Immunology

IntroductionCandidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date.MethodsIn this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics.ResultsUsing Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples.ConclusionThis study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.

AbstractMethanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.

AbstractCandidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.

Se identificaron nuevos haplotipos de Diaphorina citri también conocido como el psílido asiático de los cítricos, denominados DcitACC-1, DcitACC-2 y DcitACC-3. Los estudios se basaron en la amplificación de ADN del gen COI mitocondrial y se utilizaron individuos de diferentes zonas citrícolas del país, en algunas zonas productoras del país no se han realizado muestreos con anterioridad, específicamente en los municipios de Acatlán de Pérez, Oaxaca, Misantla y Tantoyuca, Veracruz y Huejutla, Hidalgo, por lo que se procedió a colectar insectos adultos sin distinción de género. El número de individuos de cada sitio colectado dependió de la disponibilidad de insectos en el lugar. Se obtuvieron en total 60 individuos colectados. La amplificación del ADN se realizó con los iniciadores específicos DCITRI COI-L y DCITRI COI-R, el producto de la reacción PCR se secuenció en el Instituto Potosino de Investigación Científica y Tecnológica, AC (IPICYT). Las secuencias obtenidas se compararon con las reportadas en el Genebank y se determinó que existe una línea matriz que corresponde a los haplotipos Dcit-01 y Dcit-04 con número de identificación FJ190300 y FJ190306 (Boykin, 2007). Se obtuvieron 22 secuencias que se analizaron con los programas Oligo analizer y Clustal Omega y se identificaron 11 secuencias iguales a los haplotipos Dcit-01 y Dcit-04. Los resultados mostraron 13 secuencias con diferencias en tres nucleótidos específicos: 61, 253 y 636, mismos que son reportados en este trabajo como nuevos haplotipos.

El objetivo de este trabajo fue identificar en el genoma de Candidatus Liberibacter asiaticus (CLas), proteínas de membrana externa con potencial para el desarrollo y optimización de un método de detección inmunoenzimático. El estudio se realizó durante 2019 y se utilizó el servidor web Predict Protein, así como las bases de datos HhPred/HhSearch y Pfam. Se detectaron 52 proteínas de membrana externa en el genoma completo de CLas, de las cuales, 11 no habían sido caracterizadas previamente. Los análisis predictivos realizados en la proteína B8Y674 generaron ocho posibles epítopos y cuatro de ellos evaluados experimentalmente en células B, mostraron porcentajes de identidad entre 80 a 90%. Se detectó a CLas mediante PCR-punto final a partir del ADN extraído de limón mexicano con síntomas de Huanglongbing utilizando iniciadores diseñados sobre la secuencia del gen Omp que codifica para la proteína B8Y674 y se registró 95% de identidad entre las secuencias generadas y secuencias de CLas previamente reportadas. Los resultados obtenidos nos permiten inferir que la proteína B8Y674 es un candidato potencial para ser utilizada en la detección inmunoenzimática de CLas.

AbstractMost prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.

AbstractAsgard archaea have recently been identified as the closest archaeal relatives of eukaryotes. Their ecology, and particularly their virome, remain enigmatic. We reassembled and closed the chromosome of Candidatus Odinarchaeum yellowstonii LCB_4, through long-range PCR, revealing CRISPR spacers targeting viral contigs. We found related viruses in the genomes of diverse prokaryotes from geothermal environments, including other Asgard archaea. These viruses open research avenues into the ecology and evolution of Asgard archaea.