“Parvarchaeales” “Haiyanarchaeum thermophilum” “Jingweiarchaeum tengchongense” “Parvarchaeum tengchongense” “Haiyanarchaeum” “Jingweiarchaeum” “Haiyanarchaeaceae” “Jingweiarchaeales” “Rehaiarchaeum”
Abstract
“ Candidatus Parvarchaeales” microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments.

Identification of the Actin-Binding Region and Binding to Host Plant Apple Actin of Immunodominant Transmembrane Protein of ‘Candidatus Phytoplasma mali’

Citation
Boonrod et al. (2023). International Journal of Molecular Sciences 24 (2)
Names
Ca. Phytoplasma mali
Abstract
‘Candidatus Phytoplasma mali’ (‘Ca. P. mali’) has only one major membrane protein, the immunodominant membrane protein (Imp), which is regarded as being close to the ancestor of all phytoplasma immunodominant membrane proteins. Imp binds to actin and possibly facilitates its movement in the plant or insect host cells. However, protein sequences of Imp are quite diverse among phytoplasma species, thus resulting in difficulties in identifying conserved domains across species. In this work, we comp

Comparative Genomic Insights into the Evolution of Halobacteria -Associated “ Candidatus Nanohaloarchaeota”

Citation
Zhao et al. (2022). mSystems 7 (6)
Names
Ca. Nanohaloarchaeota
Abstract
The DPANN superphylum is a group of archaea widely distributed in various habitats. They generally have small cells and have a symbiotic lifestyle with other archaea.