16S rRNA sequences reveal numerous uncultured microorganisms in a natural community

Exploring the correlation of microbial community diversity and succession with protein degradation and impact on the production of volatile compounds during cold storage of grouper (Epinephelus coioides)

Microorganisms, proteins, and lipids play crucial and intricate roles in the aroma generation of aquatic products. To explore the impact of the interaction between microorganisms and proteins on the volatile compounds (VOCs) in grouper, this study employed whey protein isolate (WPI) to inhibit lipid oxidation and reduce mutual interference. Changes in bacterial profiles, metabolites, and VOCs were detected. Eighteen key VOCs associated with the overall flavor of grouper were identified, and the potential relationships among microorganisms, proteins, and VOCs were explored using a correlation network. Five microorganisms (Vibrio, Vagococcus, Pseudomonas, Psychrobacter, and Shewanella) closely related to characteristic flavor compounds were identified. Additionally, 30 differential metabolites related to proteins and six metabolic pathways were screened. Therefore, this study unveils the potential interaction between microorganisms and proteins in flavor formation and provides new insights into the relationships among microorganisms, proteins, and VOCs.

Cultivation of Diverse Novel Marine Bacteria from Deep Ocean Sediment Using Spent Culture Supernatant of Ca. Bathyarchaeia Enrichment

Most microorganisms resist pure cultivation under conventional laboratory conditions. One of the primary issues for this un-culturability is the absence of biologically produced growth-promoting factors in traditionally defined growth media. However, whether cultivating microbes by providing spent culture supernatant of pivotal microbes in the growth medium can be an effective approach to overcome this limitation is still an under-explored area of research. Here, we used the spent culture medium (SCM) method to isolate previously uncultivated marine bacteria and compared the efficiency of this method with the traditional cultivation (TC) method. In the SCM method, Ca. Bathyarchaeia-enriched supernatant (10%) was used along with recalcitrant organic substrates such as lignin, humic acid, and organic carbon mixture. Ca. Bathyarchaeia, a ubiquitous class of archaea, have the capacity to produce metabolites, making their spent culture supernatant a key source to recover new bacterial stains. Both cultivation methods resulted in the recovery of bacterial species from the phyla Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota. However, our SCM approach also led to the recovery of species from rarely cultivated groups, such as Planctomycetota, Deinococcota, and Balneolota. In terms of the isolation of new taxa, the SCM method resulted in the cultivation of 80 potential new strains, including one at the family, 16 at the genus, and 63 at the species level, with a novelty ratio of ~ 35% (80/219). In contrast, the TC method allowed the isolation of ~ 10% (19/171) novel strains at species level only. These findings suggest that the SCM approach improved the cultivation of novel and diverse bacteria.

Dominance by cyanobacteria in the newly formed biofilms on stone monuments under a protective shade at the Beishiku Temple in China

Following the installation of a protective shade, rapid propagation of microorganisms showing in black and grey colors occurred at Beishiku Temple in Gansu Province of China. This study employed a combination of high-throughput sequencing technology, morphological examinations, and an assessment of the surrounding environmental condition to analyze newly formed microbial disease spots. The investigation unveiled the responsible microorganisms and the instigating factors of the microbial outbreak that subsequently to the erection of the shade. Through comparison of bioinformatics, the ASV method surpasses the OTU method in characterizing community compositional changes by the dominant microbial groups, the phylum Cyanobacteria emerged as the most dominant ones in the microbial community accountable for the post-shade microbial deterioration. The black spot and grey spot are predominantly composed of Mastigocladopsis and Scytonema, respectively. Validation analysis, based on the active RNA-level community results, supported and validated these conclusions. Comparative scrutiny of the microbial community before shade installation and the background environmental data disclosed that the erection of the shade prompted a decrease in temperatures and an increase in humidity within the protected area. Consequently, this spurred the exponential proliferation of indigenous cyanobacteria in the spots observed. The outcomes of this study carry considerable significance in devising preventive conservation strategies for cultural heritage and in managing the process of biodeterioration.

The potential of soil microbial communities to transform deoxynivalenol in agricultural soils-a soil microcosm study

Infestation of cereal fields with toxigenic Fusarium species is identified as an environmental source for the mycotoxin deoxynivalenol (DON). During rain events, DON may be washed off from infested plants and enter the soil, where microbial transformation may occur. Although some studies showed DON transformation potential of soil microbial communities in liquid soil extracts, these findings can not be transferred to environmental conditions. Accordingly, microbial transformation of DON in soil has to be investigated under realistic conditions, e.g., microcosms mimicking field situations. In this study, we investigated the potential of soil microbial communities to transform DON in six different agricultural soils at two levels (0.5 and 5 µg g-1). The dissipation and the formation of transformation products were investigated in a period of 35 days and compared to a sterilized control. In addition, we measured soil respiration and applied the phospholipid-derived fatty acid (PLFA) analysis to assess whether soil microbial community characteristics are related to the microbial transformation potential. Dissipation of DON in non-sterilized soils was fast (50% dissipation within 0.6-3.7 days) compared to the sterile control where almost no dissipation was observed. Thus, dissipation was mainly attributed to microbial transformation. We verified that small amounts of DON are transformed to 3-keto-deoxynivalenol (3-keto-DON) and 3-epi-deoxynivalenol (3-epi-DON), which were not detectable after 16-day incubation, indicating further transformation processes. There was a trend towards faster transformation in soils with active and large microbial communities and low fungi-to-bacteria ratio.

Changes in the Physicochemical Properties and Microbial Communities of Air-Fried Hairtail Fillets during Storage

This study assessed the physicochemical properties of air-fried hairtail fillets (190 °C, 24 min) under different storage temperatures (4, 25, and 35 °C). The findings revealed a gradual decline in sensory scores across all samples during storage, accompanied by a corresponding decrease in thiobarbituric acid reactive substances (TBARS) and total viable count over time. Lower storage temperatures exhibited an effective capacity to delay lipid oxidation and microbiological growth in air-fried hairtail fillets. Subsequently, alterations in the microbiota composition of air-fried hairtail fillets during cold storage were examined. Throughout the storage duration, Achromobacter, Escherichia-Shigella, and Pseudomonas emerged as the three dominant genera in the air-fried hairtail samples. Additionally, Pearson correlation analysis demonstrated that among the most prevalent microbial genera in air-fried hairtail samples, Achromobacter and Psychrobacter exhibited positive correlations with the L* value, a* value, and sensory scores. Conversely, they displayed negative correlations with pH, b* value, and TBARS. Notably, air-fried samples stored at 4 °C exhibited prolonged freshness compared with those stored at 25 °C and 35 °C, suggesting that 4 °C is an optimal storage temperature. This study offers valuable insights into alterations in the physicochemical properties and microbial distribution in air-fried hairtail fillets during storage, facilitating the improvement of meat quality by adjusting microbial communities in air-fried hairtail fillets.

Cellulolytic Aerobic Bacteria Isolated from Agricultural and Forest Soils: An Overview

This review provides insights into cellulolytic bacteria present in global forest and agricultural soils over a period of 11 years. It delves into the study of soil-dwelling cellulolytic bacteria and the enzymes they produce, cellulases, which are crucial in both soil formation and the carbon cycle. Forests and agricultural activities are significant contributors to the production of lignocellulosic biomass. Forest ecosystems, which are key carbon sinks, contain 20-30% cellulose in their leaf litter. Concurrently, the agricultural sector generates approximately 998 million tons of lignocellulosic waste annually. Predominant genera include Bacillus, Pseudomonas, Stenotrophomonas, and Streptomyces in forests and Bacillus, Streptomyces, Pseudomonas, and Arthrobacter in agricultural soils. Selection of cellulolytic bacteria is based on their hydrolysis ability, using artificial cellulose media and dyes like Congo red or iodine for detection. Some studies also measure cellulolytic activity in vitro. Notably, bacterial cellulose hydrolysis capability may not align with their cellulolytic enzyme production. Enzymes such as GH1, GH3, GH5, GH6, GH8, GH9, GH10, GH12, GH26, GH44, GH45, GH48, GH51, GH74, GH124, and GH148 are crucial, particularly GH48 for crystalline cellulose degradation. Conversely, bacteria with GH5 and GH9 often fail to degrade crystalline cellulose. Accurate identification of cellulolytic bacteria necessitates comprehensive genomic analysis, supplemented by additional proteomic and transcriptomic techniques. Cellulases, known for degrading cellulose, are also significant in healthcare, food, textiles, bio-washing, bleaching, paper production, ink removal, and biotechnology, emphasizing the importance of discovering novel cellulolytic strains in soil.

Identification and drug resistance of pathogen of ulcerative skin disease and its immune responses and protective efficacy after vaccination in a giant spiny frog, Quasipaa spinosa

OBJECTIVE

In order to explore the pathogen of the ulcerative skin disease in giant spiny frog (Quasipaa spinosa), and to provide theoretical basis for the prevention and control of the disease in practical production, this study was carried out to isolate and identify the pathogenic bacteria from the sick frogs suffering from rotting skin disease and to carry out the immunization test of the inactivated vaccine.

METHODS

Physiological and biochemical characterization, and molecular biology of the pathogenic bacteria were identified, and drug screening and immunization responses were also carried out.

RESULTS

The dominant bacterium QS01 was isolated from the lesions of diseased giant spiny frogs, which was confirmed to be the causative agent of the rotting skin disease of giant spiny frogs by artificial regression infection test. Based on the fact that the pathogen is a gram-negative short bacterium, its phenotypic characteristics and 16S rRNA and gyrB gene sequences were analyzed, and the bacterium was determined to be Citrobacter freundii. The results of the drug sensitivity test showed that the bacterium was sensitive to 11 antibiotics, including Enrofloxacin, Fleroxacin and Ciprofloxacin, including three non-polluting drugs such as Florfenicol, Roxithromycin and Thiamphenicol, as well as three Chinese herbal medicines such as Rheum officinale Baill, Coptis chinensis Franch and Scutellaria baicalensis Georgi. Most non-specific immune responses could go to recovery in 24h. The frogs were vaccinated with QS01 formaldehyde inactivated vaccine by injection, immersion and spraying, and the serum antibody potency of the three immunized groups with the average potency reached the peak at the 20th d after immunization, and the serum antibody potency of the injected immunized group was at the highest ratio of 1:64-128 (101.6), while the immersed group and the spraying group attained the ratio of 1:16-32 (20.2) and 1:16-32 (16) respectively, and lasted until the 30th d. The control group that was not immunized had the highest serum antibody potency of 1:16-32 (20.2) and 1:16-32 (16), and continued until the 30th d. The control group that was not immunized was not immunized. The serum antibody potency of the unimmunized control group was 1:2 to 2(2). The immunoprotection rates after takedown were 100 %, 85.71 % and 71.43 %, respectively.

CONCLUSION

C. freundii is the pathogen of the disease in this farm, and the vaccination by immersion and spraying can effectively prevent and control the rotting skin disease in frogs. These results revealed pathogenicity of C. freundii and its activation of host immune response, which will provide a scientific reference for the aquaculture and disease prevention in Q. spinosa culture.

ITS and 16S rDNA metagenomic dataset of different soils from flax fields

Flax (Linum usitatissimum L.), one of the important and versatile crops, is used for the production of oil and fiber. To obtain high and stable yields of flax products, L. usitatissimum varieties should be cultivated under optimal conditions, including the composition of the soil microbiome. We evaluated the diversity of microorganisms in soils under conditions unfavorable for flax cultivation (suboptimal acidity or herbicide treatment) or infected with causative agents of harmful flax diseases (Septoria linicola, Colletotrichum lini, Melampsora lini, or Fusarium oxysporum f. sp. lini). For this purpose, twenty-two sod-podzolic soil samples were collected from flax fields and their metagenomes were analyzed using the regions of 16S ribosomal RNA gene (16S rDNA) and internal transcribed spacers (ITS) of the ribosomal RNA genes, which are used in phylogenetic studies of bacteria and fungi. Amplicons were sequenced on the Illumina MiSeq platform (reads of 300 + 300 bp). On average, we obtained 8,400 reads for ITS and 43,300 reads for 16S rDNA per sample. For identification of microorganisms in the soil samples, the Illumina reads were processed using DADA2. The raw data are deposited in the Sequence Read Archive under the BioProject accession number PRJNA956957. Tables listing the microorganisms identified in the soil samples are available in this article. The obtained dataset can be used to analyze the fungal and bacterial composition of flax field soils and their relationship to environmental conditions, including suboptimal soil acidity and infection with fungal pathogens. In addition, it can help to understand the influence of herbicide treatment on the microbial diversity of flax fields. Another useful application of our data is the ability to assess the suitability of the soil microbiome for flax cultivation.

Innovative approaches to accurately assess the effectiveness of biocide-based treatments to fight biodeterioration of Cultural Heritage monuments

The development of diagnostic methods to accurately assess the effects of treatments on lithobiont colonization remains a challenge for the conservation of Cultural Heritage monuments. In this study, we tested the efficacy of biocide-based treatments on microbial colonization of a dolostone quarry, in the short and long-term, using a dual analytical strategy. We applied a metabarcoding approach to characterize fungal and bacterial communities over time, integrated with microscopy techniques to analyze the interactions of microorganisms with the substrate and evaluate the effectiveness. These communities were dominated by the bacterial phyla Actinobacteriota, Proteobacteria and Cyanobacteria, and the fungal order Verrucariales, which include taxa previously reported as biodeteriogenic agents and observed here associated with biodeterioration processes. Following the treatments, changes over time in the abundance profiles depend on taxa. While Cyanobacteriales, Cytophagales and Verrucariales decreased in abundance, other groups, such as Solirubrobacteriales, Thermomicrobiales and Pleosporales increased. These patterns could be related not only to the specific effects of the biocide on the different taxa, but also to different recolonization abilities of those organisms. The different susceptibility to treatments could be associated with the inherent cellular properties of different taxa, but differences in biocide penetration to endolithic microhabitats could be involved. Our results demonstrate the importance of both removing epilithic colonization and applying biocides to act against endolithic forms. Recolonization processes could also explain some of the taxon-dependent responses, especially in the long-term. Taxa showing resistance, and those benefiting from nutrient accumulation in the form of cellular debris following treatments, may have an advantage in colonizing treated areas, pointing to the need for long-term monitoring of a wide range of taxa. This study highlights the potential utility of combining metabarcoding and microscopy to analyze the effects of treatments and design appropriate strategies to combat biodeterioration and establish preventive conservation protocols.

Diverse Microbial Hot Spring Mat Communities at Black Canyon of the Colorado River

The thermophilic microbial mat communities at hot springs in the Black Canyon of the Colorado River, thought to harbor the protistan human pathogen Naegleria fowleri, were surveyed using both culture-independent and -dependent methods to further understand the ecology of these hot spring microbiomes. Originating from Lake Mead source water, seven spring sites were sampled, varying in temperature from 25 to 55 °C. Amplicon-based high-throughput sequencing of twelve samples using 16S rRNA primers (hypervariable V4 region) revealed that most mats are dominated by cyanobacterial taxa, some but not all similar to those dominating the mats at other studied hot spring systems. 18S rRNA amplicon sequencing (V9 region) demonstrated a diverse community of protists and other eukaryotes including a highly abundant amoebal sequence related to Echinamoeba thermarum. Additional taxonomic and diversity metric analyses using near full-length 16S and 18S rRNA gene sequencing allowed a higher sequence-based resolution of the community. The mat sequence data suggest a major diversification of the cyanobacterial orders Leptolyngbyales, as well as microdiversity among several cyanobacterial taxa. Cyanobacterial isolates included some representatives of ecologically abundant taxa. A Spearman correlation analysis of short-read amplicon sequencing data supported the co-occurrences of populations of cyanobacteria, chloroflexi, and bacteroidetes providing evidence of common microbial co-occurrences across the Black Canyon hot springs.

Characterization of microbiomic and geochemical compositions across the photosynthetic fringe

Hot spring outflow channels provide geochemical gradients that are reflected in microbial community compositions. In many hot spring outflows, there is a distinct visual demarcation as the community transitions from predominantly chemotrophs to having visible pigments from phototrophs. It has been hypothesized that this transition to phototrophy, known as the photosynthetic fringe, is a result of the pH, temperature, and/or sulfide concentration gradients in the hot spring outflows. Here, we explicitly evaluated the predictive capability of geochemistry in determining the location of the photosynthetic fringe in hot spring outflows. A total of 46 samples were taken from 12 hot spring outflows in Yellowstone National Park that spanned pH values from 1.9 to 9.0 and temperatures from 28.9 to 92.2°C. Sampling locations were selected to be equidistant in geochemical space above and below the photosynthetic fringe based on linear discriminant analysis. Although pH, temperature, and total sulfide concentrations have all previously been cited as determining factors for microbial community composition, total sulfide did not correlate with microbial community composition with statistical significance in non-metric multidimensional scaling. In contrast, pH, temperature, ammonia, dissolved organic carbon, dissolved inorganic carbon, and dissolved oxygen did correlate with the microbial community composition with statistical significance. Additionally, there was observed statistical significance between beta diversity and the relative position to the photosynthetic fringe with sites above the photosynthetic fringe being significantly different from those at or below the photosynthetic fringe according to canonical correspondence analysis. However, in combination, the geochemical parameters considered in this study only accounted for 35% of the variation in microbial community composition determined by redundancy analysis. In co-occurrence network analyses, each clique correlated with either pH and/or temperature, whereas sulfide concentrations only correlated with individual nodes. These results indicate that there is a complex interplay between geochemical variables and the position of the photosynthetic fringe that cannot be fully explained by statistical correlations with the individual geochemical variables included in this study.

Microbes in fingerprints: A source for dating crime evidence?

Interest in the human microbiome has grown in recent years because of increasing applications to biomedicine and forensic science. However, the potential for dating evidence at a crime scene based upon time-dependent changes in microbial signatures has not been established, despite a relatively straightforward scientific process for isolating the microbiome. We hypothesize that modifications in microbial diversity, abundance, and succession can provide estimates of the time a surface was touched for investigative purposes. In this proof-of-concept research, the sequencing and analysis of the 16 S rRNA gene from microbes present in fresh and aged latent fingerprints deposited by three donors with pre- and post-washed hands is reported. The stability of major microbial phyla is confirmed while the dynamics of less abundant groups is described up to 21 days post-deposition. Most importantly, a phylum is suggested as the source for possible biological markers to date fingerprints: Deinococcus-Thermus.

Analysis of microbial community and biodeterioration of maritime cultural relics (ironware, porcelain, axes, hull wood) from the Nanhai No. 1 shipwreck

Purpose

Maritime cultural relics from the Nanhai No. 1 shipwreck were immersed in a buffer to maintain stability. To better monitor the changes in the composition of microorganisms in the buffer and, thus, prevent the damage to artifacts caused by harmful microorganisms.

Methods

In September and November 2019, we conducted high-throughput sequencing of water samples from four types of maritime cultural relics (ironware, porcelain, axe, and hull wood) to reveal the composition and changes in microbial communities. In addition, we isolated culturable microorganisms and conducted biocide sensitivity tests and lignin and cellulose degradation tests.

Results

Visible microbial colonization was observed in the water samples collected from the buffer solutions of ironware, porcelain, axe, and hull wood of the Nanhai No. 1 shipwreck; additionally, apparent differences in the composition of microorganisms in the water samples collected from different cultural relics and different collection times of the same cultural relics were noted. Few species of bacteria and fungi from the microbial community observed in the maritime cultural relics were cultured, and it was noted that various biocides had certain inhibitory effects on them. Some dominant strains had lignin and cellulose degradation abilities and could only grow under specific environmental conditions.

Conclusion

We found apparent differences in the composition of microorganisms obtained from different cultural relics and different collection times of the same cultural relics. This study can provide data support for better protection of maritime cultural relics obtained from the Nanhai No. 1 shipwreck and provide a theoretical basis for the biological protection of other maritime cultural relics.

Periodontal microbiology and microbial etiology of periodontal diseases: Historical concepts and contemporary perspectives

This narrative review summarizes the collective knowledge on periodontal microbiology, through a historical timeline that highlights the European contribution in the global field. The etiological concepts on periodontal disease culminate to the ecological plaque hypothesis and its dysbiosis-centered interpretation. Reference is made to anerobic microbiology and to the discovery of select periodontal pathogens and their virulence factors, as well as to biofilms. The evolution of contemporary molecular methods and high-throughput platforms is highlighted in appreciating the breadth and depth of the periodontal microbiome. Finally clinical microbiology is brought into perspective with the contribution of different microbial species in periodontal diagnosis, the combination of microbial and host biomarkers for this purpose, and the use of antimicrobials in the treatment of the disease.

Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy

The human gut microbiome is associated with a large number of disease etiologies. As such, it is a natural candidate for machine-learning-based biomarker development for multiple diseases and conditions. The microbiome is often analyzed using 16S rRNA gene sequencing or shotgun metagenomics. However, several properties of microbial sequence-based studies hinder machine learning (ML), including non-uniform representation, a small number of samples compared with the dimension of each sample, and sparsity of the data, with the majority of taxa present in a small subset of samples. We show here using a graph representation that the cladogram structure is as informative as the taxa frequency. We then suggest a novel method to combine information from different taxa and improve data representation for ML using microbial taxonomy. iMic (image microbiome) translates the microbiome to images through an iterative ordering scheme, and applies convolutional neural networks to the resulting image. We show that iMic has a higher precision in static microbiome gene sequence-based ML than state-of-the-art methods. iMic also facilitates the interpretation of the classifiers through an explainable artificial intelligence (AI) algorithm to iMic to detect taxa relevant to each condition. iMic is then extended to dynamic microbiome samples by translating them to movies.

Distribution and Genomic Variation of Thermophilic Cyanobacteria in Diverse Microbial Mats at the Upper Temperature Limits of Photosynthesis

Thermophilic cyanobacteria have been extensively studied in Yellowstone National Park (YNP) hot springs, particularly during decades of work on the thick laminated mats of Octopus and Mushroom springs. However, focused studies of cyanobacteria outside these two hot springs have been lacking, especially regarding how physical and chemical parameters along with community morphology influence the genomic makeup of these organisms. Here, we used a metagenomic approach to examine cyanobacteria existing at the upper temperature limit of photosynthesis. We examined 15 alkaline hot spring samples across six geographic areas of YNP, all with various physical and chemical parameters and community morphology. We recovered 22 metagenome-assembled genomes (MAGs) belonging to thermophilic cyanobacteria, notably an uncultured Synechococcus-like taxon recovered from a setting at the upper temperature limit of photosynthesis, 73°C, in addition to thermophilic Gloeomargarita. Furthermore, we found that three distinct groups of Synechococcus-like MAGs recovered from different temperature ranges vary in their genomic makeup. MAGs from the uncultured very-high-temperature (up to 73°C) Synechococcus-like taxon lack key nitrogen metabolism genes and have genes implicated in cellular stress responses that diverge from other Synechococcus-like MAGs. Across all parameters measured, temperature was the primary determinant of taxonomic makeup of recovered cyanobacterial MAGs. However, total Fe, community morphology, and biogeography played an additional role in the distribution and abundance of upper-temperature-limit-adapted Synechococcus-like MAGs. These findings expand our understanding of cyanobacterial diversity in YNP and provide a basis for interrogation of understudied thermophilic cyanobacteria. IMPORTANCE Oxygenic photosynthesis arose early in microbial evolution-approximately 2.5 to 3.5 billion years ago-and entirely reshaped the biological makeup of Earth. However, despite the span of time in which photosynthesis has been refined, it is strictly limited to temperatures below 73°C, a barrier that many other biological processes have been able to overcome. Furthermore, photosynthesis at temperatures above 56°C is limited to circumneutral and alkaline pH. Hot springs in Yellowstone National Park (YNP), which have a large diversity in temperatures, pH, and geochemistry, provide a natural laboratory to study thermophilic microbial mats and the cyanobacteria within. While cyanobacteria in YNP microbial mats have been studied for decades, a vast majority of the work has focused on two springs within the same geyser basin, both containing similar community morphologies. Thus, the drivers of cyanobacterial adaptations to the upper limits of photosynthesis across a variety of environmental parameters have been understudied. Our findings provide new insights into the influence of these parameters on both taxonomic diversity and genomic content of cyanobacteria across a range of hot spring samples.

Nasal microbiome in chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is defined as an inflammatory disorder of the paranasal sinuses and of the nasal mucosa that lasts 12 weeks or longer. In CRS microbes contribute to the disease pathogenesis. Clinical microbiology is focused on finding single pathogens that causes the disease and the main goal is the use of antibiotics to kill bacteria. Efforts to achieve a better understanding of CRS include the study of the sinus microbiome, and to evaluate the ability of probiotics to augment homeostasis and modulate the immune response of the host mucosa. This review provides an update on the role of the microbiome in CRS. The study was conducted using two databases: PubMed and Science Direct. We searched for articles in English that matched the review topic. We first used the abstracts of articles to assess whether they met the inclusion criteria. We also reviewed the references of the selected articles and read those with titles that might be of interest. Several studies have shown that endogenous microbiome dysbiosis can impact mucosa health and disease severity. Some bacterial species presenting protective or pathogenic effect. Antimicrobial agents can create a similar disruption and impact the nasal microbiome balance. On the other hand, probiotics offers a promising avenue for developing systemic and topical therapies geared towards strategic manipulation of the biological host load, thereby augmenting immune homeostasis. A better comprehension of sinus-nasal microbiome in healthy and in CRS patients and the link with different CRS phenotype can help in developing new prognostics, diagnostics, and therapeutics strategies. Going forward, the use of probiotics can restore the native sinus ecology with significant therapeutic and preventive implications.

Microfabrication of a micron-scale microbial-domestication pod for in situ cultivation of marine bacteria

Through the hyphenation of microfabrication, microfluidics and microbiology, we report the development of a μMicrobial-Domestication Pod (μMD Pod). This in situ cultivation device facilitates cell signaling from neighbouring species and interactions with environmental stimuli for marine bacterial growth to overcome current barriers faced by standard laboratory cultivation methods.

Cultivating marine bacteria under laboratory conditions: Overcoming the “unculturable” dogma

Underexplored seawater environments may contain biological resources with potential for new biotechnological applications. Metagenomic techniques revolutionized the study of bacterial communities but culture dependent methods will still be important to help the biodiscovery of new products and enzymes from marine bacteria. In this context, we promoted the growth of bacteria from a marine rock pond by culture dependent techniques and compared the results with culture independent methods. The total number of bacteria and diversity were studied in different agar plate media during 6 weeks. Agar plate counting was of the same order of magnitude of direct microscopy counts. The highest efficiency of cultivation was 45% attained in marine agar medium. Molecular analysis revealed 10 different phyla of which only four were isolated by the culture dependent method. On the other hand, four taxonomic orders were detected by cultivation but not by the molecular technique. These include bacteria from the phyla Bacillota and Actinomycetota. Our study shows that it is possible to grow more than the traditionally considered 1% of bacteria from a seawater sample using standard agar plate techniques and laboratorial conditions. The results also demonstrate the importance of culture methods to grow bacteria not detected by molecular approaches for future biotechnological applications.

High-throughput Method for Novel Medium Development for Culture of Anaerobic Gut Bacteria

Gut microbiota play important roles in the health of their host and detailed investigation of these organisms requires in vitro culture. Culturing strictly anaerobic bacteria can be a challenge as the gut environment they inhabit is nutritionally complex. Use of complex media containing nutritionally rich but undefined gut fluid reduces the accuracy of physiological and metabolomic studies. Here we present a high-throughput protocol for comparing growth rates of fastidiously anaerobic bacteria on different media. These protocols can be used to develop a solid medium made up of commercially sourced ingredients, providing replicable growth conditions for previously uncultured anaerobic bacteria. As many fastidious bacteria grow poorly in a liquid broth, these protocols measure bacterial growth rate on solid media. These protocols speed up and simplify the growth rate measurement process by using a multiwell format and equations in place of physical McFarland standards to calculate approximate cell density. Bacterial strains belonging to the families Erysipelotrichaceae and Lachnospiraceae (phylum Firmicutes) isolated from the hindgut of Kyphosus sydneyanus were used to demonstrate the efficacy of these protocols. Bacterial growth rates were compared between a nutritionally rich medium with gut fluid versus a novel replicable medium with mannitol. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of solid YCFA growth medium Basic Protocol 2: Collection of fish gut samples and plating to single isolates Basic Protocol 3: Genetic identification of single isolates with colony PCR and 16S rRNA gene sequencing Basic Protocol 4: Measurement of bacterial growth rates on solid media.

Microbial diversity in extreme environments

A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.

Fungal communities in feces of the frugivorous bat Ectophylla alba and its highly specialized Ficus colubrinae diet

BACKGROUND

Bats are important long-distance dispersers of many tropical plants, yet, by consuming fruits, they may disperse not only the plant's seeds, but also the mycobiota within those fruits. We characterized the culture-dependent and independent fungal communities in fruits of Ficus colubrinae and feces of Ectophylla alba to determine if passage through the digestive tract of bats affected the total mycobiota.

RESULTS

Using presence/absence and normalized abundance data from fruits and feces, we demonstrate that the fungal communities were significantly different, even though there was an overlap of ca. 38% of Amplicon Sequence Variants (ASVs). We show that some of the fungi from fruits were also present and grew from fecal samples. Fecal fungal communities were dominated by Agaricomycetes, followed by Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Malasseziomycetes, while fruit samples were dominated by Dothideomycetes, followed by Sordariomycetes, Agaricomycetes, Eurotiomycetes, and Laboulbeniomycetes. Linear discriminant analyses (LDA) show that, for bat feces, the indicator taxa include Basidiomycota (i.e., Agaricomycetes: Polyporales and Agaricales), and the ascomycetous class Eurotiomycetes (i.e., Eurotiales, Aspergillaceae). For fruits, indicator taxa are in the Ascomycota (i.e., Dothideomycetes: Botryosphaeriales; Laboulbeniomycetes: Pyxidiophorales; and Sordariomycetes: Glomerellales). In our study, the differences in fungal species composition between the two communities (fruits vs. feces) reflected on the changes in the functional diversity. For example, the core community in bat feces is constituted by saprobes and animal commensals, while that of fruits is composed mostly of phytopathogens and arthropod-associated fungi.

CONCLUSIONS

Our study provides the groundwork to continue disentangling the direct and indirect symbiotic relationships in an ecological network that has not received enough attention: fungi-plants-bats. Findings also suggest that the role of frugivores in plant-animal mutualistic networks may extend beyond seed dispersal: they may also promote the dispersal of potentially beneficial microbial symbionts while, for example, hindering those that can cause plant disease.

Biodiversity and Enzyme Activity of Marine Fungi with 28 New Records from the Tropical Coastal Ecosystems in Vietnam

The coastal marine ecosystems of Vietnam are one of the global biodiversity hotspots, but the biodiversity of marine fungi is not well known. To fill this major gap of knowledge, we assessed the genetic diversity (ITS sequence) of 75 fungal strains isolated from 11 surface coastal marine and deeper waters in Nha Trang Bay and Van Phong Bay using a culture-dependent approach and 5 OTUs (Operational Taxonomic Units) of fungi in three representative sampling sites using next-generation sequencing. The results from both approaches shared similar fungal taxonomy to the most abundant phylum (Ascomycota), genera (Candida and Aspergillus) and species (Candida blankii) but were different at less common taxa. Culturable fungal strains in this study belong to 3 phyla, 5 subdivisions, 7 classes, 12 orders, 17 families, 22 genera and at least 40 species, of which 29 species have been identified and several species are likely novel. Among identified species, 12 and 28 are new records in global and Vietnamese marine areas, respectively. The analysis of enzyme activity and the checklist of trophic mode and guild assignment provided valuable additional biological information and suggested the ecological function of planktonic fungi in the marine food web. This is the largest dataset of marine fungal biodiversity on morphology, phylogeny and enzyme activity in the tropical coastal ecosystems of Vietnam and Southeast Asia. Biogeographic aspects, ecological factors and human impact may structure mycoplankton communities in such aquatic habitats.

Dysbiotic microbiota interactions in Crohn's disease

Crohn's disease (CD) is a major form of inflammatory bowel disease characterized by transmural inflammation along the alimentary tract. Changes in the microbial composition and reduction in species diversity are recognized as pivotal hallmarks in disease dynamics, challenging the gut barrier function and shaping a pathological immune response in genetically influenced subjects. The purpose of this review is to delve into the modification of the gut microbiota cluster network during CD progression and to discuss how this shift compromises the gut barrier integrity, granting the translocation of microbes and their products. We then complete the scope of the review by retracing gut microbiota dysbiosis interactions with the main pathophysiologic factors of CD, starting from the host's genetic background to the immune inflammatory and fibrotic processes, providing a standpoint on the lifestyle/exogenous factors and the potential benefits of targeting a specific gut microbiota.

The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects

Rocks that react with liquid water are widespread but spatiotemporally limited throughout the solar system, except for Earth. Rock-forming minerals with high iron content and accessory minerals with high amounts of radioactive elements are essential to support rock-hosted microbial life by supplying organics, molecular hydrogen, and/or oxidants. Recent technological advances have broadened our understanding of the rocky biosphere, where microbial inhabitation appears to be difficult without nutrient and energy inputs from minerals. In particular, microbial proliferation in igneous rock basements has been revealed using innovative geomicrobiological techniques. These recent findings have dramatically changed our perspective on the nature and the extent of microbial life in the rocky biosphere, microbial interactions with minerals, and the influence of external factors on habitability. This study aimed to gather information from scientific and/or technological innovations, such as omics-based and single-cell level characterizations, targeting deep rocky habitats of organisms with minimal dependence on photosynthesis. By synthesizing pieces of rock-hosted life, we can explore the evo-phylogeny and ecophysiology of microbial life on Earth and the life’s potential on other planetary bodies.

Application of Deep Learning in Plant-Microbiota Association Analysis

Unraveling the association between microbiome and plant phenotype can illustrate the effect of microbiome on host and then guide the agriculture management. Adequate identification of species and appropriate choice of models are two challenges in microbiome data analysis. Computational models of microbiome data could help in association analysis between the microbiome and plant host. The deep learning methods have been widely used to learn the microbiome data due to their powerful strength of handling the complex, sparse, noisy, and high-dimensional data. Here, we review the analytic strategies in the microbiome data analysis and describe the applications of deep learning models for plant–microbiome correlation studies. We also introduce the application cases of different models in plant–microbiome correlation analysis and discuss how to adapt the models on the critical steps in data processing. From the aspect of data processing manner, model structure, and operating principle, most deep learning models are suitable for the plant microbiome data analysis. The ability of feature representation and pattern recognition is the advantage of deep learning methods in modeling and interpretation for association analysis. Based on published computational experiments, the convolutional neural network and graph neural networks could be recommended for plant microbiome analysis.

Bacterial Endophytes from Vitis vinifera L. - Metabolomics Characterization of Plant-Endophyte Crosstalk

Bacterial endophytes are known to protect Vitis vinifera L. against various harmful effects of the environment and support its growth. However, for the most part, biochemical responses of such co-existence have not yet been fully elucidated. In this work, we aimed to characterize the activities of endophytic consortia in a plant-endophyte extract by measuring five indicators of colonization (overall endophyte metabolic activity, microbial ACC deaminase activity, ability to solubilize phosphorus, ability to convert atmospheric nitrogen to ammonia ions, and ability to produce growth promoting indole acetic acid), and find relationships between these activities and metabolome. The V. vinifera canes for the metabolomics fingerprinting were extracted successively with water and methanol, and analysed by ultra-high performance liquid chromatography coupled with high resolution mass spectrometry. For data processing, the MS-DIAL - MS-CleanR - MS-FINDER software platform was used, and the data matrix was processed by PCA and PLS-DA multivariate statistical methods. The metabolites that were upregulated with the heavy endophyte colonization were mainly chlorins, phenolics, flavonoid and terpenoid glycosides, tannins, dihydropyranones, sesquiterpene lactones, and long-chain unsaturated fatty acids.

Risks, characteristics, and control strategies of disinfection-residual-bacteria (DRB) from the perspective of microbial community structure

The epidemic of COVID-19 has aroused people's particular attention to biosafety. A growing number of disinfection products have been consumed during this period. However, the flaw of disinfection has not received enough attention, especially in water treatment processes. While cutting down the quantity of microorganisms, disinfection processes exert a considerable selection effect on bacteria and thus reshape the microbial community structure to a great extent, causing the problem of disinfection-residual-bacteria (DRB). These systematic and profound changes could lead to the shift in regrowth potential, bio fouling potential, as well as antibiotic resistance level and might cause a series of potential risks. In this review, we collected and summarized the data from the literature in recent 10 years about the microbial community structure shifting of natural water or wastewater in full-scale treatment plants caused by disinfection. Based on these data, typical DRB with the most reporting frequency after disinfection by chlorine-containing disinfectants, ozone disinfection, and ultraviolet disinfection were identified and summarized, which were the bacteria with a relative abundance of over 5% in the residual bacteria community and the bacteria with an increasing rate of relative abundance over 100% after disinfection. Furthermore, the phylogenic relationship and potential risks of these typical DRB were also analyzed. Twelve out of fifteen typical DRB genera contain pathogenic strains, and many were reported of great secretion ability. Pseudomonas and Acinetobacter possess multiple disinfection resistance and could be considered as model bacteria in future studies of disinfection. We also discussed the growth, secretion, and antibiotic resistance characteristics of DRB, as well as possible control strategies. The DRB phenomenon is not limited to water treatment but also exists in the air and solid disinfection processes, which need more attention and more profound research, especially in the period of COVID-19.

Role of Yeasts in the Cranberry Fruit Rot Disease Complex

Cranberry fruit rot (CFR) is an economically important disease caused by at least 10 species of filamentous fungi. Despite the application of fungicides, incidence of CFR is sometimes high, raising the possibility of a role for microbes other than fungi in the CFR complex. Isolation of microbes from rotten berries on culture media that favor either bacteria or yeasts resulted in mucoid colonies from <15% of dry-harvested rotten berries but up to 60% of wet-harvested berries. The mucoid colonies were identified as yeasts, primarily in the family Saccharomycetaceae. Inoculation of sound berries with three yeasts, Hanseniaspora uvarum, Pichia fermentans, and Pichia terricola, resulted in significantly higher incidence and severity of rot symptoms compared with mock-inoculated controls; these yeasts were recovered from inoculated berries, providing evidence of their pathogenicity. The minimum concentrations of azoxystrobin, chlorothalonil, and prothioconazole that resulted in 80% inhibition of growth compared with untreated controls (MIC80) were determined for a subset of yeasts. In general, MIC80s were higher for azoxystrobin and prothioconazole (usually >64 µg/ml) than for chlorothalonil (usually ≤1 µg/ml). To complement culture-dependent studies, DNA was isolated from wet- and dry-harvested rotten berries, and fungi were identified to the level of family by high-throughput sequencing of the fungal internal transcribed spacer region. There were no fungal families consistently detected among samples by one method (culturing or high-throughput sequencing) and missed by the other that have not previously been reported in cranberry; however, some fungal families were found to be more abundant by one method versus the other. Harvest method (wet or dry) had a significant effect on the composition of fungal communities of rotten berries (P < 0.001), and operational taxonomic units representing the Saccharomycetaceae were more abundant in wet- than dry-harvested berries. Taken together, the results suggest that some yeasts are pathogenic to cranberry and may be especially relevant in wet-harvested berries.

Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin

Background

Staphylococci are important members of the human skin microbiome. Many staphylococcal species and strains are commensals of the healthy skin microbiota, while few play essential roles in skin diseases such as atopic dermatitis. To study the involvement of staphylococci in health and disease, it is essential to determine staphylococcal populations in skin samples beyond the genus and species level. Culture-independent approaches such as amplicon next-generation sequencing (NGS) are time- and cost-effective options. However, their suitability depends on the power of resolution.

Results

Here we compare three amplicon NGS schemes that rely on different targets within the genes tuf and rpsK, designated tuf1, tuf2 and rpsK schemes. The schemes were tested on mock communities and on human skin samples. To obtain skin samples and build mock communities, skin swab samples of healthy volunteers were taken. In total, 254 staphylococcal strains were isolated and identified to the species level by MALDI-TOF mass spectrometry. A subset of ten strains belonging to different staphylococcal species were genome-sequenced. Two mock communities with nine and eighteen strains, respectively, as well as eight randomly selected skin samples were analysed with the three amplicon NGS methods. Our results imply that all three methods are suitable for species-level determination of staphylococcal populations. However, the novel tuf2-NGS scheme was superior in resolution power. It unambiguously allowed identification of Staphylococcus saccharolyticus and distinguish phylogenetically distinct clusters of Staphylococcus epidermidis.

Conclusions

Powerful amplicon NGS approaches for the detection and relative quantification of staphylococci in human samples exist that can resolve populations to the species and, to some extent, to the subspecies level. Our study highlights strengths, weaknesses and pitfalls of three currently available amplicon NGS approaches to determine staphylococcal populations. Applied to the analysis of healthy and diseased skin, these approaches can be useful to attribute host-beneficial and -detrimental roles to skin-resident staphylococcal species and subspecies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02284-1.

Current Knowledge on the Fungal Degradation Abilities Profiled through Biodeteriorative Plate Essays

Fungi are known to contribute to the development of drastic biodeterioration of historical and valuable cultural heritage materials. Understandably, studies in this area are increasingly reliant on modern molecular biology techniques due to the enormous benefits they offer. However, classical culture dependent methodologies still offer the advantage of allowing fungal species biodeteriorative profiles to be studied in great detail. Both the essays available and the results concerning distinct fungal species biodeteriorative profiles obtained by amended plate essays, remain scattered and in need of a deep summarization. As such, the present work attempts to provide an overview of available options for this profiling, while also providing a summary of currently known fungal species putative biodeteriorative abilities solely obtained by the application of these methodologies. Consequently, this work also provides a series of checklists that can be helpful to microbiologists, restorers and conservation workers when attempting to safeguard cultural heritage materials worldwide from biodeterioration.

Gut microbiota-mediated pesticide toxicity in humans: Methodological issues and challenges in the risk assessment of pesticides

Many in vivo and in vitro studies have shown that pesticides can disrupt the functioning of gut microbiota (GM), which can lead to many diseases in humans. While the tests developed by the Organization of Economic Cooperation and Development (OECD) are expected to capture most apical effects resulting from GM disruptions, exclusion of GM in the risk assessment might mischaracterize hazards or overestimate/underestimate risks, especially when extrapolating results from one species to another species or population with a substantially different GM. On the other hand, direct assessment of GM-mediated effects may face challenges in identifying hazards, since not all GM perturbations will lead to human adverse effects. In this regard, reliable and validated biomarkers for common GM-mediated adverse effects may be very useful in the identification of GM-mediated pesticide toxicity. Nevertheless, proving causality of GM-mediated effects will need modifications of Bradford Hill criteria as well as Koch's postulates, which are more suitable for the "one-pathogen" paradigm. Furthermore, risk assessment of GM-mediated effects may require pesticide toxicokinetics along the gut, possibly through modeling, and the establishment of the involvement of GM in the mechanism of action (MOA) of the pesticide. Risk assessment of GM mediated effects also requires the standardization of experimental approaches as well as the establishment of microbial reference communities, since variations exist among GM in human populations.

Role of Exposure on the Microbial Consortiums on Historical Rural Granite Buildings

Local granite has been used throughout history in Galicia (NW Spain), forming the basis of much of the region’s architecture. Like any other rock, granite provides an ecological niche for a multitude of organisms that form biofilms that can affect the physical integrity of the stone. In this study, for the first time, characterization of the microbial consortium forming biofilms that developed on historical rural granite buildings is carried out using a combination of culture-dependent and next generation sequencing (NGS) techniques. Results pointed to differences in biofilm composition on the studied rural granite buildings and that of previously analyzed urban granite buildings, especially in terms of abundance of cyanobacteria and lichenized fungi. Exposure was corroborated as an important factor, controlling both the diversity and abundance of microorganisms on walls, with environmental factors associated with a northern orientation favoring a higher diversity of fungi and green algae, and environmental factors associated with the west orientation determining the abundance of lichenized fungi. The orientation also affected the distribution of green algae, with one of the two most abundant species, Trentepohlia cf. umbrina, colonizing north-facing walls, while the other, Desmococcus olivaceus, predominated on west-facing walls.

The microbial rare biosphere: current concepts, methods and ecological principles

Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.

Effects of Different Continuous Cropping Years on Bacterial Community and Diversity of Cucumber Rhizosphere Soil in Solar-Greenhouse

The rhizosphere soils from 1, 3, 5, and 7 years of cucumber continuous cropping in solar-greenhouse were used as the research objects. The region of bacterial 16S rRNA was analyzed by Illumina MiSeq high-throughput sequencing technology. The effect of continuous cropping years on the microbial community structure and diversity in cucumber soil in the greenhouse was investigated. The physical and chemical properties of soil and the activities of urease and catalase were determined. The results showed that cucumber crop succession for different years affected the community composition of the bacteria at the phylum level, and the abundance of Proteobacteria, Chloroflexi, Gemmatimonadetes, Patescibacteria and Firmicutes gradually increased, while Actinobacteria in the soil significantly decreased. Among the top 15 significantly different genera, with the extension of successive years, the relative abundance of most genera in bacteria decreased after a small increase in year 3. The diversity results indicated that soil samples from continuous cropping for 7 years had the lowest community diversity. PICRUSt analysis showed a decreasing trend in soil bacterial function as the cucumber crop succession age increased. In environmental factor clustering analysis, the soil bacterial community was significantly correlated with pH, available nitrogen (AN), soil urease (SUR) and available phosphorus (AP), and the effect on the bacterial community was expressed as SUR > AP > AN > pH.

Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences

With the advent of next-generation sequencing technology, it has become convenient and cost efficient to thoroughly characterize the microbial diversity and taxonomic composition in various environmental samples. Millions of sequencing data can be generated, and how to utilize this enormous sequence resource has become a critical concern for microbial ecologists. One particular challenge is the OTUs (operational taxonomic units) picking in 16S rRNA sequence analysis. Lucky, this challenge can be directly addressed by sequence clustering that attempts to group similar sequences. Therefore, numerous clustering methods have been proposed to help to cluster 16S rRNA sequences into OTUs. However, each method has its clustering mechanism, and different methods produce diverse outputs. Even a slight parameter change for the same method can also generate distinct results, and how to choose an appropriate method has become a challenge for inexperienced users. A lot of time and resources can be wasted in selecting clustering tools and analyzing the clustering results. In this study, we introduced the recent advance of clustering methods for OTUs picking, which mainly focus on three aspects: (i) the principles of existing clustering algorithms, (ii) benchmark dataset construction for OTU picking and evaluation metrics, and (iii) the performance of different methods with various distance thresholds on benchmark datasets. This paper aims to assist biological researchers to select the reasonable clustering methods for analyzing their collected sequences and help algorithm developers to design more efficient sequences clustering methods.

Impact of encapsulating a probiotic (Pediococcus pentosaceus Li05) within gastro-responsive microgels on Clostridium difficile infections

Antibiotic treatment is often followed by Clostridium difficile infection (CDI), which causes severe diarrhea and other health issues. Oral administration of Pediococcus pentosaceus Li05 (Li05) has been shown to have great potential in preventing CDI. However, the viability of Li05 is greatly reduced during storage and passage through the gastrointestinal (GI) tract, which limits its biological activity. In this study, a gastro-responsive microgel was designed to encapsulate and protect Li05 to enhance its efficacy against CDI. The viability of Li05 encapsulated within the microgels was significantly enhanced during long-term storage and after exposure to simulated GI fluids. Moreover, this gastro-responsive microgel led to greater sustained release of the probiotic. In a mouse CDI model, we found that encapsulated Li05 was better at inhibiting C. difficile infection than nonencapsulated Li05, as demonstrated through analysis of the probiotic survival rate, spleen weight, colonic histology, and inflammatory cytokine levels. Moreover, the gut microbial diversity was enriched by treatment with encapsulated Li05. These results suggest that encapsulating Li05 within biopolymer microgels may enhance its ability to prevent and treat CDI using functional foods, supplements, or pharmaceuticals.

Significance of lysogeny for the metabolism of Desulfovibrio spp. strains isolated from aquatic environments of Georgia

AIMS

Sulphate-reducing bacteria (SRB) are ecologically important group of anaerobic micro-organisms that can reduce sulphate to form hydrogen sulphide-a toxic gas causing iron corrosion on metal surfaces. In this work, SRB strains were isolated from aquatic environments in the country of Georgia to determine their lysogenicity and the role of temperate phages in host metabolism.

METHODS AND RESULTS

SRB strains were isolated in samples from the Black Sea coast of Georgia. Based on their genetic, cytological and physiological properties of bacteria, 10 Georgian isolates were assigned to the genus Desulfovibrio. Temperate bacteriophages were induced from three out of ten strains by UV-exposure. Comparison of metal (Fe and Cr) reduction and utilization of various carbon sources by the wild-type (lysogenic) bacterial strains and their UV-irradiated counterparts was done.

CONCLUSIONS

Temperate phage in the cells of SRB could alter significant functions of bacteria and may have a contribution in the acquisition of different traits by SRB.

SIGNIFICANCE AND IMPACT OF THE STUDY

This article pointed to a significant role for temperate bacteriophages in the metabolism and metabolic potential of host strains of SRB, which were first isolated from the aquatic environment of Georgia.

PPIT: an R package for inferring microbial taxonomy from nifH sequences

MOTIVATION

Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale.

RESULTS

We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes.

AVAILABILITY

PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Fungal Community and Biodeterioration Analysis of Hull Wood and Its Storage Environment of the Nanhai No. 1 Shipwreck

The Nanhai No. 1 shipwreck is a Chinese merchant ship in the Southern Song Dynasty, and now it is stored in a huge enclosed glass warehouse in Maritime Silk Road Museum in Guangdong Province. At present, the hull of the Nanhai No. 1 shipwreck is still being excavated, and a small part of the hull wood is soaked in a specific solution to desalt. Through long-term exploration, we found that the above two states of hull wood had undergone biodeterioration, so the purpose of this study is to analyze the fungal community of exposed and soaked wood from the Nanhai No. 1 shipwreck. We sampled 10 exposed hull wood and sea mud samples, two wood storage water samples, and air samples in the glass warehouse. We used scanning electron microscope and optical microscope to find that there were obvious fungal structures in exposed wood and wood storing water samples. High-throughput sequencing of fungi revealed that the most abundant genera in exposed and soaked wood were Fusarium sp., and Scedosporium sp., respectively. In addition, Fusarium solani and Scedosporium apiospermum were successfully isolated from the hull wood surface and wood storing water samples, and the degradation tests of lignin and cellulose, the sensitivity tests of biocides and growth curve assay were carried out. We also found that Penicillium sp. and Cladosporium sp. are the most abundant in the glass warehouse air. Our research results show that F. solani and S. apiospermum should be regarded as a major threat to the preservation of the Nanhai No. 1 shipwreck. These results provide a reference for our protection of shipwrecks and other similar artifacts.

Diversity and succession of the microbial community and its correlation with lipid oxidation in dry-cured black carp (Mylopharyngodon piceus) during storage

This study aimed to achieve deeper insights into the microbiota composition and dynamic succession of the dry-cured black carp during storage using a high-throughput sequencing technique (HTS). The effect of lipid oxidation on microorganisms was also evaluated. Over 651 bacterial genera belonging to 37 phyla were identified. Firmicutes, Proteobacteria and Actinobacteria were the main bacterial phylum, some are highly associated with meat spoilage. Staphylococcus, Macrococcus and Acinetobacter were the most three microbial genera throughout the entire storage period (30 days). Between two different storage temperature, refrigeration at 4 °C could facilitate maintaining the microbial diversity, while 25 °C storage led to the formation of dominant microflora and the reduction of community diversity. Canonical correspondence analysis (CCA) showed that acid value (AV), malondialdehyde (MDA) and 4-hydroxy-2-hexenal (HHE) contents were three key environmental factors (oxidation products) affecting the profile of the microbiota. Staphylococcus presented a positive correlation with HHE content, while Macrococcus and Acinetobacter were negatively correlated with HHE content. These results could expand our knowledge on the effect of lipid oxidation on change of microbial distribution, it could also present an guideline to develop advanced storage methods for the vacuum packed dry-cured fish products.

Taisui TS-2007S, a Large Microbial Mat Discovered in Soil in China

In this study, Taisui TS-2007S, a previously unidentified biological object discovered in soil in China, was identified. TS-2007S was shown to contain abundant carbohydrates but a scarcity of protein, fat, and minerals. The exopolymers of TS-2007S showed FT-IR spectra that were similar to those of xanthan gum (XG) but that were dissimilar to those of polyvinyl alcohol (PVA). The NMR spectra of TS-2007S exopolymers in D₂O were similar to those of PVA but differed from those of xanthan gum. Unlike PVA, TS-2007S exopolymers and xanthan gum were not soluble in dimethyl sulfoxide (DMSO). Furthermore, the exopolymers contained many monosaccharide components, including fucose, rhamnose, mannose, and glucuronic acid in a molar ratio of 87.90:7.49:4.45:0.15. The exopolymers also included traces of glucuronic acid, galactose, and xylose. Taken together, these results suggest that the exopolymers are microbial extracellular polymeric substances (EPSs). The microbial community structure in TS-2007S showed that the predominant bacterial, archaeal, and fungal phyla were Proteobacteria, Euryarchaeota, and Ascomycota at high relative abundances of 90.77, 97.15, and 87.43%, respectively, different from those observed in water and soil environments. Based on these results, we strongly propose that TS-2007S should be defined as a microbial mat formed in soil.

Oyster Calcifying Fluid Harbors Persistent and Dynamic Autochthonous Bacterial Populations That May Aid in Shell Formation

The eastern oyster (Crassostrea virginica) is a keystone species in estuarine environments but faces threats to shell formation associated with warming temperatures and acidification. Extrapallial fluid (EF), which is responsible for shell formation, harbors diverse and abundant microbial communities. Commensal microbial communities are vital to host health and fitness, yet long-term studies investigating temporal responses of the EF microbiome and its function in oyster fitness are lacking. In this study, bacterial communities of oyster EF and the water column were characterized monthly from October 2010 to September 2011. We investigated the selection, composition, and dynamics of resident and transient community members, evaluated the impact of temperature on EF microbial communities, and examined the functional role of the EF microbiome. Oyster EF communities were significantly different from the water column and were enriched for several taxa, including the Deltaproteobacteria, Epsilonproteobacteria, and Gammaproteobacteria. Overall, 94 resident members were identified in oyster EF. These members were persistent and abundant, comprising on average 33% of EF communities. Resident EF communities formed high-temperature and low-temperature groups and were more abundant overall at colder temperatures. Oyster EF resident communities were predicted to be enriched for dissimilatory nitrate reduction, nitrogen fixation, nitrification, and sulfite reductase genes. Sulfate and nitrate reduction may have a synergistic effect on calcium carbonate precipitation and indirectly aid in shell formation. Therefore, the potential role of the oyster EF microbiome in shell formation warrants further investigation as oysters and other shellfish face the future impacts of ocean warming and acidification.

Effects of soil preservation for biodiversity monitoring using environmental DNA

Environmental DNA (eDNA) metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa such as soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guideline for best practices so far. Here, we assessed the impact of four methods of soil sample preservation that can be conveniently used also in metabarcoding studies targeting remote or difficult to access areas. Tested methods include: preservation at room temperature for 6 hr, preservation at 4°C for 3 days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6 hr at room temperature and preservation for 21 days. For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under ideal conditions (i.e., extraction of eDNA immediately after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in molecular operational taxonomic units (MOTU) richness of bacteria, fungi and eukaryotes across treatments, but MOTU richness was similar across preservation methods if rare taxa were not considered. All the approaches were able to identify differences in community structure among habitats, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.

Assessment of Bacterial Contamination of Air at the Museum of King John III’s Palace at Wilanow (Warsaw, Poland): Selection of an Optimal Growth Medium for Analyzing Airborne Bacteria Diversity

There is no standardized protocol for the assessment of microbial air contamination in museums and other cultural heritage sites. Therefore, most museums conduct such assessments based on their own guidelines or good practices. Usually, microbial air contamination is assessed using only classical microbiology methods with the application of a single growth medium. Therefore, this medium should be carefully selected to limit any selective cultivation bias. Metabarcoding, i.e., a next-generation sequencing (NGS)-based method, combined with classical microbiological culturing was used to assess the effectiveness of various media applications in microbiological screening at the Museum of King John III’s Palace at Wilanow (Warsaw, Poland). The obtained results indicated that when using a classical microbiology approach to assess the microbial air contamination at the museum, the selection of a proper growth medium was critical. It was shown that the use of rich media (commonly applied by museum conservators) introduced significant bias by severely underreporting putative human pathogens and the bacterial species involved in biodeterioration. Therefore, we recommend the use of other media, such as Frazier or Reasoner’s 2A (R2A) medium, as they could yield more diverse communities and recovered the highest number of genera containing human pathogens, which may be suitable for public health assessments.

Identification of microbial interaction network: zero-inflated latent Ising model based approach

BACKGROUND

Throughout their lifespans, humans continually interact with the microbial world, including those organisms which live in and on the human body. Research in this domain has revealed the extensive links between the human-associated microbiota and health. In particular, the microbiota of the human gut plays essential roles in digestion, nutrient metabolism, immune maturation and homeostasis, neurological signaling, and endocrine regulation. Microbial interaction networks are frequently estimated from data and are an indispensable tool for representing and understanding the conditional correlation between the microbes. In this high-dimensional setting, zero-inflation and unit-sum constraint for relative abundance data pose challenges to the reliable estimation of microbial interaction networks.

METHODS AND RESULTS

To identify the microbial interaction network, the zero-inflated latent Ising (ZILI) model is proposed which assumes the distribution of relative abundance relies only on finite latent states and provides a novel way to solve issues induced by the unit-sum and zero-inflation constrains. A two-step algorithm is proposed for the model selection of ZILI. ZILI is evaluated through simulated data and subsequently applied to an infant gut microbiota dataset from New Hampshire Birth Cohort Study. The results are compared with results from Gaussian graphical model (GGM) and dichotomous Ising model (DIS). Providing ZILI is the true data-generating model, the simulation studies show that the two-step algorithm can identify the graphical structure effectively and is robust to a range of parameter settings. For the infant gut microbiota dataset, the final estimated networks from GGM and ZILI turn out to have significant overlap in which the ZILI tends to select the sparser network than those from GGM. From the shared subnetwork, a hub taxon Lachnospiraceae is identified whose involvement in human disease development has been discovered recently in literature.

CONCLUSIONS

Constrains induced by relative abundance of microbiota such as zero inflation and unit sum render the conditional correlation analysis unreliable for conventional methods such as GGM. The proposed optimal categoricalization based ZILI model provides an alternative yet elegant way to deal with these difficulties. The results from ZILI have reasonable biological interpretation. This model can also be used to study the microbial interaction in other body parts.

The benefit of culture-independent methods to detect bacteria and fungi in re-infected root filled teeth: a pilot study

AIM

To identify dominant microorganisms in root filled teeth with apical periodontitis by Pan-PCRs in comparison with a culture-dependent approach, focusing on fungal species profiling.

METHODOLOGY

The root filling material (gutta-percha) removed from 42 teeth with periapical radiolucencies undergoing root canal retreatments was analysed by molecular genetics techniques. Real-Time Pan-PCRs were conducted for the diagnosis of predominant bacteria (targeting 16S rDNA) and fungi (targeting ITS1-2 region). Identification of microorganisms was performed by Sanger sequencing of the PCR products and BLAST analysis. Additionally, subgingival plaque samples were collected and cultured to review the composition of the microbial flora. The McNemar test and the repeated measures anova were used for statistical analyses (significance level was set at P < 0.05).

RESULTS

Overall, 42/42 plaque samples had bacterial growth, whereas 32/42 gutta-percha samples had bacterial growth with a dominance of Streptococcus spp. (12/42) and Enterococcus faecalis (9/42). The mean number of bacterial taxa per gutta-percha sample was 1.6 cultivatable taxa, significantly lower than in the plaque sample that had six taxa/sample (P < 0.001). Fungus-specific cultures were negative for gutta-percha samples, and only one plaque sample had growth of a fungus. In total, 36/42 plaque samples were positive in bacterial Pan-PCRs. In bacterial Pan-PCRs of 31/42 gutta-percha samples, dominant microorganisms were identified including Streptococcus spp. (5/42) and E. faecalis (4/42). Moreover, in 7/42 gutta-percha samples, DNA of bacteria which are difficult-to-cultivate in microbiology routine culture (Acinetobacter,Pyramidobacter,Bacteroidetes,Synergistes,Atopobium and Pseudoramibacter) was found. DNA of Candida spp. was detected in 5/42 root canals by fungal Pan-PCR (1/5) and genus-specific Candida-PCR (5/5).

CONCLUSIONS

Pan-PCR assays remain appropriate as a broad-range approach for the detection of a dominant pathogen in gutta-percha samples which have less diverse microbial composition. The molecular genetic Pan-PCR approach has the advantage of detecting microorganisms that are as-yet-uncultivable or difficult-to-cultivate and should be therefore complement conventional microbiological diagnostics.

Molecular Detection of Campylobacter Species: Comparision of 16SrRNA with slyD, cadF, rpoA, and dnaJ Sequencing

Background

Campylobacter spp. are the main cause of human gastroenteritis. The 16SrRNA sequencing is one of fast molecualr method to detect this fastidious. In this study, we compared the sequencing of 16srRNA genewith four housekeeping genestodetect Campylobacter spp. in patients with diarrhea and healthy people.

Methods

60 samples of Campylobacter DNA extracted from stool samples of 30 patients with diarrhea and 30 healthy people were used. In order to detect Campylobacter, we designed primers for proliferation of 16SrRNA, cadF, dnaJ, slyD , and rpoA genes using Primer 3, Mega 4.0 and Blast software. Then the PCR products were sequenced using ABI system.

Results

The sequencing showed concordance of PCR-products with deposited sequences in the Gene Bank. Among diarrhea patients, 53.3% of samples were significantly (p< 0.05) positive for slyD and cadF genes and 50% of samples were positive using 16SrRNA, rpoA, and dnaJ genes by PCR assay. The average of sensitivity and specificity were found 53.33% and 83.33%, respectively.

Conclusion

Due to various copies of repeated sequences of 16SrRNA gene, analyzing its amplicons on electrophoresis may be more difficult than the slyD and cadF genes. According to our results, among the 5 studied genes; the highest detection rate was related to slyD and cadF genes. Although, dnaJ and rpoA genes,instead of 16SrRNA gene, can be considered as appropriate genes for molecular detection of Campylobacter bacteria.

Oligotrophic Nitrification and Denitrification Bacterial Communities in a Constructed Sewage Treatment Ecosystem and Nitrogen Removal of Delftia tsuruhatensis NF4

Oligotrophic nitrifiers and denitrifiers play important roles in the removal of nitrogen from wastewater. Here, we studied the dominant bacterial populations of the sewage treatment ecosystem (STE) water from different processes and those of culture on oligotrophic heterotrophic nitrification (OHN) medium and oligotrophic aerobic denitrification (OAD) medium, using co-analysis of Illumina HiSeq DNA sequencing and traditional culture methods. The results showed that the STE water had no dominant population of oligotrophic nitrifiers or oligotrophic denitrifiers. However, after culturing on OHN medium and OAD medium, the core genera Pseudomonas, Aeromonas, and Acinetobacter that have the nitrogen removal capacity in oligotrophic environments, dominated in the bacterial community. The principal component analysis (PCA) showed that the bacterial community in the constructed rapid infiltration (CRI) effluent water of STE had high similarity with those of cultures on OHN medium and OAD medium, which prompt the special purification role of nitrogen in the CRI system. The sodium alginate immobilized OAD bacteria strain Delftia tsuruhatensis NF4 was isolated from the CRI system, with total nitrogen (TN) removal efficiency of 43.3% in sterilized STE influent water, and 60.1% in OAD medium on day three. The immobilization significantly influenced the TN and nitrate removal efficiency in OAD medium (p < 0.05), but not in sterilized STE influent water (p > 0.05). This study would lay the foundation for resource discovery of oligotrophic heterotrophic nitrifiers and aerobic denitrifiers in STE and further functional application of them on the bioremediation of wastewater.

Oligotrophic nitrifiers and denitrifiers play important roles in the removal of nitrogen from wastewater. Here, we studied the dominant bacterial populations of the sewage treatment ecosystem (STE) water from different processes and those of culture on oligotrophic heterotrophic nitrification (OHN) medium and oligotrophic aerobic denitrification (OAD) medium, using co-analysis of Illumina HiSeq DNA sequencing and traditional culture methods. The results showed that the STE water had no dominant population of oligotrophic nitrifiers or oligotrophic denitrifiers. However, after culturing on OHN medium and OAD medium, the core genera Pseudomonas, Aeromonas, and Acinetobacter that have the nitrogen removal capacity in oligotrophic environments, dominated in the bacterial community. The principal component analysis (PCA) showed that the bacterial community in the constructed rapid infiltration (CRI) effluent water of STE had high similarity with those of cultures on OHN medium and OAD medium, which prompt the special purification role of nitrogen in the CRI system. The sodium alginate immobilized OAD bacteria strain Delftia tsuruhatensis NF4 was isolated from the CRI system, with total nitrogen (TN) removal efficiency of 43.3% in sterilized STE influent water, and 60.1% in OAD medium on day three. The immobilization significantly influenced the TN and nitrate removal efficiency in OAD medium (p < 0.05), but not in sterilized STE influent water (p > 0.05). This study would lay the foundation for resource discovery of oligotrophic heterotrophic nitrifiers and aerobic denitrifiers in STE and further functional application of them on the bioremediation of wastewater.