An Overview on Nocardiopsis Species Originating From North African Biotopes as a Promising Source of Bioactive Compounds and In Silico Genome Mining Analysis of Three Sequenced Genomes.

Actinobacteria are renowned for their prolific production of diverse bioactive secondary metabolites. In recent years, there has been an increasing focus on exploring "rare" genera within this phylum for biodiscovery purposes, notably the Nocardiopsis genus, which will be the subject of the present study. Recognizing the absence of articles describing the research process of finding bioactive molecules from the genus Nocardiopsis in North African environments. We, therefore, present a historical overview of the discoveries of bioactive molecules of the genus Nocardiopsis originating from the region, highlighting their biological activities and associated reported molecules, providing a snapshot of the current state of the field, and offering insights into future opportunities and challenges for drug discovery. Additionally, we present a genome mining analysis of three genomes deposited in public databases that have been reported to be bioactive. A total of 36 biosynthetic gene clusters (BGCs) were identified, including those known to encode bioactive molecules. Notably, a substantial portion of the BGCs showed little to no similarity to those previously described, suggesting the possibility that the analyzed strains could be potential producers of new compounds. Further research on these genomes is essential to fully uncovering their biotechnological potential. Moving forward, we discuss the experimental designs adopted in the reported studies, as well as new avenues to guide the exploration of the Nocardiopsis genus in North Africa.

Selective isolation, antimicrobial screening and phylogenetic diversity of marine actinomycetes derived from the Coast of Bejaia City (Algeria), a polluted and microbiologically unexplored environment.

AIMS: The current study aimed to evaluate the occurrence of actinomycetes in the Coast of Bejaia City using selective isolation, as well as their bioactivity and phylogenitic diversity. METHODS AND RESULTS: Different selective media and methods were used, leading to the isolation of 103 actinomycete strains. The number of strains was influenced by isolation procedures and their interactions based on a three-way ANOVA and a post hoc Tukey test, which revealed that using M2 medium, dilution of samples followed by moderate heat treatment, and sampling at 10-20 m yielded the highest numbers of actinomycetes. The isolates were screened for their antimicrobial activity against human pathogenic microorganisms using agar and well diffusion methods. Of all the isolates, ten displayed activity against at least one Gram-positive bacterium, of which P21 showed the highest activity against Staphylococcus aureus, Methicillin-resistant S. aureus and Bacillus subtilis, with a diameter of 32, 28 and 25 mm respectively. Subsequently, active isolates were assigned to Streptomyces spp. and Nocardiopsis spp. based on 16S rRNA gene sequencing, including a putative new Streptomyces species (S3). The phenotypic characteristics of the P21 strain were determined, and interesting enzymatic capacities were shown. CONCLUSION: The recovery of actinomycetes along the Coast of Bejaia City was influenced by the isolation procedure. Ten strains displayed interesting antibacterial activity against Gram-positive bacteria, of which the P21 strain was selected as the most active strain. SIGNIFICANCE AND IMPACT OF THE STUDY: This work provides a new insight into the occurrence of actinobacteria in the Coast of Bejaia. It suggests also that polluted environments such as Bejaia Bay could provide access to interesting actinomycetes as sources of antibiotic leads.

Impact of IBD-Associated Dysbiosis on Bacterial Quorum Sensing Mediated by Acyl-Homoserine Lactone in Human Gut Microbiota.

Intestinal dysbiosis is a key feature in the pathogenesis of inflammatory bowel disease (IBD). Acyl-homoserine lactones (AHL) are bacterial quorum-sensing metabolites that may play a role in the changes in host cells-gut microbiota interaction observed during IBD. The objective of our study was to investigate the presence and expression of AHL synthases and receptor genes in the human gut ecosystem during IBD. We used an in silico approach, applied to the Inflammatory Bowel Disease Multi'omics Database comprising bacterial metagenomic and metatranscriptomic data from stools of patients with Crohn's disease (CD) (n = 50), ulcerative colitis (UC) (n = 27) and non-IBD controls (n = 26). No known putative AHL synthase gene was identified; however, several putative luxR receptors were observed. Regarding the expression of these receptor genes, the luxR gene from Bacteroides dorei was under-expressed in IBD patients (p = 0.02) compared to non-IBD patients, especially in CD patients (p = 0.02). In the dysbiosis situation, one luxR receptor gene from Bacteroides fragilis appeared to be over-expressed (p = 0.04) compared to that of non-dysbiotic patients. Targeting LuxR receptors of bacterial quorum sensing might represent a new approach to modulate the gut microbiota in IBD.

Characterization of N-Acyl Homoserine Lactones in Vibrio tasmaniensis LGP32 by a Biosensor-Based UHPLC-HRMS/MS Method.

Since the discovery of quorum sensing (QS) in the 1970s, many studies have demonstrated that Vibrio species coordinate activities such as biofilm formation, virulence, pathogenesis, and bioluminescence, through a large group of molecules called N-acyl homoserine lactones (AHLs). However, despite the extensive knowledge on the involved molecules and the biological processes controlled by QS in a few selected Vibrio strains, less is known about the overall diversity of AHLs produced by a broader range of environmental strains. To investigate the prevalence of QS capability of Vibrio environmental strains we analyzed 87 Vibrio spp. strains from the Banyuls Bacterial Culture Collection (WDCM911) for their ability to produce AHLs. This screening was based on three biosensors, which cover a large spectrum of AHLs, and revealed that only 9% of the screened isolates produced AHLs in the defined experimental conditions. Among these AHL-producing strains, Vibrio tasmaniensis LGP32 is a well-known pathogen of bivalves. We further analyzed the diversity of AHLs produced by this strain using a sensitive bioguided UHPLC-HRMS/MS approach (Ultra-High-Performance Liquid Chromatography followed by High-Resolution tandem Mass Spectrometry) and we identified C10-HSL, OH-C12-HSL, oxo-C12-HSL and C14:1-HSL as QS molecules. This is the first report that documents the production of AHL by Vibrio tasmaniensis LGP32.

Lichens as natural sources of biotechnologically relevant bacteria.

The search for microorganisms from novel sources and in particular microbial symbioses represents a promising approach in biotechnology. In this context, lichens have increasingly become a subject of research in microbial biotechnology, particularly after the recognition that a diverse community of bacteria other than cyanobacteria is an additional partner to the traditionally recognized algae-fungus mutualism. Here, we review recent studies using culture-dependent as well as culture-independent approaches showing that lichens can harbor diverse bacterial families known for the production of compounds of biotechnological interest and that several microorganisms isolated from lichens, in particular Actinobacteria and Cyanobacteria, can produce a number of bioactive compounds, many of them with biotechnological potential.

Review - Lichen-Associated Bacteria as a Hot Spot of Chemodiversity: Focus on Uncialamycin, a Promising Compound for Future Medicinal Applications.

This review presents the state of knowledge on the medicinal potential of bacteria associated with lichens. In fact, besides the classical symbiotic partners (photobiont and mycobiont) forming the lichen thallus, associated bacteria have been recently described as a third partner. Various studies demonstrated the diversity of these communities with a predominance of Alphaproteobacteria. Bacterial groups more relevant for secondary metabolite synthesis have also been revealed. This article summarizes studies reporting the abilities of these communities to produce metabolites with relevant bioactivities. The biotechnological interest of these bacteria for drug discovery is highlighted regarding the production of compounds with therapeutic potential. Special focus is given to the synthesis of the most promising compound, uncialamycin, a potent enediyne isolated from a Streptomyces sp. associated with Cladonia uncialis.

Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater.

A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115(T), was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115(T) was shown to belong to the Gammaproteobacteria, adjacent to members of the genera Marinicella, Arenicella and Kangiella, sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the Gammaproteobacteria. The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115(T) included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115(T) should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115(T) ( = CIP 110343(T) = DSM 25350(T)).

Integrated Metabolomic, Molecular Networking, and Genome Mining Analyses Uncover Novel Angucyclines From Streptomyces sp. RO-S4 Strain Isolated From Bejaia Bay, Algeria.

Multi-omic approaches have recently made big strides toward the effective exploration of microorganisms, accelerating the discovery of new bioactive compounds. We combined metabolomic, molecular networking, and genomic-based approaches to investigate the metabolic potential of the Streptomyces sp. RO-S4 strain isolated from the polluted waters of Bejaia Bay in Algeria. Antagonistic assays against methicillin-resistant Staphylococcus aureus with RO-S4 organic extracts showed an inhibition zone of 20 mm by using the agar diffusion method, and its minimum inhibitory concentration was 16 µg/ml. A molecular network was created using GNPS and annotated through the comparison of MS/MS spectra against several databases. The predominant compounds in the RO-S4 extract belonged to the angucycline family. Three compounds were annotated as known metabolites, while all the others were putatively new to Science. Notably, all compounds had fridamycin-like aglycones, and several of them had a lactonized D ring analogous to that of urdamycin L. The whole genome of Streptomyces RO-S4 was sequenced to identify the biosynthetic gene cluster (BGC) linked to these angucyclines, which yielded a draft genome of 7,497,846 bp with 72.4% G+C content. Subsequently, a genome mining analysis revealed 19 putative biosynthetic gene clusters, including a grincamycin-like BGC with high similarity to that of Streptomyces sp. CZN-748, that was previously reported to also produce mostly open fridamycin-like aglycones. As the ring-opening process leading to these compounds is still not defined, we performed a comparative analysis with other angucycline BGCs and advanced some hypotheses to explain the ring-opening and lactonization, possibly linked to the uncoupling between the activity of GcnE and GcnM homologs in the RO-S4 strain. The combination of metabolomic and genomic approaches greatly improved the interpretation of the metabolic potential of the RO-S4 strain.

Current and future chemical treatments to fight biodeterioration of outdoor building materials and associated biofilms: Moving away from ecotoxic and towards efficient, sustainable solutions.

All types of building materials are rapidly colonized by microorganisms, initially through an invisible and then later a visible biofilm that leads to their biodeterioration. Over centuries, this natural phenomenon has been managed using mechanical procedures, oils, or even wax. In modern history, many treatments such as high-pressure cleaners, biocides (mainly isothiazolinones and quaternary ammonium compounds) are commercially available, as well as preventive ones, such as the use of water-repellent coatings in the fabrication process. While all these cleaning techniques offer excellent cost-benefit ratios, their limitations are numerous. Indeed, building materials are often quickly recolonized after application, and microorganisms are increasingly reported as resistant to chemical treatments. Furthermore, many antifouling compounds are ecotoxic, harmful to human health and the environment, and new regulations tend to limit their use and constrain their commercialization. The current state-of-the-art highlights an urgent need to develop innovative antifouling strategies and the widespread use of safe and eco-friendly solutions to biodeterioration. Interestingly, innovative approaches and compounds have recently been identified, including the use of photocatalysts or natural compounds such as essential oils or quorum sensing inhibitors. Most of these solutions developed in laboratory settings appear very promising, although their efficiency and ecotoxicological features remain to be further tested before being widely marketed. This review highlights the complexity of choosing the adequate antifouling compounds when fighting biodeterioration and proposes developing case-to-case innovative strategies to raise this challenge, relying on integrative and multidisciplinary approaches.

In situ activity of NAC11-7 roseobacters in coastal waters off the Chesapeake Bay based on ftsZ expression.

Determining in situ growth rates for specific bacterioplankton is of critical importance to understanding their contributions to energy and matter flow in the Ocean. Quantifying expression of genes central to cell division is a plausible approach for obtaining these measurements. In order to test this approach's assumptions, a quantitative PCR assay targeting the cell division gene ftsZ in the ubiquitous NAC11-7 group of the Rhodobacterales order of marine bacteria was developed. ftsZ genes and their corresponding mRNAs were measured in diel in situ samples and in parallel on-deck incubations. Strong correlations between ftsZ expression and gene abundance (R-squared = 0.62) were observed in situ. Rapid changes in NAC11-7 ftsZ gene copies suggested that different populations from different water types were sampled with a significant positive correlation between ftsZ expression and water temperature (R-squared = 0.68, P < 0.001). An outlier to this trend occurred at a single time point (9:00), which was remarkably consistent with a concomitant peak in ftsZ expression in on-deck incubations, suggesting the possibility of synchronous population growth.

Primary production in a subtropical stratified coastal lagoon--contribution of anoxygenic phototrophic bacteria.

Anaerobic anoxygenic phototrophic bacteria can be found in the suboxic waters of shallow stratified coastal systems, and may play important roles in the total primary production of subtropical stratified coastal lagoons. We investigated the spatiotemporal variability of light CO(2) fixation and net oxygen production in the stratified Conceição Lagoon (Brazil) in summer and fall of 2007, as well as the contribution of bacteriochlorophyll a (BChl a)-containing bacteria to photosynthetically driven electron transfer. Both chlorophyll a (Chl a) and BChl a varied in space, while only BChl a varied in time (three-fold increase from summer to fall). In summer, net oxygen production and light CO(2) fixation were correlated, with both having higher rates with higher Chl a concentrations in the enclosed region of the lagoon. In fall, CO(2) fixation was decoupled from oxygen production. Denaturing gradient gel electrophoresis revealed that bacterial communities of oxic site 12 and suboxic site 33 formed one cluster, different from other oxic samples within the lagoon. In addition, BChl a/Chl a ratios at these sites were high, 40% and 45%, respectively. Light acted as the main factor controlling the BChl a concentration and CO(2) fixation rates. High turbidity within the enclosed area of the lagoon explained high BChl a and decoupling between CO(2) fixation and oxygen production in oxygenated waters. Contribution of purple sulfur bacteria to total bacterial density in suboxic waters was 1.2%, and their biomass contributed to a much higher percentage (12.2%) due to their large biovolume. Our results indicate a significant contribution of anaerobic anoxygenic bacteria to the primary production of the "dead zone" of Conceição Lagoon.

Eosinopenia <100/µL as a marker of active COVID-19: An observational prospective study.

OBJECTIVES: To analyse the diagnostic performance of eosinopenia, alone or combined with polymorphonuclear neutrophils (PMN) and/or lymphocytes, as a marker of active COVID-19 in patients hospitalized for suspicion of SARS-CoV-2 infection. METHODS: A prospective observational study including patients hospitalized for suspicion of COVID-19 in a COVID unit was performed from 20th March to 5th April 2020, in Perpignan, France. Patients for which there was a doubt upon diagnosis, who were recently under oral corticosteroids, had myeloid malignancy or human immunodeficient virus infection were excluded. SARS-CoV-2 detection was performed using an RT-PCR assay, from nasopharyngeal swab specimens. Complete blood count were performed for all patients. RESULTS: One-hundred and twenty-one patient were included: 57 patients were diagnosed with COVID-19, 64 patients were not. Eosinophil count was lower in the COVID-19 group (median: 0/µL versus 70/µL, p < 0.0001). To diagnose COVID-19, eosinopenia had a sensitivity of 89.5% and a specificity of 78.1% while lymphopenia's were 73.7% and 62.5% respectively. Using area under curve (AUC) of receiving operating characteristics (ROC) curves, eosinophil's optimal cut-off level was 10/µL, sensitivity and specificity were 86%, and 79.7% respectively. Regarding the eosinophil/PMN ratio, the optimal cut-off level was 3.344, sensitivity and specificity were 87.7% and 73.4% respectively. The AUC of lymphocyte/PMN ratio was significantly lower than eosinophil/PMN ratio's (0.621 versus 0.846, p = 0.0003). CONCLUSION: Eosinopenia - <10/µL - and eosinophil/PMN ratio are useful, low-cost, reproducible tools to help diagnose COVID-19, during an epidemic period, in a population of hospitalized patients admitted for suspicion of COVID-19.

A unique approach to monitor stress in coral exposed to emerging pollutants.

Metabolomic profiling of the hexacoral Pocillopora damicornis exposed to solar filters revealed a metabolomic signature of stress in this coral. It was demonstrated that the concentration of the known steroid (3ß, 5α, 8α) -5, 8-epidioxy- ergosta- 6, 24(28) - dien- 3- ol (14) increased in response to octocrylene (OC) and ethylhexyl salicylate (ES) at 50 µg/L. Based on the overall coral response, we hypothesize that steroid 14 mediates coral response to stress. OC also specifically altered mitochondrial function at this concentration and above, while ES triggered a stress/inflammatory response at 300 µg/L and above as witnessed by the significant increases in the concentrations of polyunsaturated fatty acids, lysophosphatidylcholines and lysophosphatidylethanolamines. Benzophenone-3 increased the concentration of compound 14 at 2 mg/L, while the concentration of stress marker remained unchanged upon exposition to the other solar filters tested. Also, our results seemed to refute earlier suggestions that platelet-activating factor is involved in the coral inflammatory response.

Insights into the Natural Defenses of a Coral Reef Fish Against Gill Ectoparasites: Integrated Metabolome and Microbiome Approach.

Understanding natural defense mechanisms against parasites can be a valuable tool for the development of innovative therapies. We have previously identified a butterflyfish species (Chaetodon lunulatus) that avoids gill monogenean parasites while living amongst closely related parasitized species. The metabolome and microbiome of several sympatric butterflyfish species from the island of Moorea (French Polynesia) were previously described. In this study, we used the previously generated datasets in an attempt to identify metabolites and bacteria potentially involved in parasite defense mechanisms. We investigated the interplay between the gill mucus metabolome and microbiome of the non-susceptible C. lunulatus versus sympatric butterflyfish species that were always found parasitized in the Central and Eastern Indo-Pacific. After observing significant differences between the metabolome and bacteria of susceptible versus non-susceptible fish, we obtained the discriminant metabolites and operational taxonomic units (OTUs) using a supervised analysis. Some of the most important discriminant metabolites were identified as peptides, and three new peptides derived from ß-subunit hemoglobin from C. lunulatus (CLHbß-1, CLHbß-2, and CLHbß-3) were purified, characterized and synthesized to confirm their structures. We also identified specific bacterial families and OTUs typical from low-oxygen habitats in C. lunulatus gill mucus. By using a correlation network between the two datasets, we found a Fusobacteriaceae strain exclusively present in C. lunulatus and highly correlated to the peptides. Finally, we discuss the possible involvement of these peptides and Fusobacteriaceae in monogenean avoidance by this fish species.

Near real-time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA-targeted DNA probes.

A sandwich hybridization assay (SHA) was developed to detect 16S rRNAs indicative of phylogenetically distinct groups of marine bacterioplankton in a 96-well plate format as well as low-density arrays printed on a membrane support. The arrays were used in a field-deployable instrument, the Environmental Sample Processor (ESP). The SHA employs a chaotropic buffer for both cell homogenization and hybridization, thus target sequences are captured directly from crude homogenates. Capture probes for seven of nine different bacterioplankton clades examined reacted specifically when challenged with target and non-target 16S rRNAs derived from in vitro transcribed 16S rRNA genes cloned from natural samples. Detection limits were between 0.10-1.98 and 4.43- 12.54 fmole ml(-1) homogenate for the 96-well plate and array SHA respectively. Arrays printed with five of the bacterioplankton-specific capture probes were deployed on the ESP in Monterey Bay, CA, twice in 2006 for a total of 25 days and also utilized in a laboratory time series study. Groups detected included marine alphaproteobacteria, SAR11, marine cyanobacteria, marine group I crenarchaea, and marine group II euryarchaea. To our knowledge this represents the first report of remote in situ DNA probe-based detection of marine bacterioplankton.

Development and application of quantitative-PCR tools for subgroups of the Roseobacter clade.

Specific SYBR green-based quantitative-PCR assays targeting conserved regions in the 16S-23S rRNA internal transcribed spacer regions were developed for five subgroups of the environmentally abundant and biogeochemically active Roseobacter clade of marine bacteria. The assays were applied to field samples demonstrating their utility in investigations of abundant Roseobacter group phylotypes in the environment.

BchY-based degenerate primers target all types of anoxygenic photosynthetic bacteria in a single PCR.

To detect anoxygenic bacteria containing either type 1 or type 2 photosynthetic reaction centers in a single PCR, we designed a degenerate primer set based on the bchY gene. The new primers were validated in silico using the GenBank nucleotide database as well as by PCR on pure strains and environmental DNA.

Genetic diversity and phenotypic plasticity of AHL-mediated Quorum sensing in environmental strains of Vibrio mediterranei.

N-Acyl homoserine lactone (AHL)-mediated Quorum sensing (QS) is one of the most studied social behavior among Proteobacteria. However, despite the current knowledge on QS-associated phenotypes such as bioluminescence, biofilm formation, or pathogenesis, the characterization of environmental factors driving QS in realistic ecological settings remains scarce. We investigated the dynamics of AHL and AHL-producing Vibrio among 840 isolates  collected fortnightly from the Salses-Leucate Mediterranean lagoon in spring and summer 2015 and 2016. Vibrio isolates were characterized by gyrB gene sequencing, Enterobacterial repetitive intergenic consensus polymerase chain reaction, and genome sequencing, and AHL production was investigated by a biosensors-based UHPLC-HRMS/MS approach. Our results revealed, for the first time, a succession of V. mediterranei isolates with different AHL production phenotypes over time and this dynamics was observed in a single genotype (average genomic nucleotide identity >99.9). A multivariate DistLM analysis revealed that 83.4% of the temporal variation of V. mediterranei QS phenotypes was explained by environmental variables. Overall, our results suggest that isolates of a single genotype are able to change their QS phenotypes in response to environmental conditions, highlighting the phenotypic plasticity of bacterial communication in the environment.

Evidence of a Large Diversity of N-acyl-Homoserine Lactones in Symbiotic Vibrio fischeri Strains Associated with the Squid Euprymna scolopes.

Vibrio fischeri possesses a complex AHL-mediated Quorum-sensing (QS) system including two pathways, LuxI/R (3-oxo-C6-HSL and C6-HSL) and AinS/R (C8-HSL), which are important for the regulation of physiological traits. Diverse QS-dependent functional phenotypes have been described in V. fischeri; however, AHL diversity is still underestimated. In the present study, we investigated AHL diversity in five symbiotic V. fischeri strains with distinct phenotypic properties using UHPLC-HRMS/MS. The results obtained (1) revealed an unexpectedly high diversity of signaling molecules, (2) emphasized the complexity of QS in V. fischeri, and (3) highlight the importance of understanding the specificity of AHL-mediated QS.

Low-diversity bacterial microbiota in Southern Ocean representatives of lanternfish genera Electrona, Protomyctophum and Gymnoscopelus (family Myctophidae).

Myctophids are among the most abundant mesopelagic teleost fishes worldwide. They are dominant in the Southern Ocean, an extreme environment where they are important both as consumers of zooplankton as well as food items for larger predators. Various studies have investigated myctophids diet, but no data is yet available regarding their associated microbiota, despite that the significance of bacterial communities to fish health and adaptation is increasingly acknowledged. In order to document microbiota in key fish groups from the Southern Ocean, the bacterial communities associated with the gut, fin, gills and light organs of members of six species within the three myctophid genera Electrona, Protomyctophum and Gymnoscopelus were characterized using a 16S rRNA-based metabarcoding approach. Gut communities display limited diversity of mostly fish-specific lineages likely involved in food processing. Fin and skin communities display diversity levels and compositions resembling more those found in surrounding seawater. Community compositions are similar between genera Electrona and Protomyctophum, that differ from those found in Gymnoscopelus and in water. Low abundances of potentially light-emitting bacteria in light organs support the hypothesis of host production of light. This first description of myctophid-associated microbiota, and among the first on fish from the Southern Ocean, emphasizes the need to extend microbiome research beyond economically-important species, and start addressing ecologically-relevant species.