Nature Communications


Publications
17

The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus

Citation
Carter et al. (2023). Nature Communications 14 (1)
Names
Ca. Liberibacter asiaticus
Abstract
AbstractThe bacterium Candidatus Liberibacter asiaticus (CLas) causes citrus Huanglongbing disease. Our understanding of the pathogenicity and biology of this microorganism remains limited because CLas has not yet been cultivated in artificial media. Its genome is relatively small and encodes approximately 1136 proteins, of which 415 have unknown functions. Here, we use a high-throughput yeast-two-hybrid (Y2H) screen to identify interactions between CLas proteins, thus providing insights into th

Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle

Citation
Li et al. (2023). Nature Communications 14 (1)
Names
“Houyibacterium oceanica” “Houyibacterium” “Houyibacteriaceae” “Houyihalomonas phototrophica” “Xihehalomonas phototrophica” “Xihemonas sinensis” “Kuafubacteria” “Kuafubacterium phototrophica” “Kuafucaenimonas phototrophica” “Kuafuhalomonas phototrophica” “Xihepedomonas phototrophica” “Xihelimnomonas phototrophica” “Xihecaenimonas phototrophica” “Kuafubacteriales” “Kuafubacteriaceae” “Xihehalomonas” “Xihemonas” “Xihecaenibacterium” “Houyihalomonas” “Xihelimnobacterium phototrophica” “Xihelimnobacterium” “Xihemonas phototrophica” “Xihecaenibacterium phototrophica” “Xihebacterium phototrophica” “Xihebacterium glacialis” “Xihebacterium aquatica” “Xihemicrobium phototrophica” “Xihemicrobium aquatica” “Kuafubacterium” “Xihebacterium” “Xihemicrobium” “Xihecaenimonas” “Xihelimnomonas” “Xihepedomonas” “Kuafuhalomonas” “Kuafucaenimonas”
Abstract
AbstractPhotosynthesis is a fundamental biogeochemical process, thought to be restricted to a few bacterial and eukaryotic phyla. However, understanding the origin and evolution of phototrophic organisms can be impeded and biased by the difficulties of cultivation. Here, we analyzed metagenomic datasets and found potential photosynthetic abilities encoded in the genomes of uncultivated bacteria within the phylum Myxococcota. A putative photosynthesis gene cluster encoding a type-II reaction cent

Multi-heme cytochrome-mediated extracellular electron transfer by the anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’

Citation
Zhang et al. (2023). Nature Communications 14 (1)
Names
Ca. Methanoperedens nitroreducens
Abstract
AbstractAnaerobic methanotrophic archaea (ANME) carry out anaerobic oxidation of methane, thus playing a crucial role in the methane cycle. Previous genomic evidence indicates that multi-heme c-type cytochromes (MHCs) may facilitate the extracellular electron transfer (EET) from ANME to different electron sinks. Here, we provide experimental evidence supporting cytochrome-mediated EET for the reduction of metals and electrodes by ‘Candidatus Methanoperedens nitroreducens’, an ANME acclimated to

Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut

Citation
Ye et al. (2023). Nature Communications 14 (1)
Names
Taurinivorans muris Ts Taurinivorans
Abstract
AbstractTaurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dep

New globally distributed bacterial phyla within the FCB superphylum

Citation
Gong et al. (2022). Nature Communications 13 (1)
Names
“Orphanbacterum longqiense” “Joyebacterota” “Arandabacteraceae” “Arandabacterota” “Arandabacterales” “Arandabacteria” “Orphanbacterum” “Arandabacterum bohaiense” “Blakebacterota” “Orphanbacteraceae” “Joyebacterum haimaense” “Blakebacterum guaymasense” “Orphanbacterales” “Joyebacterum” “Blakebacterum” “Orphanbacteria” “Joyebacteraceae” “Blakebacteraceae” “Orphanbacterota” “Joyebacterales” “Blakebacterales” “Arandabacterum” “Joyebacteria” “Blakebacteria”
Abstract
AbstractMicrobes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbact

Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota

Citation
Sheridan et al. (2022). Nature Communications 13 (1)
Names
“Lutacidiplasmatales” “Lutacidiplasma silvani” “Lutacidiplasma” “Lutacidiplasmataceae”
Abstract
AbstractThe Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) “Lutacidiplasmatales” due to their occurrence in various

An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea

Citation
Buessecker et al. (2022). Nature Communications 13 (1)
Names
Wolframiiraptor gerlachensis Ts Wolframiiraptor Wolframiiraptoraceae Benthortus lauensis Ts Geocrenenecus dongiae Ts Geocrenenecus arthurdayi Geocrenenecus huangii Terraquivivens ruidianensis Terraquivivens tengchongensis Terraquivivens yellowstonensis Benthortus Geocrenenecus Terraquivivens Terraquivivens tikiterensis Ts Wolframiiraptor sinensis Wolframiiraptor allenii
Abstract
AbstractTrace metals have been an important ingredient for life throughout Earth’s history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredox

Genomic diversity across the Rickettsia and ‘Candidatus Megaira’ genera and proposal of genus status for the Torix group

Citation
Davison et al. (2022). Nature Communications 13 (1)
Names
Ca. Megaira “Tisiphia”
Abstract
AbstractMembers of the bacterial genusRickettsiawere originally identified as causative agents of vector-borne diseases in mammals. However, manyRickettsiaspecies are arthropod symbionts and close relatives of ‘CandidatusMegaira’, which are symbiotic associates of microeukaryotes. Here, we clarify the evolutionary relationships between these organisms by assembling 26 genomes ofRickettsiaspecies from understudied groups, including the Torix group, and two genomes of ‘Ca. Megaira’ from various in

Bacterial filamentation as a mechanism for cell-to-cell spread within an animal host

Citation
Tran et al. (2022). Nature Communications 13 (1)
Names
“Bordetella atropi”
Abstract
AbstractIntracellular pathogens are challenged with limited space and resources while replicating in a single host cell. Mechanisms for direct invasion of neighboring host cells have been discovered in cell culture, but we lack an understanding of how bacteria directly spread between host cells in vivo. Here, we describe the discovery of intracellular bacteria that use filamentation for spreading between the intestinal epithelial cells of a natural host, the rhabditid nematode Oscheius tipulae.

Plant hairy roots enable high throughput identification of antimicrobials against Candidatus Liberibacter spp

Citation
Irigoyen et al. (2020). Nature Communications 11 (1)
Names
Liberibacter
Abstract
AbstractA major bottleneck in identifying therapies to control citrus greening and other devastating plant diseases caused by fastidious pathogens is our inability to culture the pathogens in defined media or axenic cultures. As such, conventional approaches for antimicrobial evaluation (genetic or chemical) rely on time-consuming, low-throughput and inherently variable whole-plant assays. Here, we report that plant hairy roots support the growth of fastidious pathogens like Candidatus Liberibac