Cultivation strategies for growth of uncultivated bacteria

Microbial Interactions in Rearing Systems for Marine Fish Larvae

This article reviews the scientific literature discussing the microbial interactions between water microbiota, live food microbiota, fish larvae immune system and gut microbiota, and biofilm microbial communities in rearing systems for marine fish larvae. Fish gut microbiota is the first line of defense against opportunistic pathogens, and marine fish larvae are vulnerable to high mortalities during the first weeks after hatching. The bacterial colonization of fish larvae is a dynamic process influenced by environmental and host-related factors. The bacteria transferred to larvae from the eggs can influence the composition of the gut microbiota in the early stages of fish. Fish larvae ingest free-living microorganisms present in the water, as marine fish larvae drink water for osmoregulation. In marine aquaculture systems, the conventional feeding-rearing protocol consists of zooplankton (rotifers, Artemia, and copepods). These live food organisms are filter-feeders. Once transferred to a new environment, they quickly adopt the microflora of the surrounding water. So, the water microbiota is similar to the microbiota of the live food at the time of ingestion of live food by the larvae. In aquaculture rearing systems, bacterial biofilms may harbor opportunistic pathogenic bacteria and serve as a reservoir for those microbes, which may colonize the water column. The methods applied for the study of fish larvae microbiota were reviewed.

A modified iChip for in situ cultivation of bacteria in arid environments

Antimicrobial resistance is an ever-increasing problem for human health, and with only a few novel antimicrobials discovered in recent decades, an extraordinary effort is needed to circumvent this crisis. A promising source of new microbial-derived antimicrobial compounds resides in the large fraction of microbes that are not readily cultured by standard cultivation. It has previously been shown that nests of the social spider Stegodyphus dumicola contain a diverse bacterial community, where only a small fraction of the microbes could be recovered by standard cultivation. To improve the recovery of the bacterial diversity cultured from nests, we modified the previously described isolation chip (iChip) to fit the natural arid environment of S. dumicola nests. Here we provide a comprehensive analysis of the modified iChip's performance. We found that the modified iChip improved the overall culturability, performed equally or better at recovering the bacterial diversity from individual nests, and improved the recovery of rare isolates compared to standard cultivation. Furthermore, we show that the modified iChip can be used in the field. In addition, we observed that the nests contain volatile organic compounds (VOCs) that could serve as substrate for the selective enrichment of rare and iChip-specific isolates. Our modified iChip can be applied for in situ cultivation in a broad range of arid habitats that can be exploited for future drug discovery.IMPORTANCEThe demand for novel antimicrobial compounds is an ever-increasing problem due to the rapid spread of antibiotic-resistant microbes. Therefore, exploring new habitats for microbial-derived antimicrobial compounds is crucial. The nest microbiome of Stegodyphus dumicola remains largely unexplored and could potentially serve as a new source of antimicrobial compounds. To access the nest's microbial diversity, we designed a modified iChip for in situ cultivation inside spider nests and tested its applications in both field and laboratory settings. Our study shows that the iChip's ability to recover in situ abundant genera was comparable or superior to standard cultivation, while the recovery of rare (low-abundant genera) was higher. We argue that these low-abundant and iChip-specific isolates are enriched from naturally occurring nest volatile organic compounds (VOCs) during iChip incubation.

A Methodological Study on Microbial In Vivo Sampling Methods of Root Canal Microbiota for Next-Generation Gene Sequencing Analysis

INTRODUCTION

The aim was to evaluate the suitability of paper points or endodontic nickel-titanium files to sample microorganisms for in vivo investigation of endodontic microbiota by 16S ribosomal DNA (rDNA) sequencing.

METHODS

Forty-five patients presenting clinical and radiological signs of apical periodontitis were recruited for sampling, giving their written informed consent. Glide paths were assessed using C-Pilot Files and K-Files under electronic root canal length control under aseptic conditions. Microbial samples were taken from 84 root canals in duplicate, the first sample with a sterile paper point (size 15), the second with a sterile file (size 20/.06). After DNA extraction, the hypervariable region V4 of the bacterial 16 S rRNA gene was amplified and sequenced (Illumina MiSeq). Sequencing data were trimmed with Cutadapt and exact amplicon sequence variants generated by DADA2. Taxonomy was assigned based on the Human Oral Microbiome Database (eHOMD). Statistical analysis of diversity parameters comprised Wilcoxon signed-rank tests and permutational analysis of variance (PERMANOVA). Compositional differences were evaluated by differential abundance analysis (DESeq2). Microbial contamination during the sampling process and analysis were evaluated.

RESULTS

Concerning alpha diversity, richness and dissimilarity differed nonsignificantly between paper point and instrument samples (P > .05), whereas a significant difference was observed in the Shannon index (P < .05). Regarding beta diversity, paper point and instrument samples presented with similar microbial community compositions (P = 1.0, PERMANOVA). Paper point controls contained significantly higher proportions of Pseudomonadales (P < .05).

CONCLUSIONS

Paper point and endodontic instrument sampling generate valid specimens for 16S rDNA community profiling. Endodontic instrument sampling is easier to execute and, therefore, could be the technique of choice.

A decade of advances in human gut microbiome-derived biotherapeutics

Microbiome science has evolved rapidly in the past decade, with high-profile publications suggesting that the gut microbiome is a causal determinant of human health. This has led to the emergence of microbiome-focused biotechnology companies and pharmaceutical company investment in the research and development of gut-derived therapeutics. Despite the early promise of this field, the first generation of microbiome-derived therapeutics (faecal microbiota products) have only recently been approved for clinical use. Next-generation therapies based on readily culturable and as-yet-unculturable colonic bacterial species (with the latter estimated to comprise 63% of all detected species) have not yet progressed to pivotal phase 3 trials. This reflects the many challenges involved in developing a new class of drugs in an evolving field. Here we discuss the evolution of the live biotherapeutics field over the past decade, from the development of first-generation products to the emergence of rationally designed second- and third-generation live biotherapeutics. Finally, we present our outlook for the future of this field.

A metagenomic perspective on the microbial prokaryotic genome census

Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.

Boar semen microbiome: Insights and potential implications

The pioneers of next-generation sequencing technology and bioinformatic analyses initiated a new era in microbiology research by offering profound insights into bacterial microbiome communities. In the pig farming sector, while considerable attention has been devoted to the gut microbiome and the microbiome of the female reproductive tract, research on the microbiome of boar semen remains limited. Nonetheless, published studies have provided valuable insights, serving as important references and sparking ideas for further investigations into the seminal microbiome. Factors such as breed, seasons, feed additives, hygiene management, and antibiotic use are believed to exert a notable influence on the diversity and richness of bacterial genera in the boar seminal microbiome, potentially affecting semen quality. Moreover, current shifts towards sustainability in the swine industry, coupled with global guidelines concerning the prudent use of antibiotics in stored boar semen for artificial insemination, underscore the need for insights into factors influencing seminal bacteria. The objective of this review is to elucidate the current understanding of boar bacterial contents using conventional culture methods, as well as the boar seminal microbiome through metagenomics and bioinformatics. It also aims to review specific microbiome communities, such as those in the reproductive tract and gut, and their connections to semen quality. In addition, strategic enhancements for processing boar semen doses through alternative methods to improve seminal quality are proposed.

Mini review: antimicrobial compounds produced by bacteria associated with marine invertebrates

The marine environment is considered one of the most important ecosystems with high biodiversity. Microorganisms in this environment are variable and coexist with other marine organisms. The microbes associated with other marine organisms produce compounds with biological activity that may help the host's defense against invading organisms. The symbiotic association of bacteria with marine invertebrates is of ecological and biotechnological importance. Biologically active metabolites isolated from bacteria associated with marine invertebrates are considered potential sources of natural antimicrobial molecules for treating infectious diseases. Many studies have been conducted to screen the antimicrobial activity of metabolites produced by bacteria associated with marine invertebrates. This work provides an overview of the advancements in antimicrobial compound research on bacteria associated with marine invertebrates.

Utility of Serial Microbial Cell-free DNA Sequencing for Inpatient and Outpatient Pathogen Surveillance Among Allogeneic Hematopoietic Stem Cell Transplant Recipients

Background

This study characterizes the clinical utility and validity of the Karius test (KT), a plasma microbial cell-free DNA sequencing platform, as an infection surveillance tool among hematopoietic stem cell transplant (HCT) recipients, including monitoring for cytomegalovirus (CMV) and detecting infections relative to standard microbiologic testing (SMT).

Methods

A prospective, observational cohort study was performed among adult HCT recipients as inpatients and outpatients. Serial KTs were performed starting with 1 sample within 14 days before HCT, then weekly from 7-63 days posttransplant then monthly from 3-12 months post-HCT. Diagnostic performance of KT versus CMV polymerase chain reaction was evaluated with positive percent agreement and negative percent agreement. Infectious events (<12 months post-HCT) were extracted from medical records. For infectious events without positive SMT, 2 clinicians adjudicated KT results to determine if any detections were a probable cause. Difference in time from KT pathogen detection and infection onset was calculated.

Results

Of the 70 participants, mean age was 49.9 years. For CMV surveillance, positive percent agreement was 100% and negative percent agreement was 90%. There was strong correlation between CMV DNA and KT molecules per microliter (r 2: 0.84, P < .001). Of the 32 SMT+/KT+ infectious events, KT identified 26 earlier than SMT (median: -12 days) and an additional 5 diagnostically difficult pathogens identified by KT but not SMT.

Conclusions

KT detected CMV with high accuracy and correlation with quantitative polymerase chain reaction. Among infectious events, KT demonstrated additive clinical utility by detecting pathogens earlier than SMT and those not detected by SMT.

Diversity and Functionality of Bacteria Associated with Different Tissues of Spider Heteropoda venatoria Revealed through Integration of High-Throughput Sequencing and Culturomics Approaches

Spiders host a diverse range of bacteria in their guts and other tissues, which have been found to play a significant role in their fitness. This study aimed to investigate the community diversity and functional characteristics of spider-associated bacteria in four tissues of Heteropoda venatoria using HTS of the 16S rRNA gene and culturomics technologies, as well as the functional verification of the isolated strains. The results of HTS showed that the spider-associated bacteria in different tissues belonged to 34 phyla, 72 classes, 170 orders, 277 families, and 458 genera. Bacillus was found to be the most abundant bacteria in the venom gland, silk gland, and ovary, while Stenotrophomonas, Acinetobacter, and Sphingomonas were dominant in the gut microbiota. Based on the amplicon sequencing results, 21 distinct cultivation conditions were developed using culturomics to isolate bacteria from the ovary, gut, venom gland, and silk gland. A total of 119 bacterial strains, representing 4 phyla and 25 genera, with Bacillus and Serratia as the dominant genera, were isolated. Five strains exhibited high efficiency in degrading pesticides in the in vitro experiments. Out of the 119 isolates, 28 exhibited antibacterial activity against at least one of the tested bacterial strains, including the pathogenic bacteria Staphylococcus aureus, Acinetobacter baumanii, and Enterococcus faecalis. The study also identified three strains, GL312, PL211, and PL316, which exhibited significant cytotoxicity against MGC-803. The crude extract from the fermentation broth of strain PL316 was found to effectively induce apoptosis in MGC-803 cells. Overall, this study offers a comprehensive understanding of the bacterial community structure associated with H. venatoria. It also provides valuable insights into discovering novel antitumor natural products for gastric cancer and xenobiotic-degrading bacteria of spiders.

Enterotype-Dependent Probiotic-Mediated Changes in the Male Rat Intestinal Microbiome In Vivo and In Vitro

Beneficial properties of lactic acid bacteria have been known long ago, but particular interest in probiotics has arisen in the last two decades due to the understanding of the important role of intestinal microflora in human life. Thus, the ability of probiotics to support healthy homeostasis of gut microbiomes has received particular attention. Here, we evaluated the effect of a probiotic consisting of Bifidobacterium longum and Lacticaseibacillus paracasei on the gut microbiome of male rats, assessed their persistence in the fecal biota, and compared probiotic-mediated changes in vitro and in vivo. As expected, microbiomes of two enterotypes were identified in the feces of 21 animals, and it turned out that even a single dose of the probiotic altered the microbial composition. Upon repeated administration, the E1 biota temporarily acquired properties of the E2 type. Being highly sensitive to the intervention of probiotic bacteria at the phylum and genus levels, the fecal microbiomes retained the identity of their enterotypes when transferred to a medium optimized for gut bacteria. For the E2 biota, even similarities between probiotic-mediated reactions in vitro and in vivo were detected. Therefore, fecal-derived microbial communities are proposed as model consortia to optimize the response of resident bacteria to various agents.

Uncultured Microorganisms and Their Functions in the Fermentation Systems of Traditional Chinese Fermented Foods

Traditional Chinese fermented foods are diverse and loved by people for their rich nutrition and unique flavors. In the fermentation processes of these foods, the microorganisms in the fermentation systems play a crucial role in determining the flavor and quality. Currently, some microorganisms in the fermentation systems of traditional Chinese fermented foods are in a state of being unculturable or difficult to culture, which hinders the comprehensive analysis and resource development of the microbial communities in the fermentation systems. This article provides an overview of the uncultured microorganisms in the natural environment, in the fermentation systems of traditional Chinese fermented foods, and the research methods for studying such microorganisms. It also discusses the prospects of utilizing the uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods. The aim is to gain a comprehensive understanding of the microbial diversity and uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods in order to better exploit and utilize these microorganisms and promote the development of traditional Chinese fermented foods.

Atlas of mRNA translation and decay for bacteria

Regulation of messenger RNA stability is pivotal for programmed gene expression in bacteria and is achieved by a myriad of molecular mechanisms. By bulk sequencing of 5' monophosphorylated mRNA decay intermediates (5'P), we show that cotranslational mRNA degradation is conserved among both Gram-positive and -negative bacteria. We demonstrate that, in species with 5'-3' exonucleases, the exoribonuclease RNase J tracks the trailing ribosome to produce an in vivo single-nucleotide toeprint of the 5' position of the ribosome. In other species lacking 5'-3' exonucleases, ribosome positioning alters endonucleolytic cleavage sites. Using our metadegradome (5'P degradome) sequencing approach, we characterize 5'P mRNA decay intermediates in 96 species including Bacillus subtilis, Escherichia coli, Synechocystis spp. and Prevotella copri and identify codon- and gene-level ribosome stalling responses to stress and drug treatment. We also apply 5'P sequencing to complex clinical and environmental microbiomes and demonstrate that metadegradome sequencing provides fast, species-specific posttranscriptional characterization of responses to drug or environmental perturbations. Finally we produce a degradome atlas for 96 species to enable analysis of mechanisms of RNA degradation in bacteria. Our work paves the way for the application of metadegradome sequencing to investigation of posttranscriptional regulation in unculturable species and complex microbial communities.

Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease

Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm³ and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.

Effects of Matrix Composition and Temperature on Viability and Metabolic Activity of Microencapsulated Marine Bacteria

To enhance the discovery of novel natural products, various innovations have been developed to aid in the cultivation of previously unculturable microbial species. One approach involving the microencapsulation of bacteria has been gaining popularity as a new cultivation technique, with promising applications. Previous studies demonstrated the success of bacterial encapsulation; however, they highlighted that a key limitation of encapsulating bacteria within agarose is the high temperature required for encapsulation. Encapsulation of bacteria within agarose typically requires a temperature high enough to maintain the flow of agarose through microfluidic devices without premature gelation. Given the sensitivity of many bacterial taxa to temperature, the effect of various agarose-based encapsulating matrices on marine bacterial viability was assessed to further develop this approach to bacterial culture. It was determined that lowering the temperature of encapsulation via the use of low-gelling-temperature agarose, as well as the addition of nutrients to the matrix, significantly improved the viability of representative marine sediment bacteria in terms of abundance and metabolic activity. Based on these findings, the use of low-gelling-temperature agarose with supplemental nutrients is recommended for the encapsulation of marine bacteria obtained from temperate habitats.

Culturing and Molecular Approaches for Identifying Microbiota Taxa Impacting Children's Obesogenic Phenotypes Related to Xenobiotic Dietary Exposure

Integrated data from molecular and improved culturomics studies might offer holistic insights on gut microbiome dysbiosis triggered by xenobiotics, such as obesity and metabolic disorders. Bisphenol A (BPA), a dietary xenobiotic obesogen, was chosen for a directed culturing approach using microbiota specimens from 46 children with obesity and normal-weight profiles. In parallel, a complementary molecular analysis was carried out to estimate the BPA metabolising capacities. Firstly, catalogues of 237 BPA directed-cultured microorganisms were isolated using five selected media and several BPA treatments and conditions. Taxa from Firmicutes, Proteobacteria, and Actinobacteria were the most abundant in normal-weight and overweight/obese children, with species belonging to the genera Enterococcus, Escherichia, Staphylococcus, Bacillus, and Clostridium. Secondly, the representative isolated taxa from normal-weight vs. overweight/obese were grouped as BPA biodegrader, tolerant, or resistant bacteria, according to the presence of genes encoding BPA enzymes in their whole genome sequences. Remarkably, the presence of sporobiota and concretely Bacillus spp. showed the higher BPA biodegradation potential in overweight/obese group compared to normal-weight, which could drive a relevant role in obesity and metabolic dysbiosis triggered by these xenobiotics.

Diversity pattern of marine culturable heterotrophic bacteria in a region with coexisting upwelling and mud banks in the southeastern Arabian Sea

Mud banks and upwelling are two important oceanographic features occurring along the southwest coast of India during the southwest monsoon period. The study region, Alappuzha lying on the southwest coast of India, is unique due to the co-existence of upwelling and mud banks during the monsoon (MON) season. Water samples were collected from three stations, M1, M2, and M3, from April to September 2014, at weekly/biweekly intervals to determine the total bacterial abundance, viable prokaryotic counts, and total plate counts, along with measurements on physico-chemical parameters. For determining the heterotrophic culturable bacterial diversity, water samples were collected during two seasons, monsoon and pre-monsoon (PRM), from three stations. Water samples were inoculated into two non-selective broths for enrichment, DNA was extracted, and next-generation sequencing analysis was performed using Illumina Miseq sequencing. The sequence analysis revealed that dominant communities were Proteobacteria, followed by Firmicutes and Fusobacteria. Proportions of Fusobacteria increased during monsoon and proportions of Firmicutes were high in premonsoon season. Among Proteobacteria, Gammaproteobacteri is presented more than 99% of all the classes, irrespective of seasons. Vibrio was the most dominant genus during both seasons. The presence of anaerobic genera such as Propionigenium and Cetobacterium at all the stations during MON indicated the presence of upwelled waters. The genus Stenotrophomonas was observed in the M2 station alone. This study provides an overview of the culturable heterotrophic bacterial communities in a region in the southeastern Arabian Sea with coexisting mud banks and upwelling. The results of this study were compared with a published report on culture-independent bacterial diversity (from environmental DNA) from the same region. The study demonstrates that the use of culture media underrepresented the phylogenetic diversity and selectively enriched the class Gammaproteobacteria alone.

Comparative Analyses of the Subgingival Microbiome in Chronic Periodontitis Patients with and without Gingival Erosive Oral Lichen Planus Based on 16S rRNA Gene Sequencing

The aim of the study was to compare the microbiota composition and bacterial diversity of subgingival plaque in chronic periodontitis patients with and without gingival erosive oral lichen planus. The subgingival plaque samples of 20 chronic periodontitis patients with gingival erosive oral lichen planus (CP-OLP group) and 19 chronic periodontitis patients without gingival erosive oral lichen planus (CP group) were analyzed by 16S rRNA gene high-throughput sequencing. Compared with the CP group, the richness and diversity of subgingival plaque microflora in the CP-OLP group decreased significantly. There were some differences between the two groups in the composition of microflora on the levels of phylum and genus. Distributions of Prevotella and Leptotrichia in the CP-OLP group were significantly lower than those in the CP group. The dominant genera in CP-OLP group were Pseudomonas and Granulicatella. These results indicated that gingival erosive oral lichen planus may influence the structure and proportion of subgingival plaque microflora.

Spatial scale in analysis of the dental plaque microbiome

Ecologists have long recognized the importance of spatial scale in understanding structure-function relationships among communities of organisms within their environment. Here, we review historical and contemporary studies of dental plaque community structure in the context of three distinct scales: the micro (1-10 µm), meso (10-100 µm) and macroscale (100 µm to ≥1 cm). Within this framework, we analyze the compositional nature of dental plaque at the macroscale, the molecular interactions of microbes at the microscale, and the emergent properties of dental plaque biofilms at the mesoscale. Throughout our analysis of dental plaque across spatial scales, we draw attention to disease and health-associated structure-function relationships and include a discussion of host immune involvement in the mesoscale structure of periodontal disease-associated biofilms. We end with a discussion of two filamentous organisms, Fusobacterium nucleatum and Corynebacterium matruchotii, and their relevant contributions in structuring dental plaque biofilms.

Development of a microbe domestication pod (MD Pod) for in situ cultivation of micro-encapsulated marine bacteria

Microbial marine natural products hold significant potential for the discovery of new bioactive therapeutics such as antibiotics. Unfortunately, this discovery is hindered by the inability to culture the majority of microbes using traditional laboratory approaches. While many new methods have been developed to increase cultivability, a high-throughput in situ incubation chamber capable of simultaneously isolating individual microbes while allowing cellular communication has not previously been reported. Development of such a device would expedite the discovery of new microbial taxa and, thus, facilitate access to their associated natural products. In this study, this concept is achieved by the development of a new device termed by the authors as the microbe domestication (MD) Pod. The MD Pod enables single-cell cultivation by isolating marine bacterial cells in agarose microbeads produced using microfluidics, while allowing potential transmission of chemical signals between cells during in situ incubation in a chamber, or "Pod," that is deployed in the environment. The design of the MD Pod was optimized to ensure the use of biocompatible materials, allow for simple assembly in a field setting, and maintain sterility throughout incubation. The encapsulation process was designed to ensure that the viability of marine sediment bacteria was not adversely impacted by the encapsulation process. The process was validated using representative bacteria isolated from temperate marine sediment samples: Marinomonas polaris, Psychrobacter aquimaris, and Bacillus licheniformis. The overall process appeared to promote metabolic activity of most representative species. Thus, microfluidic encapsulation of marine bacteria and subsequent in situ incubation in the MD Pod is expected to accelerate marine natural products discovery by increasing the cultivability of marine bacteria.

Metatranscriptomic analyses of the oral microbiome

Although the composition of the oral human microbiome is now well studied, regulation of genes within oral microbial communities remains mostly uncharacterized. Current concepts of periodontal disease and caries highlight the importance of oral biofilms and their role as etiological agents of those diseases. Currently, there is increased interest in exploring and characterizing changes in the composition and gene-expression profiles of oral microbial communities. These efforts aim to identify changes in functional activities that could explain the transition from health to disease and the reason for the chronicity of those infections. It is now clear that the functions of distinct species within the subgingival microbiota are intimately intertwined with the rest of the microbial community. This point highlights the relevance of examining the expression profile of specific species within the subgingival microbiota in the case of periodontal disease or caries lesions, in the context of the other members of the biofilm in vivo. Metatranscriptomic analysis of the oral community is the starting point for identifying environmental signals that modulate the shift in metabolism of the community from commensal to dysbiotic. These studies give a snapshot of the expression patterns of microbial communities and also allow us to determine triggers to diseases. For example, in the case of caries, studies have unveiled a potential new pathway of sugar metabolism, namely the use of sorbitol as an additional source of carbon by Streptococcus mutans; and in the case of periodontal disease, high levels of extracellular potassium could be a signal of disease. Longitudinal studies are needed to identify the real markers of the initial stages of caries and periodontal disease. More information on the gene-expression profiles of the host, along with the patterns from the microbiome, will lead to a clearer understanding of the modulation of health and disease. This review presents a summary of these initial studies, which have opened the door to a new understanding of the dynamics of the oral community during the dysbiotic process in the oral cavity.

Prokaryotic community composition in a great shallow soda lake covered by large reed stands (Neusiedler See/Lake Fertő) as revealed by cultivation- and DNA-based analyses

Little is known about the detailed community composition of heterotrophic bacterioplankton in macrophyte-dominated littoral systems, where a considerable amount of dissolved organic carbon originates from aquatic macrophytes instead of phytoplankton. The aim of the present study was to reveal the effect of macrophytes on the microbial community and to elucidate their role in a macrophyte-dominated shallow soda lake, which can be characterised by a mosaic of open waters and reed marsh. Therefore, 16S rRNA gene amplicon sequencing, the most probable number method, cultivation of bacterial strains, EcoPlate and cultivation-based substrate utilisation techniques were applied. Differences in the structures of microbial communities were detected between the water and the sediment samples and between vegetated and unvegetated water samples. Planktonic bacterial communities of an inner pond and a reed-covered area showed significant similarities to each other. Woesearchaeia was the dominant archaeal taxon in the water samples, while Bathyarchaeia, 'Marine Benthic Group D' and 'DHVEG-1' were abundant in the sediment samples. The most probable number of heterotrophic bacteria was lower in the open water than in the reed-associated areas. The vast majority (83%) of the isolated bacterial strains from the water samples of the reed-covered area were able to grow on a medium containing reed extract as the sole source of carbon.

From nature to nurture: Essence and methods to isolate robust methanotrophic bacteria

Methanotrophic bacteria are entities with innate biocatalytic potential to biofilter and oxidize methane into simpler compounds concomitantly conserving energy, which can contribute to copious industrial applications. The future and efficacy of such industrial applications relies upon acquiring and/or securing robust methanotrophs with taxonomic and phenotypic diversity. Despite several dramatic advances, isolation of robust methanotrophs is still a long-way challenging task with several lacunae to be filled in sequentially. Methanotrophs with high tolerance to methane can be isolated and cultivated by mimicking natural environs, and adopting strategies like adaptive metabolic evolution. This review summarizes existent and innovative methods for methanotrophic isolation and purification, and their respective applications. A comprehensive description of new insights shedding light upon how to isolate and concomitantly augment robust methanotrophic metabolism in an orchestrated fashion follows.

Nonulosonic acids contribute to the pathogenicity of the oral bacterium Tannerella forsythia

Periodontitis is a polymicrobial, biofilm-caused, inflammatory disease affecting the tooth-supporting tissues. It is not only the leading cause of tooth loss worldwide, but can also impact systemic health. The development of effective treatment strategies is hampered by the complicated disease pathogenesis which is best described by a polymicrobial synergy and dysbiosis model. This model classifies the Gram-negative anaerobe Tannerella forsythia as a periodontal pathogen, making it a prime candidate for interference with the disease. Tannerella forsythia employs a protein O-glycosylation system that enables high-density display of nonulosonic acids via the bacterium's two-dimensional crystalline cell surface layer. Nonulosonic acids are sialic acid-like sugars which are well known for their pivotal biological roles. This review summarizes the current knowledge of T. forsythia's unique cell envelope with a focus on composition, biosynthesis and functional implications of the cell surface O-glycan. We have obtained evidence that glycobiology affects the bacterium's immunogenicity and capability to establish itself in the polymicrobial oral biofilm. Analysis of the genomes of different T. forsythia isolates revealed that complex protein O-glycosylation involving nonulosonic acids is a hallmark of pathogenic T. forsythia strains and, thus, constitutes a valuable target for the design of novel anti-infective strategies to combat periodontitis.

Natural Products from Mammalian Gut Microbiota

The mammalian gut has a remarkable abundance of microbes. These microbes have strong potential to biosynthesize distinct metabolites that are promising drugs, and many more bioactive compounds have yet to be explored as potential drug candidates. These small bioactive molecules often mediate important host-microbe and microbe-microbe interactions. In this review, we provide perspectives on and challenges associated with three mining strategies - culture-based, (meta)genomics-based, and metabolomics-based mining approaches - for discovering natural products derived from biosynthetic gene clusters (BGCs) in mammalian gut microbiota. In addition, we comprehensively summarize the structures, biological functions, and BGCs of these compounds. Improving these techniques, including by using combinatorial approaches, may accelerate drug discovery from gut microbes.

A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications

The cell surface of the oral pathogen Tannerella forsythia is heavily glycosylated with a unique, complex decasaccharide that is O-glycosidically linked to the bacterium's abundant surface (S-) layer, as well as other proteins. The S-layer glycoproteins are virulence factors of T. forsythia and there is evidence that protein O-glycosylation underpins the bacterium's pathogenicity. To elucidate the protein O-glycosylation pathway, genes suspected of encoding pathway components were first identified in the genome sequence of the ATCC 43037 type strain, revealing a 27-kb gene cluster that was shown to be polycistronic. Using a gene deletion approach targeted at predicted glycosyltransferases (Gtfs) and methyltransferases encoded in this gene cluster, in combination with mass spectrometry of the protein-released O-glycans, we show that the gene cluster encodes the species-specific part of the T. forsythia ATCC 43037 decasaccharide and that this is assembled step-wise on a pentasaccharide core. The core was previously proposed to be conserved within the Bacteroidetes phylum, to which T. forsythia is affiliated, and its biosynthesis is encoded elsewhere on the bacterial genome. Next, to assess the prevalence of protein O-glycosylation among Tannerella sp., the publicly available genome sequences of six T. forsythia strains were compared, revealing gene clusters of similar size and organization as found in the ATCC 43037 type strain. The corresponding region in the genome of a periodontal health-associated Tannerella isolate showed a different gene composition lacking most of the genes commonly found in the pathogenic strains. Finally, we investigated whether differential cell surface glycosylation impacts T. forsythia's overall immunogenicity. Release of proinflammatory cytokines by dendritic cells (DCs) upon stimulation with defined Gtf-deficient mutants of the type strain was measured and their T cell-priming potential post-stimulation was explored. This revealed that the O-glycan is pivotal to modulating DC effector functions, with the T. forsythia-specific glycan portion suppressing and the pentasaccharide core activating a Th17 response. We conclude that complex protein O-glycosylation is a hallmark of pathogenic T. forsythia strains and propose it as a valuable target for the design of novel antimicrobials against periodontitis.

Introducing the sporobiota and sporobiome

Unrelated spore-forming bacteria share unique characteristics stemming from the presence of highly resistant endospores, leading to similar challenges in health and disease. These characteristics are related to the presence of these highly transmissible spores, which are commonly spread within the environment and are implicated in host-to-host transmission. In humans, spore-forming bacteria contribute to a variety of pathological processes that share similar characteristics, including persistence, chronicity, relapses and the maintenance of the resistome. We first outline the necessity of characterizing the totality of the spore-forming bacteria as the sporobiota based on their unique common characteristics. We further propose that the collection of all genes of spore-forming bacteria be known as the sporobiome. Such differentiation is critical for exploring the cross-talk between the sporobiota and other members of the gut microbiota, and will allow for a better understanding of the implications of the sporobiota and sporobiome in a variety of pathologies and the spread of antibiotic resistance.