Genomic and metagenomic insights into the microbial community of a thermal spring

Isolation of Sphingopyxis kveilinensis sp. nov., a Potential Antibiotic-Degrading Bacterium, from a Karst Wetland

A Gram-stain-negative, aerobic, mesophilic, motile, rod-shaped bacterium, designated strain TUF1T, was isolated from a karst wetland in south-west China. It was demonstrated to be capable of growing on plates containing oxytetracycline, streptomycin, or ofloxacin as the sole carbon source. Phylogenetic analysis of the 16S rRNA gene sequence revealed that this organism belongs to the genus Sphingopyxis and is closely related to S. chilensis S37T (99.17%) and S. alaskensis RB2256T (99.12%). The orthologous average nucleotide identity values (OrthoANIu, 84.42% and 87.53%) and digital DNA-DNA hybridization values (dDDH, 41.7% and 48.9%) between strain TUF1T and its close relatives were all below the standard recommended threshold values for species discrimination. The genomic DNA G + C content was determined to be 64.7%. The predominant cellular fatty acids were identified as summed feature 8 (C18:1ω7c and/or C18:1ω6c) and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The major polar lipids found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, and sphingoglycolipid. The sole respiratory quinone present was ubiquinone Q10. Based on the phylogenetic, biochemical, physiological, and chemotaxonomic analyses, strain TUF1T represents a novel species of the genus Sphingopyxis. The designation "Sphingopyxis kveilinensis sp. nov." is proposed as the name for this novel species, and the strain TUF1T (= CGMCC1.62043 T = JCM36394T) is designated as the type strain.

Characterization of thermostable carboxypeptidase from high-altitude hot spring metagenome

This study explored the metagenome of the Pir Panjal Hot Spring (PPHS) to identify thermostable hydrolases. The carboxypeptidase (CarP) gene was successfully amplified and cloned into Escherichia coli DH5-α cells, followed by expression in E. coli BL21-DE3 cells. The CarP enzyme was comprehensively characterized in vitro. Sequencing analysis revealed an open reading frame encoding a functional protein of 504 amino acids, with a molecular weight of 58.65 kDa and an isoelectric point of 4.81. The CarP protein was purified using Ni-His affinity chromatography, and the experimental molecular weight matched in silico predictions. The enzyme exhibited significant thermostability and alkaliphilic properties, with optimal activity at 70 °C and pH 10.0. Additionally, the presence of Zn+2 ions at concentrations of 5 and 10 mmol/L enhanced protease activity by 1.4 and 1.5-fold, respectively. This study reports the discovery of a novel, multifunctional, and thermostable CarP from hot-spring metagenomes. The enzyme's stability against high temperatures, metal ions, surfactants, and inhibitors, along with its specific substrate interactions, highlights its potential for various biotechnological applications.

Genomic analysis of the class Phycisphaerae reveals a versatile group of complex carbon-degrading bacteria

Bacteria of the phylum Planctomycetota have received much attention over the years due to their unique cell biology and potential for biotechnological application. Within the phylum, bacteria of the class Phycisphaerae have been found in a multitude of environmental datasets. However, only a few species have been brought into culture so far and even enrichments are scarce. Therefore, very little is known about their lifestyle, which has hindered efforts to estimate their environmental relevance. Here, we analysed all medium- and high-quality Phycisphaerae genomes represented in the genome taxonomy database to learn more about their physiology. We combined automatic and manual annotation efforts to provide a bird's eye view of their diverse energy metabolisms. Contrasting previous reports, we did not find indications for the presence of genes for anaerobic ammonium oxidation in any Phycisphaerae genome. Instead, we found that many members of this class are adapted to a facultative anaerobic or strictly fermentative lifestyle and may be specialized in the breakdown of carbon compounds produced by other organisms. Based on these findings, we provide a practical overview of organic carbon substrates predicted to be utilized by Phycisphaerae families.

Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode

Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.

Natural Changbai mineral water reduces obesity risk through regulating metabolism and gut microbiome in a hyperuricemia male mouse model

Access to clean and safe drinking water is essential. This study aimed to evaluate the effect of a kind of small molecular natural mineral water, C-cell mineral water on hyperuricemia male mice metabolism condition. A 13-week drinking water intervention study was conducted in Uox-knockout mice (KO). The hepatic metabolite profiling and related genes expression were detected by UPLC-TOF-MS and transcriptomic, and the gut microbiota of KO mice was determined by metagenomics sequencing. Results showed that the body weight of mice fed with C-cell water was remarkably lower than that of control mice on D 77 and D 91. Hepatic metabolite profiling revealed a shift in the pathway of glycine, serine and threonine metabolism, pantothenate and CoA biosynthesis, and biosynthesis of cofactors in KO mice fed with C-cell mineral water. Increased energy metabolism levels were related to increased hepatic expression of genes responsible for coenzyme metabolism and lipid metabolism. Gut microbiota was characterized by increasing activity of beneficial bacteria Blautia, and reducing activity of pathobiont bacteria Parasutterella. These genera have been reported to be associated with obesity. Small molecular mineral-rich natural water ingestion regulates metabolism and gut microbiota, protecting against obesity induced by hyperuricemia through mediating a microbiota-liver axis.

Metagenome-assembled genomes reveal carbohydrate degradation and element metabolism of microorganisms inhabiting Tengchong hot springs, China

A hot spring is a distinctive aquatic environment that provides an excellent system to investigate microorganisms and their function in elemental cycling processes. Previous studies of terrestrial hot springs have been mostly focused on the microbial community, one special phylum or category, or genes involved in a particular metabolic step, while little is known about the overall functional metabolic profiles of microorganisms inhabiting the terrestrial hot springs. Here, we analyzed the microbial community structure and their functional genes based on metagenomic sequencing of six selected hot springs with different temperature and pH conditions. We sequenced a total of 11 samples from six hot springs and constructed 162 metagenome-assembled genomes (MAGs) with completeness above 70% and contamination lower than 10%. Crenarchaeota, Euryarchaeota and Aquificae were found to be the dominant phyla. Functional annotation revealed that bacteria encode versatile carbohydrate-active enzymes (CAZYmes) for the degradation of complex polysaccharides, while archaea tend to assimilate C1 compounds through carbon fixation. Under nitrogen-deficient conditions, there were correspondingly fewer genes involved in nitrogen metabolism, while abundant and diverse set of genes participating in sulfur metabolism, particularly those associated with sulfide oxidation and thiosulfate disproportionation. In summary, archaea and bacteria residing in the hot springs display distinct carbon metabolism fate, while sharing the common energy preference through sulfur metabolism. Overall, this research contributes to a better comprehension of biogeochemistry of terrestrial hot springs.

Effects of Comano Spring Water-derived Bacterial Lysates on Skin Regeneration: An Ex-vivo Study

BACKGROUND/AIM

A native non-pathogenic bacterial microflora was identified in Comano (TN, Italy) spring water. The aim of this study was to investigate the regenerative effects of some of the bacterial lysates extracted from this water in a human ex-vivo skin experimental wound model.

MATERIALS AND METHODS

Bacterial lysates were extracted from four new isolates: lysate 1 (L1) - closest relative Rudaea cellulosilytica, phylum Proteobacteria; lysate 2 (L2) - closest relative Mesorhizobium erdmanii, phylum Proteobacteria; lysate 3 (L3) - closest relative Herbiconiux ginseng, phylum Actinobacteria; lysate 4 (L4) - closest relative Fictibacillus phosphorivorans, phylum Firmicutes. Their regenerative effects were investigated in a human ex-vivo skin experimental wound healing model at 3 (T1), 5 (T2), and 10 days (T3).

RESULTS

The samples cultured with the L2 lysate displayed both an earlier and complete restoration of all the skin layers and their features were the closest to the normal skin. The regenerated epidermis demonstrated a complete maturation as the normal epidermis. The papillary dermis appeared mature, and the reticular dermis displayed both collagen and elastic fibres regularly parallel to the skin surface. An anti-inflammatory effect was displayed by the L1 lysate, but this action did not constitute a regenerative effect, suggesting that pathways for inflammation and regeneration might be different.

CONCLUSION

The therapeutic power of spring waters is not exclusively related to their mineral composition, but it may also be attributable to their native non-pathogenic bacterial microflora.

Thermal Therapy Modulation of the Psoriasis-Associated Skin and Gut Microbiome

INTRODUCTION

Psoriasis is a systemic immune-mediated disease primarily manifesting as skin redness and inflammation. Balneotherapy proved to be a successful non-pharmacological option to reduce the skin areas affected by the disease, but the specific mechanisms underlying this effect have not been elucidated yet. Here we test the hypothesis that the effect of thermal treatments on psoriatic lesions could be partially mediated by changes in the resident microbial population, i.e., the microbiome.

METHODS

In this study, we enrolled patients with psoriasis and monitored changes in their skin and gut microbiome after a 12-bath balneotherapy course with a combination of 16S rRNA amplicon sequencing and metagenomics. Changes in the resident microbiome were then correlated with thermal therapy outcomes evaluated as changes in Psoriasis Area and Severity Index (PASI) and Body Surface Area index (BSA).

RESULTS

The amplicon sequencing analysis of the skin microbiome showed that after thermal treatment the microbiome composition of affected areas improved to approach that typical of unaffected skin. We moreover identified some low-abundance bacterial biomarkers indicative of disease status and treatment efficacy, and we showed via metagenomic sequencing that thermal treatments and thermal water drinking affect the fecal microbiome to host more species associated with favorable metabolic health.

CONCLUSIONS

Changes in lower-abundance microbial taxa presence and abundance could be the basis for the positive effect of thermal water treatment and drinking on the cutaneous and systemic symptomatology of psoriasis.

The Effects of Lakitelek Thermal Water and Tap Water on Skin Microbiome, a Randomized Control Pilot Study

The beneficial effects of balneotherapy have been proven by numerous clinical studies on locomotor disorders. To date, there is only scant data on changes in the microbiome system of the skin during balneotherapy. The aim of this study was to compare the effects of thermal water and tap water on the skin’s microbiome in healthy volunteers. 30 healthy female volunteers participated in the study. The experimental group (of 15 women) spent 30-min 10 times, in Gabriella Spring’s thermal baths (i.e., mineral water containing sodium hydrogen carbonate).The controlled group (15 women) had the same, but in tap water. The results of this study have proven that there is a difference in the influencing effects of tap water and medicinal water on the microbiome of the skin. After bathing in the thermal water of Lakitelek, Deinococcus increased significantly at the genus level, and the tendency for Rothia mucilaginosa bacteria also increased. At the species level, Rothia mucilaginosa increased significantly, while Paracoccus aminovorans and the tendency for Paracoccus marcusii decreased. When the values of the two trial groups after bathing at the genus level were compared, Rothia bacteria increased significantly, while Haemophilus tended to increase, Pseudomonas tended to decrease, Neisseria tended to increase significantly, and Flavobacterium tended to decrease. At the species level, Geobacillus vulcani decreased significantly, and the tendency for Burkholderia gladioli decreased. The growth of Rothia mucilaginosa and the decrease in the tendency of Paracoccus, Pseudomonas, Flavobacteroium, and Burkholderia gladioli confirm the beneficial effect of balneotherapy. In this study, trends are represented by the uncorrected p value. The main result was that the thermal water changed certain bacteria of the skin, both on the genus and species levels, but there were no significant changes in the tap water used, either at the genus or species level. We first compared the worlds of thermal water and tap water’s microbiome systems. The thermal water decreased the number of certain inflammatory infectious agents and could enhance some of their positive effects, which have been proven at the molecular level. Our results can provide an important clue in the treatment of certain skin diseases. The research of the skin microbiome during balneotherapy can be one of the most intriguing and exciting topics of the future and can bring us closer to understanding the mechanism of action of balneotherapy.

Post-monsoon seasonal variation of prokaryotic diversity in solfataric soil from the North Sikkim hot spring

The solfataric soil sediments of the hot springs of Sikkim located at Yume Samdung and Lachen valley were studied for deciphering the bacterial diversity. The main aim here is to present a comparative study and generate a baseline data on the post-monsoon seasonal variation for the months of October and December, analyzed through 16S rRNA V3-V4 amplicon sequencing. The results have shown that there is not much variation at phylum level in the month of October in all the three hot springs such as New Yume Samdung (NYS), Old Yume Samdung (OYS), and Tarum (TAR) hot spring. The abundant phyla mainly present were Firmicutes, followed by Proteobacteria, Actinobacteria, and Bacteroidetes. Similarly, in the month of December, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were prevalent; however, the percent relative abundance of these phyla in the month of December is relatively less. Besides this decrease in percent abundance, it was interestingly seen that relatively more phyla were found contributing towards the bacterial diversity in the month of December. Similar to phylum level, at genus level, there was not much variation seen among various prevalent genera of the three studied hot springs in both months. The major genera prevalent in both months among all the three hot springs were followed by Bacillus, Desulfotomaculum, Lactobacillus, and Paenibacillus. A similar trend was also seen at gene level that relative abundance of various genera was higher in the month of October but more genera were found to be contributing towards bacterial diversity in the month of December. Few distinct genera were found to be more abundant in the month of December such as Rhodopirellula and Blastopirellula. The results may conclude that there is not much variation in the abundance and type of bacterial communities during the post-monsoon season in the month of October and December. However, this may be assumed that there is the accumulation or increase in the bacterial communities during the winter (relatively higher temperature among hot springs) and may favor few mesophilic and more thermophilic communities as well.

Culturomics of Bacteria from Radon-Saturated Water of the World's Oldest Radium Mine

Balneotherapeutic water springs, such as those with thermal, saline, sulfur, or any other characteristics, have recently been the subject of phylogenetic studies with a closer focus on the description and/or isolation of phylogenetically novel or biotechnologically interesting microorganisms. Generally, however, most such microorganisms are rarely obtained in pure culture or are even, for now, unculturable under laboratory conditions. In this culture-dependent study of radioactive water springs of Jáchymov (Joachimstahl), Czech Republic, we investigated a combination of classical cultivation approaches with those imitating sampling source conditions. Using these environmentally relevant cultivation approaches, over 1,000 pure cultures were successfully isolated from 4 radioactive springs. Subsequent dereplication yielded 121 unique taxonomic units spanning 44 genera and 9 taxonomic classes, ~10% of which were identified as hitherto undescribed taxa. Genomes of the latter were sequenced and analyzed, with a special focus on endogenous defense systems to withstand oxidative stress and aid in radiotolerance. Due to their origin from radioactive waters, we determined the resistance of the isolates to oxidative stress. Most of the isolates were more resistant to menadione than the model strain Deinococcus radiodurans DSM 20539T. Moreover, isolates of the Deinococcacecae, Micrococcaceae, Bacillaceae, Moraxellaceae, and Pseudomonadaceae families even exhibited higher resistance in the presence of hydrogen peroxide. In summary, our culturomic analysis shows that subsurface water springs contain diverse bacterial populations, including as-yet-undescribed taxa and strains with promising biotechnological potential. Furthermore, this study suggests that environmentally relevant cultivation techniques increase the efficiency of cultivation, thus enhancing the chance of isolating hitherto uncultured microorganisms. IMPORTANCE The mine Svornost in Jáchymov (Joachimstahl), Czech Republic is a former silver-uranium mine and the world's first and for a long time only radium mine, nowadays the deepest mine devoted to the extraction of water which is saturated with radon and has therapeutic benefits given its chemical properties. This healing water, which is approximately 13 thousand years old, is used under medical supervision for the treatment of patients with neurological and rheumatic disorders. Our culturomic approach using low concentrations of growth substrates or the environmental matrix itself (i.e., water filtrate) in culturing media combined with prolonged cultivation time resulted in the isolation of a broad spectrum of microorganisms from 4 radioactive springs of Jáchymov which are phylogenetically novel and/or bear various adaptive or coping mechanisms to thrive under selective pressure and can thus provide a wide spectrum of capabilities potentially exploitable in diverse scientific, biotechnological, or medical disciplines.

Genome-centric insight into metabolically active microbial population in shallow-sea hydrothermal vents

BACKGROUND

Geothermal systems have contributed greatly to both our understanding of the functions of extreme life and the evolutionary history of life itself. Shallow-sea hydrothermal systems are ecological intermediates of deep-sea systems and terrestrial springs, harboring unique and complexed ecosystems, which are well-lit and present physicochemical gradients. The microbial communities of deep-sea and terrestrial geothermal systems have been well-studied at the population genome level, yet little is known about the communities inhabiting the shallow-sea hydrothermal systems and how they compare to those inhabiting other geothermal systems.

RESULTS

Here, we used genome-resolved metagenomic and metaproteomic approaches to probe into the genetic potential and protein expression of microorganisms from the shallow-sea vent fluids off Kueishantao Island. The families Nautiliaceae and Campylobacteraceae within the Epsilonbacteraeota and the Thiomicrospiraceae within the Gammaproteobacteria were prevalent in vent fluids over a 3-year sampling period. We successfully reconstructed the in situ metabolic modules of the predominant populations within the Epsilonbacteraeota and Gammaproteobacteria by mapping the metaproteomic data back to metagenome-assembled genomes. Those active bacteria could use the reductive tricarboxylic acid cycle or Calvin-Benson-Bassham cycle for autotrophic carbon fixation, with the ability to use reduced sulfur species, hydrogen or formate as electron donors, and oxygen as a terminal electron acceptor via cytochrome bd oxidase or cytochrome bb3 oxidase. Comparative metagenomic and genomic analyses revealed dramatic differences between submarine and terrestrial geothermal systems, including microbial functional potentials for carbon fixation and energy conversion. Furthermore, shallow-sea hydrothermal systems shared many of the major microbial genera that were first isolated from deep-sea and terrestrial geothermal systems, while deep-sea and terrestrial geothermal systems shared few genera.

CONCLUSIONS

The metabolic machinery of the active populations within Epsilonbacteraeota and Gammaproteobacteria at shallow-sea vents can mirror those living at deep-sea vents. With respect to specific taxa and metabolic potentials, the microbial realm in the shallow-sea hydrothermal system presented ecological linkage to both deep-sea and terrestrial geothermal systems. Video Abstract.

Microbiome characterization of alpine water springs for human consumption reveals site- and usage-specific microbial signatures

The microbiome of water springs is gaining increasing interest, especially in water intended for human consumption. However, the knowledge about large-scale patterns in water springs microbiome is still incomplete. The presence of bacteria in water sources used for human consumption is a major concern for health authorities; nonetheless, the standard microbiological quality checks are focused only on pathogenic species and total microbial load. Using 16S rRNA high throughput sequencing, we characterized the microbiome from 38 water springs in Trentino (Northern Italy) for 2 consecutive years in order to gain precious insights on the microbiome composition of these unexplored yet hardly exploited environments. The microbiological studies were integrated with standard measurements of physico-chemical parameters performed by the Provincial Office for Environmental Monitoring in order to highlight some of the dynamics influencing the microbial communities of these waters. We found that alpha diversity showed consistent patterns of variation overtime, and showed a strong positive correlation with the water nitrate concentration and negatively with fixed residue, electrical conductivity, and calcium concentration. Surprisingly, alpha diversity did not show any significant correlation with neither pH nor temperature. We found that despite their remarkable stability, different water springs display different coefficients of variation in alpha diversity, and that springs used for similar purposes showed similar microbiomes. Furthermore, the springs could be grouped according to the number of shared species into three major groups: low, mid, and high number of shared taxa, and those three groups of springs were consistent with the spring usage. Species belonging to the phyla Planctomycetes and Verrucomicrobia were prevalent and at relatively high abundance in springs classified as low number of shared species, whereas the phylum Lentisphaerae and the Candidate Phyla radiation were prevalent at higher abundance in the mineral and potable springs. The present study constitutes an example for standard water spring monitoring integrated with microbial community composition on a regional scale, and provides information which could be useful in the design and application of future water management policies in Trentino.

Geochemical and microbiological profiles in hydrothermal extreme acidic environments (Pisciarelli Spring, Campi Flegrei, Italy)

Although terrestrial hydrothermal systems are considered among the most fascinating environments, how their unique and extreme conditions can affect microorganisms selection and the role in biogeochemical cycles has not yet been well elucidated. A combined geochemical and microbiological exploration in waters and sediments from ten sampling points along a sharp temperature gradient (15-90 °C) within an extremely acidic hydrothermal system (Pisciarelli Spring, Campi Flegrei area, southern Italy) displayed how hydrothermal fluids influence the microbial dynamics. This area was characterized by high levels of reduced gaseous species (e.g. H2S, H2, CH4, CO), and very low pH values (<2.3). Thermodynamic calculations revealed a high microbial catabolic potential in oxidation/reduction reactions of N-, S-, and Fe-bearing species. Overall, an increase of the archaeal/bacterial abundance ratio was observed by decreasing temperature and pH values. In particular, Archaea and Bacteria were present in almost equal cell abundance (up to 1.1 × 109 and 9.3 × 108 cell/g, respectively) in the <70 °C sampling points (average pH = 2.09); on the contrary, highest temperature waters (85-90 °C; average pH = 2.26) were characterized by low abundance of archaeal cells. The high-throughput sequencing of 16S rRNA gene indicated strong differences in archaeal and bacterial communities' composition along temperature gradient. However, the microbiome in this extreme environment was mainly constituted by chemoautotrophic microorganisms that were likely involved in N-, S-, and Fe-bearing species transformations (e.g. Acidianus infernus, Ferroplasma acidarmanus, Acidithiobacillus, Sulfobacillus, Thaumarchaeota), in agreement with thermodynamic calculations.

Hydrochemical, isotopic and microbiota characterization of telese mineral waters (Southern Italy)

The study deals with the analyses of springs and wells at the base of Montepugliano Hill that represents the SE edge of the wide carbonate Matese massif (Campania, southern Italy). At the base of the hill, from west to east and for almost one kilometre, cold springs HCO₃-Ca type (Grassano springs, ~ 4.5 m³/s; TDS: about 0.45 g/L) pass to hypothermal, HCO₃-Ca type, sulphurous and CO₂-rich springs (~ 1 m³/s with TDS > 1 g/L). Some of the latter are widely used in Telese Spa and Centro Relax Spa. Chemical and isotopic analyses carried out for this study support the hypothesis that all these waters (mineral and non-mineral) have the same catchment area, which is located in the Matese massif. As regards the sulphurous springs, they receive both meteoric waters infiltration and uprising of deeper waters rich in endogenous CO₂ and H₂S gases through important faults systems. Far from these faults, the chemistry of groundwater is scarcely (or not at all) affected by these deep fluid enrichment processes. This scheme is very significant; in fact, when very important groundwater resources are present, it is possible to use both mineral waters in Spa and, in areas far from the faults, those not yet mineralized. Finally, at Montepugliano Hill, in the final stage of the flow path, groundwater is also affected by change in the microbiome: this could provide a basis for comparison between various mineral waters.

Narrative review on the management of moderate-severe atopic dermatitis in pediatric age of the Italian Society of Pediatric Allergology and Immunology (SIAIP), of the Italian Society of Pediatric Dermatology (SIDerP) and of the Italian Society of Pediatrics (SIP)

Currently, there are a few detailed guidelines on the overall management of children and adolescents with moderate-severe atopic dermatitis. AD ​​is a complex disease presenting with different clinical phenotypes, which require an individualized and multidisciplinary approach. Therefore, appropriate interaction between primary care pediatricians, pediatric allergists, and pediatric dermatologists is crucial to finding the best management strategy. In this manuscript, members of the Italian Society of Pediatric Allergology and Immunology (SIAIP), the Italian Society of Pediatric Dermatology (SIDerP), and the Italian Society of Pediatrics (SIP) with expertise in the management of moderate-severe atopic dermatitis have reviewed the latest scientific evidence in the field. This narrative review aims to define a pathway to appropriately managing children and adolescents with moderate-severe atopic dermatitis.

Genome-centric metagenomics provides new insights into the microbial community and metabolic potential of landfill leachate microbiota

Landfills are important sources of microorganisms associated with anaerobic digestion. However, the knowledge on microbiota along with their functional potential in this special habitat are still lacking. In this study, we recovered 1168 non-redundant metagenome-assembled genomes (MAGs) from nine landfill leachate samples collected from eight cities across China, spanning 42 phyla, 73 classes, 114 orders, 189 families, and 267 genera. Totally, 74.1% of 1168 MAGs could not be classified to any known species and 5.9% of these MAGs belonged to microbial dark matter phyla. Two putative novel classes were discovered from landfill leachate samples. The identification of thousands of novel carbohydrate-active enzymes showed similar richness level compared to the cow rumen microbiota. The methylotrophic methanogenic pathway was speculated to contribute significantly to methane production in the landfill leachate because of its co-occurrence with the acetoclastic and hydrogenotrophic methanogenic pathways. The genetic potential of dissimilatory nitrate reduction to ammonium (DNRA) was observed, implying DNRA may play a role in ammonium generation in landfill leachate. These findings implied that landfill leachate might be a valuable microbial resource repository and filled the previous understanding gaps for both methanogenesis and nitrogen cycling in landfill leachate microbiota. Our study provides a comprehensive genomic catalog and substantially provides unprecedented taxonomic and functional profiles of the landfill leachate microbiota.

Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Shotgun sequencing of environmental DNA (i.e., metagenomics) has revolutionized the field of environmental microbiology, allowing the characterization of all microorganisms in a sequencing experiment. To identify the microbes in terms of taxonomy and biological activity, the sequenced reads must necessarily be aligned on known microbial genomes/genes. However, current alignment methods are limited in terms of speed and can produce a significant number of false positives when detecting bacterial species or false negatives in specific cases (virus, plasmids, and gene detection). Moreover, recent advances in metagenomics have enabled the reconstruction of new genomes using de novo binning strategies, but these genomes, not yet fully characterized, are not used in classic approaches, whereas machine and deep learning methods can use them as models. In this article, we attempted to review the different methods and their efficiency to improve the annotation of metagenomic sequences. Deep learning models have reached the performance of the widely used k-mer alignment-based tools, with better accuracy in certain cases; however, they still must demonstrate their robustness across the variety of environmental samples and across the rapid expansion of accessible genomes in databases.

Balneotherapy year in review 2021: focus on the mechanisms of action of balneotherapy in rheumatic diseases

Balneotherapy (BT) is one of the most commonly used non-pharmacologic complementary therapies for different rheumatic diseases. Its beneficial properties probably derived from a combination of mechanical, thermal, and chemical effects, but the exact mechanism of action is not elucidated. This review aimed at summarizing the current knowledge about the effects of BT, and identifying its possible mechanism of action in different rheumatic diseases. Pubmed and Scopus were used to perform a search of the literature to extract articles including terms related to BT and rheumatic diseases published in the period from 2010 to 2021. We selected pre-clinical studies, randomized controlled trials, and clinical trials. The results of clinical studies confirmed the beneficial properties on different mediators and factors of inflammation, oxidative stress, cartilage metabolism, and humoral and cellular immune responses in patients affected by chronic degenerative musculoskeletal disorders. The data derived from OA and RA-induced murine models revealed the efficacy of different BT treatments in decreasing pain, inflammation, and improving mobility, as well as in reducing the expression of matrix-degrading enzymes and markers of oxidative stress damage. Different in vitro studies analyzed the potential effect of a mineral water, as a whole, or of a mineral element, demonstrating their anti-inflammatory, antioxidant, and chondroprotective properties in OA cartilage, synoviocytes and chondrocytes, and osteoblast and osteoclast cultures. The presented data are promising and confirm BT as an effective complementary approach in the management of several low-grade inflammation, degenerative, and stress-related pathologies, as rheumatic diseases.

The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping

Human health and disease have increasingly been shown to be impacted by the gut microbiota, and mouse models are essential for investigating these effects. However, the compositions of human and mouse gut microbiotas are distinct, limiting translation of microbiota research between these hosts. To address this, we constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC), a repository of 26,640 high-quality mouse microbiota-derived bacterial genomes. This catalog enables species-level analyses for mapping functions of interest and identifying functionally equivalent taxa between the microbiotas of humans and mice. We have complemented this with a publicly deposited collection of 223 bacterial isolates, including 62 previously uncultured species, to facilitate experimental investigation of individual commensal bacteria functions in vitro and in vivo. Together, these resources provide the ability to identify and test functionally equivalent members of the host-specific gut microbiotas of humans and mice and support the informed use of mouse models in human microbiota research.

Diversity of microbial communities in hot springs of Sri Lanka as revealed by 16S rRNA gene high-throughput sequencing analysis

Characterization of hot spring microbiota is useful as an initial platform for exploring industrially important microbes. The present study focused on characterization of microbiota in four hot springs in Sri Lanka: Maha Oya; Wahava; Madunagala; and Kivlegama using high throughput 16S amplicon sequencing. Temperatures of the selected springs were ranged from 33.7 °C to 52.4 °C, whereas pH ranged from 7.2 to 8.2. Bacteria were found to be the dominant microbial group (>99%) compared to Archaea which represented less than 1% of microbiota. Four hot springs comprised of unique microbial community structures. Proteobacteria, Firmicutes, Bacteroidetes, Cloroflexi, Deinococcus and Actenobacteria were the major bacterial phyla. Moderately thermophilic genera such as Thermodesulfobacteria and Deinococcus-Thermus were detected as major genera that could be used in industrial applications operating at temperatures around 50 °C and alkaline reaction conditions.

Mesorhizobium comanense sp. nov., isolated from groundwater

Strain 3P27G6^T was isolated from an artesian well connected to the thermal water basin of Comano Terme, Province of Trento, Italy. In phylogenetic analyses based on multilocus sequence analysis, strain 3P27G6^T clustered together with Mesorhizobium australicum WSM2073^T. Genome sequencing produced a 99.51 % complete genome, with a length of 7 363 057 bp and G+C content of 63.53 mol%, containing 6897 coding sequences, 55 tRNA and three rRNA. Average nucleotide identity analysis revealed that all distances calculated between strain 3P27G6^T and the other Mesorhizobium genomes were below 0.9, indicating that strain 3P27G6^T represents a new species. Therefore, we propose the name Mesorhizobium comanense sp. nov. with the type strain 3P27G6^T (=DSM 110654^T=CECT 30067^T). Strain 3P27G6^T is a Gram-negative, rod-shaped, aerobic bacterium. Growth condition, antibiotic susceptibility, metabolic and fatty acid-methyl esters profiles of the strain were determined. Only few nodulation and nitrogen fixation genes were found in the genome, suggesting that this strain may not be specialized in nodulation or in nitrogen fixation.

Comparative Metagenomic Analysis of Two Hot Springs From Ourense (Northwestern Spain) and Others Worldwide

With their circumneutral pH and their moderate temperature (66 and 68°C, respectively), As Burgas and Muiño da Veiga are two important human-use hot springs, previously studied with traditional culture methods, but never explored with a metagenomic approach. In the present study, we have performed metagenomic sequence-based analyses to compare the taxonomic composition and functional potential of these hot springs. Proteobacteria, Deinococcus-Thermus, Firmicutes, Nitrospirae, and Aquificae are the dominant phyla in both geothermal springs, but there is a significant difference in the abundance of these phyla between As Burgas and Muiño da Veiga. Phylum Proteobacteria dominates As Burgas ecosystem while Aquificae is the most abundant phylum in Muiño da Veiga. Taxonomic and functional analyses reveal that the variability in water geochemistry might be shaping the differences in the microbial communities inhabiting these geothermal springs. The content in organic compounds of As Burgas water promotes the presence of heterotrophic populations of the genera Acidovorax and Thermus, whereas the sulfate-rich water of Muiño da Veiga favors the co-dominance of genera Sulfurihydrogenibium and Thermodesulfovibrio. Differences in ammonia concentration exert a selective pressure toward the growth of nitrogen-fixing bacteria such as Thermodesulfovibrio in Muiño da Veiga. Temperature and pH are two important factors shaping hot springs microbial communities as was determined by comparative analysis with other thermal springs.

Genome-centric metagenomics reveals insights into the evolution and metabolism of a new free-living group in Rhizobiales

Background

The Rhizobiales (Proteobacteria) order is an abundant and diverse group of microorganisms, being extensively studied for its lifestyle based on the association with plants, animals, and humans. New studies have demonstrated that the last common ancestor (LCA) of Rhizobiales had a free-living lifestyle, but the phylogenetic and metabolism characterization of basal lineages remains unclear. Here, we used a high-resolution phylogenomic approach to test the monophyly of the Aestuariivirgaceae family, a new taxonomic group of Rhizobiales. Furthermore, a deep metabolic investigation provided an overview of the main functional traits that can be associated with its lifestyle. We hypothesized that the presence of pathways (e.g., Glycolysis/Gluconeogenesis) and the absence of pathogenic genes would be associated with a free-living lifestyle in Aestuariivirgaceae.

Results

Using high-resolution phylogenomics approaches, our results revealed a clear separation of Aestuariivirgaceae into a distinct clade of other Rhizobiales family, suggesting a basal split early group and corroborate the monophyly of this group. A deep functional annotation indicated a metabolic versatility, which includes putative genes related to sugar degradation and aerobic respiration. Furthermore, many of these traits could reflect a basal metabolism and adaptations of Rhizobiales, as such the presence of Glycolysis/Gluconeogenesis pathway and the absence of pathogenicity genes, suggesting a free-living lifestyle in the Aestuariivirgaceae members.

Conclusions

Aestuariivirgaceae (Rhizobiales) family is a monophyletic taxon of the Rhizobiales with a free-living lifestyle and a versatile metabolism that allows these microorganisms to survive in the most diverse microbiomes, demonstrating their adaptability to living in systems with different conditions, such as extremely cold environments to tropical rivers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02354-4.

Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network

Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for microbial DNA sequence data, which exploits convolutional neural networks, recurrent neural networks, and attention mechanisms to predict taxonomic classifications and sample-associated attributes, such as the relationship between the microbiome and host phenotype, on the read/sequence level. In this paper, we develop this novel deep learning approach and evaluate its application to amplicon sequences. We apply our approach to short DNA reads and full sequences of 16S ribosomal RNA (rRNA) marker genes, which identify the heterogeneity of a microbial community sample. We demonstrate that our implementation of a novel attention-based deep network architecture, Read2Pheno, achieves read-level phenotypic prediction. Training Read2Pheno models will encode sequences (reads) into dense, meaningful representations: learned embedded vectors output from the intermediate layer of the network model, which can provide biological insight when visualized. The attention layer of Read2Pheno models can also automatically identify nucleotide regions in reads/sequences which are particularly informative for classification. As such, this novel approach can avoid pre/post-processing and manual interpretation required with conventional approaches to microbiome sequence classification. We further show, as proof-of-concept, that aggregating read-level information can robustly predict microbial community properties, host phenotype, and taxonomic classification, with performance at least comparable to conventional approaches. An implementation of the attention-based deep learning network is available at https://github.com/EESI/sequence_attention (a python package) and https://github.com/EESI/seq2att (a command line tool).

Beneficial Effects of Natural Mineral Waters on Intestinal Inflammation and the Mucosa-Associated Microbiota

Natural mineral water (NMWs) intake has been traditionally used in the treatment of various gastrointestinal diseases. We investigated the effect of two French NMWs, one a calcium and magnesium sulphate, sodium chloride, carbonic, and ferruginous water (NMW1), the other a mainly bicarbonate water (NMW2) on the prevention of intestinal inflammation. Intestinal epithelial cells stimulated with heat inactivated Escherichia coli or H₂O₂ were treated with NMWs to evaluate the anti-inflammatory effects. Moderate colitis was induced by 1% dextran sulfate sodium (DSS) in Balbc/J mice drinking NMW1, NWW2, or control water. General signs and histological features of colitis, fecal lipocalin-2 and pro-inflammatory KC cytokine levels, global mucosa-associated microbiota, were analyzed. We demonstrated that both NMW1 and NMW2 exhibited anti-inflammatory effects using intestinal cells. In induced-colitis mice, NMW1 was effective in dampening intestinal inflammation, with significant reductions in disease activity scores, fecal lipocalin-2 levels, pro-inflammatory KC cytokine release, and intestinal epithelial lesion sizes. Moreover, NMW1 was sufficient to prevent alterations in the mucosa-associated microbiota. These observations, through mechanisms involving modulation of the mucosa-associated microbiota, emphasize the need of investigation of the potential clinical efficiency of such NMWs to contribute, in human beings, to a state of low inflammation in inflammatory bowel disease.

Characteristics associated with clinical response to Comano thermal spring water balneotherapy in pediatric patients with atopic dermatitis

BACKGROUND

Several studies have investigated the efficacy of balneotherapy in atopic dermatitis (AD), including a pediatric open randomized clinical trial conducted at the Comano thermal spring water center, which showed a significant reduction in AD severity and an improvement of the quality of life. However, so far many studies on balneotherapy in pediatric AD have included relatively small populations without identifying patients' characteristics associated with their response. The aim of the present study was to identify any features associated with the clinical response to the Comano thermal spring water balneotherapy in a large cohort of pediatric AD patients.

METHODS

An observational study was conducted on 867 children aged ≤16 years (females 50.5%, mean patient's age 5.9 years, standard deviation ±3.6 years) with mild to severe AD who underwent balneotherapy at the Comano thermal spring water center (Comano, Trentino, Italy) from April to October 2014. Patients were stratified according to their disease severity, which was evaluated using five SCORing Atopic Dermatitis (SCORAD) categories before and immediately after a thermal spring water balneotherapy course. Potential characteristics associated with the patients' clinical response to Comano thermal spring water balneotherapy were investigated.

RESULTS

A statistically significant improvement in AD severity was observed after Comano thermal spring water balneotherapy (p < 0.0001). A significantly higher percentage of patients achieving improvement in AD severity was reported among children ≤4 years old (p < 0.0001) with early-onset AD (p < 0.0001), severe AD (p < 0.0001) or coexistent reported food allergies (p < 0.01). The therapy was well tolerated, and no relevant adverse effects were reported during the treatment course.

CONCLUSIONS

Comano thermal spring water balneotherapy is a safe complementary treatment for pediatric patients with AD, as it was able to reduce the disease severity, especially in children ≤4 years old, with early onset AD, severe AD or concomitant food allergies.

Mining of two novel aldehyde dehydrogenases (DHY-SC-VUT5 and DHY-G-VUT7) from metagenome of hydrocarbon contaminated soils

Background

Aldehyde dehydrogenases are vital for aerobic hydrocarbon degradation and is involved in the last step of catalysing the oxidation of aldehydes to carboxylic acids. With the global increase in hydrocarbon pollution of different environments, these enzymes have the potential to be used in enzymatic bioremediation applications.

Results

Fifteen fosmid clones with hydrocarbon degrading potential were functionally screened to identify dehydrogenase enzymes. Accordingly, the fosmid insert of the positive clones were sequenced using PacBio next generation sequencing platform and de novo assembled using CLC Genomic Work Bench. The 1233 bp long open reading frame (ORF) for DHY-SC-VUT5 was found to share a protein sequence similarity of 97.7% to short-chain dehydrogenase from E. coli. The 1470 bp long ORF for DHY-G-VUT7 was found to share a protein sequence similarity of 23.9% to glycine dehydrogenase (decarboxylating) (EC 1.4.4.2) from Caulobacter vibrioides (strain NA1000 / CB15N) (Caulobacter crescentus). The in silico analyses and blast against UNIPROT protein database with the stated similarity show that the two dehydrogenases are novel. Biochemical characterization revealed, that the highest relative activity was observed at substrate concentrations of 150 mM and 50 mM for DHY-SC-VUT5 and DHY-G-VUT7, respectively. The K_m values were found to be 13.77 mM with a V_max of 0.009135 μmol.min^− 1 and 2.832 mM with a V_max of 0.005886 μmol.min^− 1 for DHY-SC-VUT5 and DHY-G-VUT7, respectively. Thus, a potent and efficient enzyme for alkyl aldehyde conversion to carboxylic acid.

Conclusion

The microorganisms overexpressing the novel aldehyde dehydrogenases could be used to make up microbial cocktails for biodegradation of alkanes. Moreover, since the discovered enzymes are novel it would be interesting to solve their structures by crystallography and explore the downstream applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12896-021-00677-8.

The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review

The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species available in List of Prokaryotic Names with Standing in Nomenclature. Sphingopyxis spp. have been isolated from diverse niches including, agricultural soil, marine and fresh water, caves, activated sludge, thermal spring, oil and pesticide contaminated soil, and heavy metal contaminated sites. Sphingopyxis species have drawn considerable attention not only for their ability to survive under extreme environments, but also for their potential to degrade number of xenobiotics and other environmental contaminants that impose serious threat to human health. At present, genome sequence of both cultivable and non-cultivable strains (metagenome assembled genome) are available in the public databases (NCBI) and genome wide studies confirms the presence of mobile genetic elements and plethora of degradation genes and pathways making them a potential candidate for bioremediation. Beside genome wide predictions there are number of experimental evidences confirm the degradation potential of bacteria belonging to genus Sphingopyxis and also the production of different secondary metabolites that help them interact and survive in their ecological niches. This review provides detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential.

Acetylene-Fueled Trichloroethene Reductive Dechlorination in a Groundwater Enrichment Culture

In aquifers, acetylene (C2H2) is a product of abiotic degradation of trichloroethene (TCE) catalyzed by in situ minerals. C2H2 can, in turn, inhibit multiple microbial processes including TCE dechlorination and metabolisms that commonly support dechlorination, in addition to supporting the growth of acetylenotrophic microorganisms. Previously, C2H2 was shown to support TCE reductive dechlorination in synthetic, laboratory-constructed cocultures containing the acetylenotroph Pelobacter sp. strain SFB93 and Dehalococcoides mccartyi strain 195 or strain BAV1. In this study, we demonstrate TCE and perchloroethene (PCE) reductive dechlorination by a microbial community enriched from contaminated groundwater and amended with C2H2 as the sole electron donor and organic carbon source. The metagenome of the stable, enriched community was analyzed to elucidate putative community functions. A novel anaerobic acetylenotroph in the phylum Actinobacteria was identified using metagenomic analysis. These results demonstrate that the coupling of acetylenotrophy and reductive dechlorination can occur in the environment with native bacteria and broaden our understanding of biotransformation at contaminated sites containing both TCE and C2H2IMPORTANCE Understanding the complex metabolisms of microbial communities in contaminated groundwaters is a challenge. PCE and TCE are among the most common groundwater contaminants in the United States that, when exposed to certain minerals, exhibit a unique abiotic degradation pathway in which C2H2 is a product. C2H2 can act as both an inhibitor of TCE dechlorination and of supporting metabolisms and an energy source for acetylenotrophic bacteria. Here, we combine laboratory microcosm studies with computational approaches to enrich and characterize an environmental microbial community that couples two uncommon metabolisms, demonstrating unique metabolic interactions only yet reported in synthetic, laboratory-constructed settings. Using this comprehensive approach, we have identified the first reported anaerobic acetylenotroph in the phylum Actinobacteria, demonstrating the yet-undescribed diversity of this metabolism that is widely considered to be uncommon.

Biases in genome reconstruction from metagenomic data

BACKGROUND

Advances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction of genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly and binning techniques are accurate when applied to environmental metagenomes due to a lack of complete reference genome sequences against which to check the resulting MAGs.

METHODS

We compared MAGs derived from an enrichment culture containing ~20 organisms to complete genome sequences of 10 organisms isolated from the enrichment culture. Factors commonly considered in binning software-nucleotide composition and sequence repetitiveness-were calculated for both the correctly binned and not-binned regions. This direct comparison revealed biases in sequence characteristics and gene content in the not-binned regions. Additionally, the composition of three public data sets representing MAGs reconstructed from the Tara Oceans metagenomic data was compared to a set of representative genomes available through NCBI RefSeq to verify that the biases identified were observable in more complex data sets and using three contemporary binning software packages.

RESULTS

Repeat sequences were frequently not binned in the genome reconstruction processes, as were sequence regions with variant nucleotide composition. Genes encoded on the not-binned regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function. Our results support genome reconstruction as a robust process and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function; however, population-level genotypic heterogeneity in natural populations, such as uneven distribution of plasmids, can lead to incorrect inferences.

A comprehensive analysis to understand the mechanism of action of balneotherapy: why, how, and where they can be used? Evidence from in vitro studies performed on human and animal samples

Balneotherapy (BT) is one of the most commonly used complementary therapies for many pathological conditions. Its beneficial effects are related to physical and chemical factors, but the exact mechanism of action is not fully understood. Recently, there has been an increased interest in the use of preclinical models to investigate the influence of BT on inflammation, immunity, and cartilage and bone metabolism. The objective of this comprehensive analysis was to summarize the current knowledge about the in vitro studies in BT and to revise the obtained results on the biological effects of mineral waters. Special attention has been paid to the main rheumatological and dermatological conditions, and to the regulation of the immune response. The objective of this review was to summarize the in vitro studies, on human and animal samples, investigating the biological effects of BT. In particular, we analyzed the properties of a thermal water, as a whole, of an inorganic molecule, such as hydrogen sulfide in different cell cultures (keratinocytes, synoviocytes, chondrocytes, and peripheral blood cells), or of the organic component. The results corroborated the scientific value of in vitro studies in demonstrating the anti-inflammatory, antioxidant, chondroprotective, and immunosuppressive role of BT at the cellular level. However, the validity of the cell culture model is limited by several sources of bias, as the differences in experimental procedures, the high heterogeneity among the available researches, and the difficulties in considering all the chemical and physical factors of BT. We would like to stimulate the scientific community to standardize the experimental procedures and enhance in vitro research in the field of BT.

Analysis of interdomain taxonomic patterns in urban street mats

Streets are constantly crossed by billions of vehicles and pedestrians. Their gutters, which convey stormwater and contribute to waste management, and are important for human health and well-being, probably play a number of ecological roles. Street surfaces may also represent an important part of city surface areas. To better characterize the ecology of this yet poorly explored compartment, we used filtration and DNA metabarcoding to address microbial community composition and assembly across the city of Paris, France. Diverse bacterial and eukaryotic taxonomic groups were identified, including members involved in key biogeochemical processes, along with a number of parasites and putative pathogens of human, animals and plants. We showed that the beta diversity patterns between bacterial and eukaryotic communities were correlated, suggesting interdomain associations. Beta diversity analyses revealed the significance of biotic factors (cohesion metrics) in shaping gutter microbial community assembly and, to a lesser extent, the contribution of abiotic factors (pH and conductivity). Co-occurrences analysis confirmed contrasting non-random patterns both within and between domains of life, specifically when comparing diatoms and fungi. Our results highlight microbial coexistence patterns in streets and reinforce the need to further explore biodiversity in urban ground transportation infrastructures.

Looking for the X Factor in Bacterial Pathogenesis: Association of orfX-p47 Gene Clusters with Toxin Genes in Clostridial and Non-Clostridial Bacterial Species

The botulinum neurotoxin (BoNT) has been extensively researched over the years in regard to its structure, mode of action, and applications. Nevertheless, the biological roles of four proteins encoded from a number of BoNT gene clusters, i.e., OrfX1-3 and P47, are unknown. Here, we investigated the diversity of orfX-p47 gene clusters using in silico analytical tools. We show that the orfX-p47 cluster was not only present in the genomes of BoNT-producing bacteria but also in a substantially wider range of bacterial species across the bacterial phylogenetic tree. Remarkably, the orfX-p47 cluster was consistently located in proximity to genes coding for various toxins, suggesting that OrfX1-3 and P47 may have a conserved function related to toxinogenesis and/or pathogenesis, regardless of the toxin produced by the bacterium. Our work also led to the identification of a putative novel BoNT-like toxin gene cluster in a Bacillus isolate. This gene cluster shares striking similarities to the BoNT cluster, encoding a bont/ntnh-like gene and orfX-p47, but also differs from it markedly, displaying additional genes putatively encoding the components of a polymorphic ABC toxin complex. These findings provide novel insights into the biological roles of OrfX1, OrfX2, OrfX3, and P47 in toxinogenesis and pathogenesis of BoNT-producing and non-producing bacteria.

Regenerative effects of spring water-derived bacterial lysates on human skin fibroblast in in vitro culture: preliminary results

Objective:

Previous studies have shown regenerative power of the skin with Comano (Trento, Italy) spring water and resident non-pathogenic microflora. This study investigated the action of bacterial lysates that were isolated from Comano spring water on in vitro culture of human skin fibroblasts.

Methods:

For this study, we selected the following four bacterial lysates: L1 (closest relative: Rudaea cellulosilytica), L2 (closest relative: Mesorhizobium erdmanii), L3 (closest relative: Herbiconiux ginsengi), and L4 (closest relative: Fictibacillus phosphorivorans). Human fibroblasts were cultured under Dulbecco’s modified Eagle’s medium (DMEM) with bacterial lysates added or DMEM (controls). Cell proliferation was evaluated by spectrophotometric absorbance analysis after the XTT-Microculture Tetrazolium Assay.

Results:

At 24 hours, cultures with L2, L3, and L4 showed a higher absorbance compared with controls. At 48 hours, cultures with L1, L2, and L3 showed slightly lower absorbance compared with controls, and culture with L4 showed a higher absorbance than in the other experimental conditions. At 72 hours, absorbance was lower in cultures with L1, L2, and L3 than in controls, and absorbance was higher in culture with L4 than in the other experimental conditions.

Conclusions:

Our study indicates a favorable action of Comano spring water microbiota on proliferation of human skin fibroblasts.

The Landscape of Genetic Content in the Gut and Oral Human Microbiome

Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.