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The distinction of CPR bacteria from other bacteria based on protein family content.

ABSTRACT: Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear. Here, we leveraged sequences from thousands of uncultivated organisms and identified protein families that co-occur in genomes, thus are likely foundational for lineage capacities. Protein family presence/absence patterns cluster CPR bacteria together, and away from all other bacteria and archaea, partly due to proteins without recognizable homology to proteins in other bacteria. Some are likely involved in cell-cell interactions and potentially important for episymbiotic lifestyles. The diversity of protein family combinations in CPR may exceed that of all other bacteria. Over the bacterial tree, protein family presence/absence patterns broadly recapitulate phylogenetic structure, suggesting persistence of core sets of proteins since lineage divergence. The CPR could have arisen in an episode of dramatic but heterogeneous genome reduction or from a protogenote community and co-evolved with other bacteria.

SUBMITTER: Meheust R

PROVIDER: S-EPMC6744442 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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The distinction of CPR bacteria from other bacteria based on protein family content.

Méheust Raphaël R Burstein David D Castelle Cindy J CJ Banfield Jillian F JF

Nature communications 20190913 1

Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear. Here, we leveraged sequences from thousands of uncultivated organisms and identified protein families that co-occur in genomes, thus are likely foundational for lineage capacities. Protein family presence/absence patterns cluster CPR bacteria together, and away from all other bacteria and archaea, partly due to proteins without recogni ...[more]

PMID: 31519891

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Project description:BACKGROUND:The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges. RESULTS:Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1 µm filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 µm fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 µm fractions. On average, Patescibacteria enriched in the smaller 0.1 µm filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2 µm fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota). CONCLUSION:Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to attach multiple hosts just long enough to loot or exchange supplies.

Project description:Cardiopulmonary resuscitation (CPR) corrupts the morphology of the electrocardiogram (ECG) signal, resulting in an inaccurate automated external defibrillator (AED) rhythm analysis. Consequently, most current AEDs prohibit CPR during the rhythm analysis period, thereby decreasing the survival rate. To overcome this limitation, we designed a condition-based filtering algorithm that consists of three stop-band filters which are turned either 'on' or 'off' depending on the ECG's spectral characteristics. Typically, removing the artifact's higher frequency peaks in addition to the highest frequency peak eliminates most of the ECG's morphological disturbance on the non-shockable rhythms. However, the shockable rhythms usually have dynamics in the frequency range of (3-6) Hz, which in certain cases coincide with CPR compression's harmonic frequencies, hence, removing them may lead to destruction of the shockable signal's dynamics. The proposed algorithm achieves CPR artifact removal without compromising the integrity of the shockable rhythm by considering three different spectral factors. The dataset from the PhysioNet archive was used to develop this condition-based approach. To quantify the performance of the approach on a separate dataset, three performance metrics were computed: the correlation coefficient, signal-to-noise ratio (SNR), and accuracy of Defibtech's shock decision algorithm. This dataset, containing 14 s ECG segments of different types of rhythms from 458 subjects, belongs to Defibtech commercial AED's validation set. The CPR artifact data from 52 different resuscitators were added to artifact-free ECG data to create 23,816 CPR-contaminated data segments. From this, 82% of the filtered shockable and 70% of the filtered non-shockable ECG data were highly correlated (>0.7) with the artifact-free ECG; this value was only 13 and 12% for CPR-contaminated shockable and non-shockable, respectively, without our filtering approach. The SNR improvement was 4.5 ± 2.5 dB, averaging over the entire dataset. Defibtech's rhythm analysis algorithm was applied to the filtered data. We found a sensitivity improvement from 67.7 to 91.3% and 62.7 to 78% for VF and rapid VT, respectively, and specificity improved from 96.2 to 96.5% and 91.5 to 92.7% for normal sinus rhythm (NSR) and other non-shockables, respectively.

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The distinction of CPR bacteria from other bacteria based on protein family content.

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The distinction of CPR bacteria from other bacteria based on protein family content.

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