The repeated failures reported in cultivating some microbial lineages are a major challenge in microbial ecology and probably linked, in the case of Frankia microsymbionts to atypical patterns of auxotrophy. Comparative genomics of the so far uncultured cluster-2 Candidatus Frankia datiscae Dg1, with cultivated Frankiae has revealed genome reduction, but no obvious physiological impairments. A direct physiological assay on nodule tissues from Coriaria myrtifolia infected with a closely-related strain permitted the identification of a requirement for alkaline conditions. A high pH growth medium permitted the recovery of a slow-growing actinobacterium. The strain obtained, called BMG5.1, has short hyphae, produced diazovesicles in nitrogen-free media, and fulfilled Koch’s postulates by inducing effective nodules on axenically grown Coriaria spp. and Datisca glomerata. Analysis of the draft genome confirmed its close proximity to the Candidatus Frankia datiscae Dg1 genome with the absence of 38 genes (trehalose synthase, fumarylacetoacetase, etc) in BMG5.1 and the presence of 77 other genes (CRISPR, lanthionine synthase, glutathione synthetase, catalase, Na+/H+ antiporter, etc) not found in Dg1. A multi-gene phylogeny placed the two cluster-2 strains together at the root of the Frankia radiation.

The Geodermatophilaceae are unique model systems to study the ability to thrive on or within stones and their proteogenomes (referring to the whole protein arsenal encoded by the genome) could provide important insight into their adaptation mechanisms. Here we report the detailed comparative genome analysis of Blastococcus saxobsidens (Bs), Modestobacter marinus (Mm) and Geodermatophilus obscurus (Go) isolated respectively from the interior and the surface of calcarenite stones and from desert sandy soils. The genome-scale analysis of Bs, Mm and Go illustrates how adaptation to these niches can be achieved through various strategies including 'molecular tinkering/ opportunism' as shown by the high proportion of lost, duplicated or horizontally transferred genes and ORFans. Using high-throughput discovery proteomics, the three proteomes under unstressed conditions were analyzed, highlighting the most abundant biomarkers and the main protein factors. Proteomic data corroborated previously demonstrated stone-related ecological distribution. For instance, these data showed starvation-inducible, biofilm-related and DNA-protection proteins as signatures of the microbes associated with the interior, surface and outside of stones, respectively.

BACKGROUND Zinc supplementation has been considered one of the potential therapies for coronavirus disease-19 (COVID-19). We aimed to examine zinc efficacy in adult patients with COVID-19 infection. METHODS We conducted a prospective, randomized, double-blind, placebo-controlled, multicenter trial. Patients tested positive for COVID-19 without end organ failure were randomized to oral zinc (n = 231) or matching placebo (n = 239) for 15 days. The primary combined outcome was death due to COVID-19 or ICU admission within 30 days after randomization. Secondary outcomes included length of hospital stay for inpatients and duration of COVID-19 symptoms with COVID-19 related hospitalization for outpatients. FINDINGS One hundred ninety patients (40.4%) were ambulatory and 280 patients (59.6%) were hospitalized. Mortality at 30-day was 6.5% in Zinc group and 9.2% in Placebo group [odds ratio (OR) 0.70 (0.37-1.32)]; ICU admission rate was respectively 5.2% and 11.3% [OR 0.46 (0.23-0.88)]. Combined outcome was lower in zinc group compared to placebo group [OR 0.62 (0.38-0.99)]. Consistent results were observed in prespecified subgroups of patients with age < 65 years, those with comorbidity, and those who needed oxygen therapy at baseline. Length of hospital stay was shorter in zinc group compared to placebo group [difference 3.5 days, 95% CI (2.76-4.23)] in inpatients group; duration of COVID-19 symptoms decreased with zinc treatment compared to placebo in outpatients [difference 1.9 days, 95% CI (0.62-2.6)]. No severe adverse events were observed during the study. INTERPRETATION Our results showed that in COVID-19 patients, oral zinc can decrease 30-day death and ICU admission rate and can shorten symptoms duration.

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A novel Gram-reaction-positive, aerobic actinobacterium, tolerant to mitomycin C, heavy metals, metalloids, hydrogen peroxide, desiccation, and ionizing- and UV-radiation, designated G18T, was isolated from dolomitic marble collected from outcrops in Samara (Namibia). The growth range was 15–35°C, at pH 5.5–9.5 and in presence of 1% NaCl, forming greenish-black coloured colonies on GYM Streptomyces agar. Chemotaxonomic and molecular characteristics of the isolate matched those described for other representatives of the genus Geodermatophilus. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diaminoacid. The main phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, and small amount of diphosphatidylglycerol. MK-9(H4) was the dominant menaquinone and galactose was detected as diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids iso-C16:0 and iso-C15:0 and the unsaturated C17:1 ω8c and C16:1 ω7c. The 16S rRNA gene showed 97.4–99.1% sequence identity with the other representatives of genus Geodermatophilus. Based on phenotypic results and 16S rRNA gene sequence analysis, strain G18T is proposed to represent a novel species, Geodermatophilus poikilotrophi. Type strain is G18T (= DSM 44209T = CCUG 63018T). The INSDC accession number is HF970583. The novel R software package was used to compute the lethal doses with confidence intervals resulting from tolerance experiments.

Summary Stone surfaces are extreme environments that support microbial life. This microbial growth occurs despite unfavourable conditions associated with stone including limited sources of nutrients and water, high pH and exposure to extreme variations in temperature, humidity and irradiation. These stone‐dwelling microbes are often resistant to extreme environments including exposure to desiccation, heavy metals, UV and Gamma irradiation. Here, we report on the effects of climate and stone geochemistry on microbiomes of Roman stone ruins in North Africa. Stone microbiomes were dominated by Actinobacteria, Cyanobacteria and Proteobacteria but were heavily impacted by climate variables that influenced water availability. Stone geochemistry also influenced community diversity, particularly through biologically available P, Mn and Zn. Functions associated with photosynthesis and UV protection were enriched in the metagenomes, indicating the significance of these functions for community survival on stones. Core members of the stone microbial communities were also identified and included Geodermatophilaceae, Rubrobacter, Sphingomonas and others. Our research has helped to expand the understanding of stone microbial community structure and functional capacity within the context of varying climates, geochemical properties and stone conditions.

A novel, non-motile, coccoid, Gram-stain-positive actinobacterium, designated BMG 862, was isolated from a marble sample collected from the Bulla Regia monument, Northern Tunisia. Its taxonomic position was determined using a polyphasic approach. Results from chemotaxonomic analyses showed MK-9(H4), MK-8(H4) and MK-9(H2) as the predominant menaquinones. The major polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, hydroxy-phosphatidylethanolamine and three unidentified phospholipids. The fatty acids consisted of significant amounts (≥10 %) of iso-C16 : 0, C17 : 1ω8c, iso-C15 : 0 and C16 : 1ω7c. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparisons showed that strain BMG 862 belongs to the genus Blastococcus, being most closely related to Blastococcus saxobsidens (=DSM 44509) (99.5 %) and Blastococcus capsensis (=DSM 46835=CECT 8876) (99.3 %). The genomic DNA G+C content of the organism was 74.7 mol%. Results of DNA-DNA hybridization and physiological tests allowed differentiation of strain BMG 862 from related species. The strain was also characterized by its ability to hydrolyse xanthine. On the basis of phenotypic and molecular characteristics, strain BMG 862 (=DSM 46842=CECT 8884) represents the type strain of a novel species of the genus Blastococcus, for which the name Blastococcus xanthinilyticus sp. nov. is proposed.

Frankia sp. strain BMG5.30 was isolated from root nodules of a Coriaria myrtifolia seedling on soil collected in Tunisia and represents the second cluster 2 isolate. Frankia sp. strain BMG5.30 was able to re-infect C. myrtifolia generating root nodules. Here, we report its 5.8-Mbp draft genome sequence with a G + C content of 70.03% and 4509 candidate protein-encoding genes.