New approaches for isolation of previously uncultivated oral bacteria

Cultivation of anaerobic bacteria: Foundations and principles

A brief history of techniques in anaerobic microbiology are presented leading up to the incorporation of several improvements we have used over the years to improve our culture of anaerobic microorganisms of environmental, industrial and clinical importance. Two overriding aspects from our combined 90 years of experience here are: the better one's control of anaerobic conditions and gas phases, the better results are obtained; techniques can and should be targeted for individual microorganisms and accompanying experiments. Continued improvements in anaerobic microbiology are expected and encouraged for the future.

Ex vivo oral biofilm model for rapid screening of antimicrobial agents including natural cranberry polyphenols

The search has been ongoing for safe and effective antimicrobial agents for control and prevention of oral biofilm associated with disease. Clinical trials for oral specific anti-bacterials are costly and often provide inconclusive results. The simple approach of ex vivo testing of these agents has not demonstrated utility, likely due to variability of effects observed even with a single donor. We show how shed oral biofilms, easily obtained from donor saliva, and tested under optimized conditions, respond reproducibly to anti-bacterial challenges measured by reductions in rRNA accumulation in susceptible taxa. Responses are in part donor specific, but many bacteria taxa were shown to be reproducibly susceptible over a group of donors. For two antibiotics, vancomycin and penicillin G tested at pharmacologic levels, a subset of Gram-positive bacteria was inhibited. A natural product with antibacterial properties, diluted Vaccinium macrocarpon (cranberry) juice, was shown to inhibit a range of oral taxa, including Alloprevotella sp__HMT_473, Granulicatella adiacens, Lachnoanaerobaculum umeaense, Lepotrichia sp__HMT_215, Peptostreptococcus stomatis, Prevotella nanceiensis, Stomatobaculum sp__HMT_097, Veillonella parvula, and kill some targets. The model discussed in this study has promise as a rapid, precise, and reproducible ex vivo method to test and identify potential clinically useful antimicrobial agents active against the oral biofilm community.

A Comprehensive Review on Bioactive Molecules and Advanced Microorganism Management Technologies

The advent of new strains of resistant microbes and the concomitant growth in multidrug resistance have made antimicrobial resistance an urgent public health concern. New antimicrobials are desperately needed to boost the success rates of treating infectious diseases and save lives. There are many intriguing biomolecules with antibacterial action, which are mostly unexplored in microorganisms. This review article describes the importance of natural compounds against microorganisms using advanced techniques to protect individuals from diseases. We have conducted an extensive literature review using databases such as SCOPUS, SCI, PUBMED, ScienceDirect, and Medline to gather relevant information. Our review covers various microorganism sources for antimicrobials, antifungal drugs, micro-culturing techniques, and microbial-based microsystems' applications. Every kind of higher trophic life depends on microorganisms for sustenance. The unseen majority is essential to understanding how humans and other living forms can survive anthropogenic climate change. The article discusses antimicrobial substances and the latest techniques and strategies for developing effective treatments. Novel model systems and cutting-edge biomolecular and computational methodologies could help researchers enhance antimicrobial resistance by completely capitalizing on lead antimicrobials.

Advances in the isolation, cultivation, and identification of gut microbes

The gut microbiome is closely associated with human health and the development of diseases. Isolating, characterizing, and identifying gut microbes are crucial for research on the gut microbiome and essential for advancing our understanding and utilization of it. Although culture-independent approaches have been developed, a pure culture is required for in-depth analysis of disease mechanisms and the development of biotherapy strategies. Currently, microbiome research faces the challenge of expanding the existing database of culturable gut microbiota and rapidly isolating target microorganisms. This review examines the advancements in gut microbe isolation and cultivation techniques, such as culturomics, droplet microfluidics, phenotypic and genomics selection, and membrane diffusion. Furthermore, we evaluate the progress made in technology for identifying gut microbes considering both non-targeted and targeted strategies. The focus of future research in gut microbial culturomics is expected to be on high-throughput, automation, and integration. Advancements in this field may facilitate strain-level investigation into the mechanisms underlying diseases related to gut microbiota.

Microbiome metabolite quantification methods enabling insights into human health and disease

Many of the health-associated impacts of the microbiome are mediated by its chemical activity, producing and modifying small molecules (metabolites). Thus, microbiome metabolite quantification has a central role in efforts to elucidate and measure microbiome function. In this review, we cover general considerations when designing experiments to quantify microbiome metabolites, including sample preparation, data acquisition and data processing, since these are critical to downstream data quality. We then discuss data analysis and experimental steps to demonstrate that a given metabolite feature is of microbial origin. We further discuss techniques used to quantify common microbial metabolites, including short-chain fatty acids (SCFA), secondary bile acids (BAs), tryptophan derivatives, N-acyl amides and trimethylamine N-oxide (TMAO). Lastly, we conclude with challenges and future directions for the field.

Application of culturomics in fungal isolation from mangrove sediments

BACKGROUND

Fungi play a crucial role in ecosystems, and they have been widely considered a promising source for natural compounds that are crucial for drug discovery. Fungi have a high diversity, but about 95% of them remain unknown to science. The description rate of fungi is very low, mainly due to the inability of most fungi to grow in artificial media, which could not provide a sufficiently similar environment to their natural habitats. Moreover, many species in nature are in a state of low metabolic activity which cannot readily proliferate without proper resuscitation. Previously developed culturomics techniques are mostly designed and applicable for bacteria, with few attempts for fungal isolation because of their significantly larger cell size and hyphal growth properties.

RESULTS

This study attempted to isolate previously uncultured and rare fungi from mangrove sediments using newly developed fungal enrichment culture method (FECM) and fungal isolation chips (FiChips). Comparison of fungal community composition at different enrichment stages showed that FECM had great influence on fungal community composition, with rare taxa increased significantly, thus improving the isolation efficiency of previously uncultured fungi. Similarly, in situ cultivation using FiChips has a significant advantage in detecting and culturing rare fungi, as compared to the conventional dilution plate method (DPM). In addition, based on morphological comparisons and phylogenetic analyses, we described and proposed 38 new ascomycetous taxa, including three new families, eight new genera, 25 new species, and two new combinations (presented in additional file 1).

CONCLUSIONS

Our study demonstrated that mangrove sediments harbor a high diversity of fungi, and our new isolation approaches (FECM and FiChips) presented a high efficiency in isolating hitherto uncultured fungi, which is potentially usable for fungal isolation in other similar environments. Video Abstract.

Oral Microbiota in Children with Cleft Lip and Palate: A Systematic Review

BACKGROUND

Cleft in the lip and/or palate (CLP) is a congenital facial deformity that significantly impacts the oral cavity's structure and function. This malformation can affect the oral microbiota. The objective of this systematic review was to examine and consolidate the current scientific evidence on the oral microflora in children with CLP.

METHODS

The search strategy included the PubMed, PubMed Central, Web of Science, Scopus, and Embase databases. The inclusion criteria were studies assessing oral microbiota in children with CLP. The Newcastle-Ottawa Scale (NOS) was used to evaluate the quality of the included studies.

RESULTS

The search strategy identified 422 potential articles. Twelve papers met the inclusion criteria. High heterogeneity was observed in methodologies, sample sites, and patient characteristics. Eight studies assessed the levels of Streptococcus mutans and Lactobacillus in saliva, with some reporting significantly higher levels in the cleft group compared to controls, while others found no differences. One study reported a significantly higher colonization rate of Candida species in patients with cleft lip and/or palate.

CONCLUSION

The results of the available studies are unclear. Further research is needed to gain a comprehensive understanding of the oral microbiota and potential implications for oral health management in this population. The review was not registered Registration Statement.

Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle

BACKGROUND

Ruminants can utilize urea as a dietary nitrogen source owing to their ability to recycle urea-N back to the rumen where numerous ureolytic bacteria hydrolyze urea into ammonia, which is used by numerous bacteria as their nitrogen source. Rumen ureolytic bacteria are the key microbes making ruminants the only type of animals independent of pre-formed amino acids for survival, thus having attracted much research interest. Sequencing-based studies have helped gain new insights into ruminal ureolytic bacterial diversity, but only a limited number of ureolytic bacteria have been isolated into pure cultures or studied, hindering the understanding of ureolytic bacteria with respect to their metabolism, physiology, and ecology, all of which are required to effectively improve urea-N utilization efficiency.

RESULTS

We established and used an integrated approach, which include urease gene (ureC) guided enrichment plus in situ agarose microsphere embedding and cultivation under rumen-simulating conditions, to isolate ureolytic bacteria from the rumen microbiome. We optimized the dilutions of the rumen microbiome during the enrichment, single-cell embedding, and then in situ cultivation of microsphere-embedded bacteria using dialysis bags placed in rumen fluid. Metabonomic analysis revealed that the dialysis bags had a fermentation profile very similar to the simulated rumen fermentation. In total, we isolated 404 unique strains of bacteria, of which 52 strains were selected for genomic sequencing. Genomic analyses revealed that 28 strains, which were classified into 12 species, contained urease genes. All these ureolytic bacteria represent new species ever identified in the rumen and represented the most abundant ureolytic species. Compared to all the previously isolated ruminal ureolytic species combined, the newly isolated ureolytic bacteria increased the number of genotypically and phenotypically characterized ureolytic species by 34.38% and 45.83%, respectively. These isolated strains have unique genes compared to the known ureolytic strains of the same species indicating their new metabolic functions, especially in energy and nitrogen metabolism. All the ureolytic species were ubiquitous in the rumen of six different species of ruminants and were correlated to dietary urea metabolism in the rumen and milk protein production. We discovered five different organizations of urease gene clusters among the new isolates, and they had varied approaches to hydrolyze urea. The key amino acid residues of the UreC protein that potentially plays critical regulatory roles in urease activation were also identified.

CONCLUSIONS

We established an integrated methodology for the efficient isolation of ureolytic bacteria, which expanded the biological resource of crucial ureolytic bacteria from the rumen. These isolates play a vital role in the incorporation of dietary nitrogen into bacterial biomass and hence contribute to ruminant growth and productivity. Moreover, this methodology can enable efficient isolation and cultivation of other bacteria of interest in the environment and help bridge the knowledge gap between genotypes and phenotypes of uncultured bacteria. Video abstract.

Advances in the oral microbiota and rapid detection of oral infectious diseases

Several studies have shown that the dysregulation of the oral microbiota plays a crucial role in human health conditions, such as dental caries, periodontal disease, oral cancer, other oral infectious diseases, cardiovascular diseases, diabetes, bacteremia, and low birth weight. The use of traditional detection methods in conjunction with rapidly advancing molecular techniques in the diagnosis of harmful oral microorganisms has expanded our understanding of the diversity, location, and function of the microbiota associated with health and disease. This review aimed to highlight the latest knowledge in this field, including microbial colonization; the most modern detection methods; and interactions in disease progression. The next decade may achieve the rapid diagnosis and precise treatment of harmful oral microorganisms.

The Oral Microbiota in Health and Disease: An Overview of Molecular Findings

Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity is even much larger. Nucleic acid technologies have also been helpful in profiling bacterial communities and identifying disease-related patterns. This chapter provides an overview of the diversity and taxonomy of oral bacteria associated with health and disease.

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.

Micro-Technologies for Assessing Microbial Dynamics in Controlled Environments

With recent advances in microfabrication technologies, the miniaturization of traditional culturing techniques has provided ideal methods for interrogating microbial communities in a confined and finely controlled environment. Micro-technologies offer high-throughput screening and analysis, reduced experimental time and resources, and have low footprint. More importantly, they provide access to culturing microbes in situ in their natural environments and similarly, offer optical access to real-time dynamics under a microscope. Utilizing micro-technologies for the discovery, isolation and cultivation of "unculturable" species will propel many fields forward; drug discovery, point-of-care diagnostics, and fundamental studies in microbial community behaviors rely on the exploration of novel metabolic pathways. However, micro-technologies are still largely proof-of-concept, and scalability and commercialization of micro-technologies will require increased accessibility to expensive equipment and resources, as well as simpler designs for usability. Here, we discuss three different miniaturized culturing practices; including microarrays, micromachined devices, and microfluidics; advancements to the field, and perceived challenges.

Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms

Periodontitis is caused by pathogenic subgingival microbial biofilm development and dysbiotic interactions between host and hosted microbes. A thorough characterization of the subgingival biofilms by deep amplicon sequencing of 121 individual periodontitis pockets of nine patients and whole metagenomic analysis of the saliva microbial community of the same subjects were carried out. Two biofilm sampling methods yielded similar microbial compositions. Taxonomic mapping of all biofilms revealed three distinct microbial clusters. Two clinical diagnostic parameters, probing pocket depth (PPD) and clinical attachment level (CAL), correlated with the cluster mapping. The dysbiotic microbiomes were less diverse than the apparently healthy ones of the same subjects. The most abundant periodontal pathogens were also present in the saliva, although in different representations. The single abundant species Tannerella forsythia was found in the diseased pockets in about 16–17-fold in excess relative to the clinically healthy sulcus, making it suitable as an indicator of periodontitis biofilms. The discrete microbial communities indicate strong selection by the host immune system and allow the design of targeted antibiotic treatment selective against the main periodontal pathogen(s) in the individual patients.

A critical analysis of research methods and experimental models to study the root canal microbiome

Endodontic microbiology deals with the study of the microbial aetiology and pathogenesis of pulpal and periradicular inflammatory diseases. Research in endodontic microbiology started almost 130 years ago and since then has mostly focussed on establishing and confirming the infectious aetiology of apical periodontitis, identifying the microbial species associated with the different types of endodontic infections and determining the efficacy of treatment procedures in eradicating or controlling infection. Diverse analytical methods have been used over the years, each one with their own advantages and limitations. In this review, the main features and applications of the most used technologies are discussed, and advice is provided to improve study designs in order to properly address the scientific questions and avoid setbacks that can compromise the results. Finally, areas of future research are described.

Study of microbiocenosis of canine dental biofilms

Dental biofilm is a complex microbial community influenced by many exogenous and endogenous factors. Despite long-term studies, its bacterial composition is still not clearly understood. While most of the research on dental biofilms was conducted in humans, much less information is available from companion animals. In this study, we analyzed the composition of canine dental biofilms using both standard cultivation on solid media and amplicon sequencing, and compared the two approaches. The 16S rRNA gene sequences were used to define the bacterial community of canine dental biofilm with both, culture-dependent and culture-independent methods. After DNA extraction from each sample, the V3-V4 region of the 16S rRNA gene was amplified and sequenced via Illumina MiSeq platform. Isolated bacteria were identified using universal primers and Sanger sequencing. Representatives of 18 bacterial genera belonging to 5 phyla were isolated from solid media. Amplicon sequencing largely expanded this information identifying in total 284 operational taxonomic units belonging to 10 bacterial phyla. Amplicon sequencing revealed much higher diversity of bacteria in the canine dental biofilms, when compared to standard cultivation approach. In contrast, cultured representatives of several bacterial families were not identified by amplicon sequencing.

Recent trend, biases and limitations of cultivation-based diversity studies of microbes

The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500-900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.

Microbiome of Odontogenic Abscesses

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

Triggering Growth via Growth Initiation Factors in Nature: A Putative Mechanism for in situ Cultivation of Previously Uncultivated Microorganisms

Most microorganisms resist cultivation under standard laboratory conditions. On the other hand, cultivating microbes in a membrane-bound device incubated in nature (in situ cultivation) can be an effective approach to overcome this limitation. In the present study, we applied in situ cultivation to isolate diverse previously uncultivated marine sponge-associated microbes and comparatively analyzed this method's efficiencies with those of the conventional method. Then, we attempted to investigate the key and previously unidentified mechanism of growing uncultivated microorganisms by in situ cultivation focusing on growth triggering via growth initiation factor. Significantly more novel and diverse microbial types were isolated via in situ cultivation than by standard direct plating (SDP). We hypothesized that some of environmental microorganisms which resist cultivation are in a non-growing state and require growth initiation factors for the recovery and that these can be provided from the environment (in this study from marine sponge). According to the hypothesis, the effect of the sponge extract on recovery on agar medium was compared between strains derived from in situ and SDP cultivation. Adding small amounts of the sponge extracts to the medium elevated the colony-formation efficiencies of the in situ strains at the starvation recovery step, while it showed no positive effect on that of SDP strains. Conversely, specific growth rates or saturated cell densities of all tested strains were not positively affected. These results indicate that, (1) the sponge extract contains chemical compounds that facilitate recovery of non-growing microbes, (2) these substances worked on the in situ strains, and (3) growth initiation factor in the sponge extract did not continuously promote growth activity but worked as triggers for regrowth (resuscitation from non-growing state).

Accessing previously uncultured marine microbial resources by a combination of alternative cultivation methods

Few microbes can grow under laboratory conditions, highlighting the fact that the majority of microbes in environment are still uncultured and untapped resources. This study used alternative cultivation methods, diffusion chambers (DC), dilution-to-extinction culture (DTE) and modified agar preparation step (PS media) to cultivate previously uncultured marine bacterial species. These methods were applied to samples from a coastal intertidal zone, and the results were compared with those from standard direct plating (SDP) cultivation. Among the strains isolated with DC, DTE and PS media methods, 28%, 48% and 33% were novel species, respectively, while the SDP method resulted in the isolation of only 9% of novel species. Most isolates were unique to the method used for their cultivation. This implies that each method is selective in its own way, which is different from SDP, thus able to access species that are difficult to obtain using conventional approaches. Comparing the diversity showed that 75 genera were recovered by the alternative methods, 2.7 times higher than that of the SDP cultivation, which constituted 45% of total diversity from culture-independent sequencing. We conclude that combining alternative cultivation methods represents a highly promising key for accessing 'microbial dark matter'.

Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine

The isolation of bacteria that represent the diversity of autochthonous taxa in the gastrointestinal tract is necessary to fully ascertain their function, but the majority of bacterial species inhabiting the intestines of mammals are fastidious and thus challenging to isolate. The goal of the current study was to isolate a diverse assemblage of anaerobic bacteria from the intestine of pigs as a model animal and to comparatively examine various novel and traditional isolation strategies. Methods used included long-term enrichments, direct plating, a modified ichip method, as well as ethanol and tyndallization treatments of samples to select for endospore-forming taxa. A total of 234 taxa (91 previously uncultured) comprising 80 genera and 7 phyla were isolated from mucosal and luminal samples from the ileum, cecum, ascending colon, and spiral colon removed from animals under anesthesia. The diversity of bacteria isolated from the large intestine was less than that detected by next-generation sequence analysis. Long-term enrichments yielded the greatest diversity of recovered bacteria (Shannon's index [SI] = 4.7). Methods designed to isolate endospore-forming bacteria produced the lowest diversity (SI ≤ 2.7), with tyndallization yielding lower diversity than the ethanol method. However, the isolation frequency of previously uncultured bacteria was highest for ethanol-treated samples (41.9%) and the ichip method (32.5%). The goal of recovering a diverse collection of enteric bacteria was achieved. Importantly, the study findings demonstrate that it is necessary to use a combination of methods in concert to isolate bacteria that are representative of the diversity within the intestines of mammals.IMPORTANCE This work determined that using a combination of anaerobic isolation methods is necessary to increase the diversity of bacteria recovered from the intestines of monogastric mammals. Direct plating methods have traditionally been used to isolate enteric bacteria, and recent methods (e.g., diffusion methods [i.e., ichip] or differential isolation of endospore-forming bacteria) have been suggested to be superior at increasing diversity, including the recovery of previously uncultured taxa. We showed that long-term enrichment of samples using a variety of media isolated the most diverse and novel bacteria. Application of the ichip method delivered a diversity of bacteria similar to those of enrichment and direct plating methods. Methods that selected for endospore-forming bacteria generated collections that differed in composition from those of other methods with reduced diversity. However, the ethanol treatment frequently isolated novel bacteria. By using a combination of methods in concert, a diverse collection of enteric bacteria was generated for ancillary experimentation.

Highly parallelized droplet cultivation and prioritization of antibiotic producers from natural microbial communities

Antibiotics from few culturable microorganisms have saved millions of lives since the 20th century. But with resistance formation, these compounds become increasingly ineffective, while the majority of microbial and with that chemical compound diversity remains inaccessible for cultivation and exploration. Culturing recalcitrant bacteria is a stochastic process. But conventional methods are limited to low throughput. By increasing (i) throughput and (ii) sensitivity by miniaturization, we innovate microbiological cultivation to comply with biological stochasticity. Here, we introduce a droplet-based microscale cultivation system, which is directly coupled to a high-throughput screening for antimicrobial activity prior to strain isolation. We demonstrate that highly parallelized in-droplet cultivation starting from single cells results in the cultivation of yet uncultured species and a significantly higher bacterial diversity than standard agar plate cultivation. Strains able to inhibit intact reporter strains were isolated from the system. A variety of antimicrobial compounds were detected for a selected potent antibiotic producer.

Screening of Marine Bioactive Antimicrobial Compounds for Plant Pathogens

Plant diseases have been threatening food production. Controlling plant pathogens has become an important strategy to ensure food security. Although chemical control is an effective disease control strategy, its application is limited by many problems, such as environmental impact and pathogen resistance. In order to overcome these problems, it is necessary to develop more chemical reagents with new functional mechanisms. Due to their special living environment, marine organisms have produced a variety of bioactive compounds with novel structures, which have the potential to develop new fungicides. In the past two decades, screening marine bioactive compounds to inhibit plant pathogens has been a hot topic. In this review, we summarize the screening methods of marine active substances from plant pathogens, the identification of marine active substances from different sources, and the structure and antibacterial mechanism of marine active natural products. Finally, the application prospect of marine bioactive substances in plant disease control was prospected.

The new microbiology: cultivating the future of microbiome-directed medicine

The discovery of human-associated microscopic life forms has captivated the scientific community since their first documentation in the 17th century. Subsequent isolation and cultivation of microorganisms have spurred great leaps in medicine, including the discovery of antibiotics, identifying pathogens that cause infectious diseases, and vaccine development. The realization that there is a vast discrepancy between the number of microscopic cell counts and how many could thrive in the laboratory motivated the advent of sequencing-based approaches to characterize the uncultured fraction of the microbiota, leading to an unprecedented view into their composition and putative function on all bodily surfaces. It soon became apparent that specific members of the microbiota can be our commensal partners with new implications on various aspects of health, as well as a rich source of therapeutic compounds and tools for biotechnology. Harnessing the immense repertoire of microbial properties, however, inadvertently requires pure cultures for validation and manipulation of candidate genes, proteins, or metabolic pathways, just as mammalian cell culture has become an indispensable tool for mechanistic understanding of host biology. Yet, this renewed interest in growing microorganisms, individually or as a consortium, is stalled by the laborious nature of conventional cultivation methods. Addressing this unmet need through implementation of improved media design and new cultivation techniques is arguably instrumental to future milestones in translational microbiome research.

Dysosmobacter welbionis gen. nov., sp. nov., isolated from human faeces and emended description of the genus Oscillibacter

A strictly anaerobic, Gram-stain-negative, non-spore-forming, non-motile, non-pigmented bacterium, strain J115^T, was isolated from human faeces. Cells of strain J115^T were straight rods, generally 1.8-3.0 µm, but could be up to 18 µm long. Growth occurred below 2 % (w/v) NaCl and 2 % (v/v) bile. Strain J115^T produced acid from myo-inositol but not from d-glucose, d-ribose or d-xylose. Butyric acid was the major end-product from myo-inositol. The genomic DNA G+C content was 58.92 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the closest cultivated neighbours of strain J115^T were Oscillibacter ruminantium GH1^T (95.4 % similarity) and Oscillibacter valericigenes Sjm18-20^T (94.1 %). Strain J115^T was also related to the not-yet-cultured bacterium Oscillospira guilliermondii(92-93 % similarity). Coherently with the 16S rRNA gene sequence results, the ANI scores don't have units of strain J115^T to O. ruminantium GH1^T and O. valericigenes Sjm18-20^T were 73.37 and 73.24, respectively, while in silico estimations of DNA-DNA hybridization were both 20.4 %, with confidence intervals of 18.2-22.9 % and 18.2-22.8 %, respectively. The major fatty acids were iso-C_15 : 0 (24.2 %), C_18 : 0 DMA (18.4 %), anteiso-C_15 : 0 (15.2 %) and C_16 : 0 DMA (7.6 %). No respiratory quinone was detected. Based on phenotypic features and phylogenetic position, it is proposed that this isolate represents a novel species in a new genus, Dysosmobacter welbionis gen. nov., sp. nov. The type strain of Dysosmobacter welbionis is J115^T (DSM 106889^T=LMG 30601^T).

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

Most microorganisms from all taxonomic levels are uncultured. Single-cell genomes and metagenomes continue to increase the known diversity of Bacteria and Archaea, but while ‘omics can be used to infer physiological or ecological roles for species in a community, most of those hypothetical roles remain unvalidated. Here we report an approach to capture specific microorganisms from complex communities into pure cultures using genome-informed antibody engineering. We apply our reverse genomics approach to isolate and sequence single cells and to cultivate three different species-level lineages of human oral Saccharibacteria/TM7. Using our pure cultures we show that all three saccharibacteria species are epibionts of diverse Actinobacteria. We also isolate and cultivate human oral SR1 bacteria, which are members of a lineage of previously uncultured bacteria. Reverse-genomics-enabled cultivation of microorganisms can be applied to any species from any environment and has the potential to unlock the isolation, cultivation and characterization of species from as-yet-uncultured branches of the microbial tree of life.

An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced "iron mound" sediments

Fe(III)-rich deposits referred to as “iron mounds” develop when Fe(II)-rich acid mine drainage (AMD) emerges at the terrestrial surface, and aeration of the fluids induces oxidation of Fe(II), with subsequent precipitation of Fe(III) phases. As Fe(III) phases accumulate in these systems, O₂ gradients may develop in the sediments and influence the distributions and extents of aerobic and anaerobic microbiological Fe metabolism, and in turn the solubility of Fe. To determine how intrusion of O₂ into iron mound sediments influences microbial community composition and Fe metabolism, we incubated samples of these sediments in a column format. O₂ was only supplied through the top of the columns, and microbiological, geochemical, and electrochemical changes at discrete depths were determined with time. Despite the development of dramatic gradients in dissolved Fe(II) concentrations, indicating Fe(II) oxidation in shallower portions and Fe(III) reduction in the deeper portions, microbial communities varied little with depth, suggesting the metabolic versatility of organisms in the sediments with respect to Fe metabolism. Additionally, the availability of O₂ in shallow portions of the sediments influenced Fe metabolism in deeper, O₂-free sediments. Total potential (E_H + self-potential) measurements at discrete depths in the columns indicated that Fe transformations and electron transfer processes were occurring through the sediments and could explain the impact of O₂ on Fe metabolism past where it penetrates into the sediments. This work shows that O₂ availability (or lack of it) minimally influences microbial communities, but influences microbial activities beyond its penetration depth in AMD-derived Fe(III) rich sediments. Our results indicate that O₂ can modulate Fe redox state and solubility in larger volumes of iron mound sediments than only those directly exposed to O₂.

Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics

BACKGROUND

The human placenta has been traditionally viewed as sterile, and microbial invasion of this organ has been associated with adverse pregnancy outcomes. Yet, recent studies that utilized sequencing techniques reported that the human placenta at term contains a unique microbiota. These conclusions are largely based on the results derived from the sequencing of placental samples. However, such an approach carries the risk of capturing background-contaminating DNA (from DNA extraction kits, polymerase chain reaction reagents, and laboratory environments) when low microbial biomass samples are studied.

OBJECTIVE

To determine whether the human placenta delivered at term in patients without labor who undergo cesarean delivery harbors a resident microbiota ("the assemblage of microorganisms present in a defined niche or environment").

STUDY DESIGN

This cross-sectional study included placentas from 29 women who had a cesarean delivery without labor at term. The study also included technical controls to account for potential background-contaminating DNA, inclusive in DNA extraction kits, polymerase chain reaction reagents, and laboratory environments. Bacterial profiles of placental tissues and background technical controls were characterized and compared with the use of bacterial culture, quantitative real-time polymerase chain reaction, 16S ribosomal RNA gene sequencing, and metagenomic surveys.

RESULTS

(1) Twenty-eight of 29 placental tissues had a negative culture for microorganisms. The microorganisms retrieved by culture from the remaining sample were likely contaminants because corresponding 16S ribosomal RNA genes were not detected in the same sample. (2) Quantitative real-time polymerase chain reaction did not indicate greater abundances of bacterial 16S ribosomal RNA genes in placental tissues than in technical controls. Therefore, there was no evidence of the presence of microorganisms above background contamination from reagents in the placentas. (3) 16S ribosomal RNA gene sequencing did not reveal consistent differences in the composition or structure of bacterial profiles between placental samples and background technical controls. (4) Most of the bacterial sequences obtained from metagenomic surveys of placental tissues were from cyanobacteria, aquatic bacteria, or plant pathogens, which are microbes unlikely to populate the human placenta. Coprobacillus, which constituted 30.5% of the bacterial sequences obtained through metagenomic sequencing of placental samples, was not identified in any of the 16S ribosomal RNA gene surveys of these samples. These observations cast doubt as to whether this organism is really present in the placenta of patients at term not in labor.

CONCLUSION

With the use of multiple modes of microbiologic inquiry, a resident microbiota could not be identified in human placentas delivered at term from women without labor. A consistently significant difference in the abundance and/or presence of a microbiota between placental tissue and background technical controls could not be found. All cultures of placental tissue, except 1, did not yield bacteria. Incorporating technical controls for potential sources of background-contaminating DNA for studies of low microbial biomass samples, such as the placenta, is necessary to derive reliable conclusions.

Butyricimonas faecalis sp. nov., isolated from human faeces and emended description of the genus Butyricimonas

A Gram-negative, strictly anaerobic, non-spore forming, non-motile, non-pigmented bacterial strain, designated H184^T, was isolated from human faeces. 16S rRNA gene sequence analysis showed that strain H184^T represents a member of the genus Butyricimonas. Strain H184^T is related to but distinct from Butyricimonasvirosa JCM 15149^T and Butyricimonasparavirosa JCM 18677^T, with 16S rRNA gene sequence similarities of 96.32 and 96.24 %, respectively. Strain H184^T shared 90.50 % hsp60 gene sequence similarity to B. virosa JCM 15149^T and B. paravirosa JCM 18677^T. Growth occurs between 25 and 42 °C with an optimum at 37 °C. Bile and NaCl concentration range allowing growth are 0-3.75 % and 0-1.8 %, respectively. pH range for growth is 5.5-8. The strain produced propionate as the major end product from glucose. The major cellular fatty acids of strain H184^T were iso-C15 : 0 (63.5 %) and iso-C17 : 0 3-OH (12.8%). The major menaquinone of the strain was MK-10 (86 %). DNA G+C content of the isolate H184^T was 44.2 mol%. The genome-based comparison between strain H184^T and B. virosa JCM 15149^T by pairwise average nucleotide identity indicated a clear distinction with a score of 87.22. On the basis of these data, strain H184^T represents a novel species of the genus Butyricimonas, for which the name Butyricimonas faecalis sp. nov. is proposed. The type strain of B. faecalis is H184^T (DSM 106867^T, LMG 30602^T).

Neutrophil Interaction with Emerging Oral Pathogens: A Novel View of the Disease Paradigm

Periodontitis is a multifactorial chronic inflammatory infectious disease that compromises the integrity of tooth-supporting tissues. The disease progression depends on the disruption of host-microbe homeostasis in the periodontal tissue. This disruption is marked by a shift in the composition of the polymicrobial oral community from a symbiotic to a dysbiotic, more complex community that is capable of evading killing while promoting inflammation. Neutrophils are the main phagocytic cell in the periodontal pocket, and the outcome of the interaction with the oral microbiota is an important determinant of oral health. Novel culture-independent techniques have facilitated the identification of new bacterial species at periodontal lesions and induced a reappraisal of the microbial etiology of periodontitis. In this chapter, we discuss how neutrophils interact with two emerging oral pathogens, Filifactor alocis and Peptoanaerobacter stomatis, and the different strategies deploy by these organisms to modulate neutrophil effector functions, with the goal to outline a new paradigm in our knowledge about neutrophil responses to putative periodontal pathogens and their contribution to disease progression.

How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota

INTRODUCTION

Describing the human hut gut microbiota is one the most exciting challenges of the 21^st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.

Studying the human oral microbiome: challenges and the evolution of solutions

Since the pioneering work of van Leeuwenhoek in 1684, subsequently built upon by other renowned microbiologists Robert Koch, Willoughby Miller and GV Black, oral microbiology has developed innovative techniques to study the oral microflora (now termed the 'oral microbiome'). The advent of molecular techniques such as DNA-DNA hybridization, polymerase chain reaction and DNA sequencing has created an array of opportunities to construct a comprehensive picture of the diversity and composition of the oral microbiome. Approximately 700 oral bacterial species have been identified, of which 50% have yet to be cultivated, and some of these are known only by their signature DNA sequences. The synergism of ever-evolving culture-based and state-of-the-art culture-independent molecular techniques has facilitated in-depth understanding of the dynamics, acquisition and transfer of oral bacteria, along with their role in oral and general health and disease. Further research is needed to not only analyse but also to make sense of the ever-increasing volumes of data which these molecular techniques (especially high-throughput DNA sequencing) are generating, as well as why particular bacteria are present and what they are 'actually doing' there. This review presents a comprehensive literature search of oral microbiology-related methods currently used to study the oral microbiome.

In situ cultivation of previously uncultivable microorganisms using the ichip

Most microbial species remain uncultivated, and modifying artificial nutrient media brings only an incremental increase in cultivability. We reasoned that an alternative way to cultivate species with unknown requirements is to use naturally occurring combinations of growth factors. To achieve this, we moved cultivation into the microbes' natural habitat by placing cells taken from varying environmental samples into diffusion chambers, which are then returned to nature for incubation. By miniaturizing the chambers and placing only one to several cells into each chamber, we can grow and isolate microorganisms in axenic culture in one step. We call this cultivation platform the 'isolation chip', or 'ichip'. This platform has been shown to increase microbial recovery from 5- to 300-fold, depending on the study. Furthermore, it provides access to a unique set of microbes that are inaccessible by standard cultivation. Here we provide a simple protocol for building and applying ichips for environmental cultivation of soil bacteria as an example; the protocol consists of (i) preparing the ichip; (ii) collecting an environmental sample; (iii) serially diluting cells and loading them into the ichip; (iv) returning the ichip to the environment for incubation; (v) retrieving the ichip and harvesting grown material; and (vi) domestication of the ichip-derived colonies for growth in the laboratory. The ichip's full assembly and deployment is a relatively simple procedure that, with experience, takes ∼2-3 h. After in situ incubation, retrieval of the ichip and processing of its contents will take ∼1-4 h, depending on which specific procedures are used.

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.

The multi-omics promise in context: from sequence to microbial isolate

The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multi-omics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment.

The Oral Microbiota in Health and Disease: An Overview of Molecular Findings

Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity may be even much larger. Nucleic acid technologies have also been helpful in profiling bacterial communities and identifying disease-related patterns. This chapter provides an overview of the diversity and taxonomy of oral bacteria associated with health and disease.

Cultivation strategies for growth of uncultivated bacteria

BACKGROUND

The majority of environmental bacteria and around a third of oral bacteria remain uncultivated. Furthermore, several bacterial phyla have no cultivable members and are recognised only by detection of their DNA by molecular methods. Possible explanations for the resistance of certain bacteria to cultivation in purity in vitro include: unmet fastidious growth requirements; inhibition by environmental conditions or chemical factors produced by neighbouring bacteria in mixed cultures; or conversely, dependence on interactions with other bacteria in the natural environment, without which they cannot survive in isolation. Auxotrophic bacteria, with small genomes lacking in the necessary genetic material to encode for essential nutrients, frequently rely on close symbiotic relationships with other bacteria for survival, and may therefore be recalcitrant to cultivation in purity.

HIGHLIGHT

Since in-vitro culture is essential for the comprehensive characterisation of bacteria, particularly with regard to virulence and antimicrobial resistance, the cultivation of uncultivated organisms has been a primary focus of several research laboratories. Many targeted and open-ended strategies have been devised and successfully used. Examples include: the targeted detection of specific bacteria in mixed plate cultures using colony hybridisation; growth in simulated natural environments or in co-culture with 'helper' strains; and modified media preparation techniques or development of customised media eg. supplementation of media with potential growth-stimulatory factors such as siderophores.

CONCLUSION

Despite significant advances in recent years in methodologies for the cultivation of previously uncultivated bacteria, a substantial proportion remain to be cultured and efforts to devise high-throughput strategies should be a high priority.

In Situ Cultivation Allows for Recovery of Bacterial Types Competitive in Their Natural Environment

Standard cultivation fails to grow most microorganisms, whereas in situ cultivation allows for the isolation of comparatively diverse and novel microorganisms. Information on similarities and differences in the physiological properties of isolates obtained from in situ cultivation and standard cultivation is limited. Therefore, we used the arctic sediment samples and compared two culture collections obtained using standard and novel cultivation techniques. Even though there was no temperature selection at the isolation step, isolates from each method showed different reactions to temperature. The results of the present study suggest that isolates from in situ cultivation are more competitive in their natural environment.

Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples

BACKGROUND

Humans suffer from infections caused by single species or more complex polymicrobial communities. Identification of infectious bacteria commonly employs microbiological culture, which depends upon the in vitro propagation and isolation of viable organisms. In contrast, detection of bacterial DNA using next generation sequencing (NGS) allows culture-independent microbial profiling, potentially providing important new insights into the microbiota in clinical specimens.

METHODS

NGS 16S rRNA gene sequencing (NGS16S) was compared with culture using (a) synthetic polymicrobial samples for which the identity and abundance of organisms present were precisely defined and (b) primary clinical specimens.

RESULTS

Complex mixtures of at least 20 organisms were well resolved by NGS16S with excellent reproducibility. In mixed bacterial suspensions (10⁷ total genomes), we observed linear detection of a target organism over a 4-log concentration range (500-3 × 10⁶ genomes). NGS16S analysis more accurately recapitulated the known composition of synthetic samples than standard microbiological culture using nonselective media, which distorted the relative abundance of organisms and frequently failed to identify low-abundance pathogens. However, extended quantitative culture using selective media for each of the component species recovered the expected organisms at the proper abundance, validating NGS16S results. In an analysis of sputa from cystic fibrosis patients, NGS16S identified more clinically relevant pathogens than standard culture.

CONCLUSIONS

Biases in standard, nonselective microbiological culture lead to a distorted characterization of polymicrobial mixtures. NGS16S demonstrates enhanced reproducibility, quantification, and classification accuracy compared with standard culture, providing a more comprehensive, accurate, and culture-free analysis of clinical specimens.

Gene Sequence Analyses of the Healthy Oral Microbiome in Humans and Companion Animals

It has long been accepted that certain oral bacterial species are responsible for the development of periodontal disease. However, the focus of microbial and immunological research is shifting from studying the organisms associated with disease to examining the indigenous microbial inhabitants that are present in health. Microbiome refers to the aggregate genetic material of all microorganisms living in, or on, a defined habitat. Recent developments in gene sequence analysis have enabled detection and identification of bacteria from polymicrobial samples, including subgingival plaque. Diversity surveys utilizing this technology have demonstrated that bacterial culture techniques have vastly underestimated the richness and diversity of microorganisms in vivo, since only certain bacteria grow in vitro. Surveys using gene sequence analysis have demonstrated that the healthy oral microbiome is composed of an unexpectedly high number of diverse species, including putative pathogens. These findings support the view that coevolution microorganisms and macroscopic hosts has occurred in which certain microorganisms have adapted to survive in the oral cavity and host immune tolerance has allowed the establishment of a symbiotic relationship in which both parties receive benefits (mutualism). This review describes gene sequence analysis as an increasingly common, culture-independent tool for detecting bacteria in vivo and describes the results of recent oral microbiome diversity surveys of clinically healthy humans, dogs, and cats. Six bacterial phyla consistently dominated the healthy oral microbiome of all 3 host species. Previous hypotheses on etiology of periodontitis are reviewed in light of new scientific findings. Finally, the consideration that clinically relevant periodontal disease occurs when immune tolerance of the symbiotic oral microbiome is altered to a proinflammatory response will be discussed.

Decoding molecular interactions in microbial communities

Microbial communities govern numerous fundamental processes on earth. Discovering and tracking molecular interactions among microbes is critical for understanding how single species and complex communities impact their associated host or natural environment. While recent technological developments in DNA sequencing and functional imaging have led to new and deeper levels of understanding, we are limited now by our inability to predict and interpret the intricate relationships and interspecies dependencies within these communities. In this review, we highlight the multifaceted approaches investigators have taken within their areas of research to decode interspecies molecular interactions that occur between microbes. Understanding these principles can give us greater insight into ecological interactions in natural environments and within synthetic consortia.

Nanoporous microscale microbial incubators

Reconstruction of phylogenetic trees based on 16S rRNA gene sequencing reveals abundant microbial diversity that has not been cultured in the laboratory. Many attribute this so-called 'great plate count anomaly' to traditional microbial cultivation techniques, which largely facilitate the growth of a single species. Yet, it is widely recognized that bacteria in nature exist in complex communities. One technique to increase the pool of cultivated bacterial species is to co-culture multiple species in a simulated natural environment. Here, we present nanoporous microscale microbial incubators (NMMI) that enable high-throughput screening and real-time observation of multi-species co-culture. The key innovation in NMMI is that they facilitate inter-species communication while maintaining physical isolation between species, which is ideal for genomic analysis. Co-culture of a quorum sensing pair demonstrates that the NMMI can be used to culture multiple species in chemical communication while monitoring the growth dynamics of individual species.

In vitro culture of previously uncultured oral bacterial phylotypes

Around a third of oral bacteria cannot be grown using conventional bacteriological culture media. Community profiling targeting 16S rRNA and shotgun metagenomics methods have proved valuable in revealing the complexity of the oral bacterial community. Studies investigating the role of oral bacteria in health and disease require phenotypic characterizations that are possible only with live cultures. The aim of this study was to develop novel culture media and use an in vitro biofilm model to culture previously uncultured oral bacteria. Subgingival plaque samples collected from subjects with periodontitis were cultured on complex mucin-containing agar plates supplemented with proteose peptone (PPA), beef extract (BEA), or Gelysate (GA) as well as on fastidious anaerobe agar plus 5% horse blood (FAA). In vitro biofilms inoculated with the subgingival plaque samples and proteose peptone broth (PPB) as the growth medium were established using the Calgary biofilm device. Specific PCR primers were designed and validated for the previously uncultivated oral taxa Bacteroidetes bacteria HOT 365 and HOT 281, Lachnospiraceae bacteria HOT 100 and HOT 500, and Clostridiales bacterium HOT 093. All agar media were able to support the growth of 10 reference strains of oral bacteria. One previously uncultivated phylotype, Actinomyces sp. HOT 525, was cultivated on FAA. Of 93 previously uncultivated phylotypes found in the inocula, 26 were detected in in vitro-cultivated biofilms. Lachnospiraceae bacterium HOT 500 was successfully cultured from biofilm material harvested from PPA plates in coculture with Parvimonas micra or Veillonella dispar/parvula after colony hybridization-directed enrichment. The establishment of in vitro biofilms from oral inocula enables the cultivation of previously uncultured oral bacteria and provides source material for isolation in coculture.

A comprehensive repertoire of prokaryotic species identified in human beings

The compilation of the complete prokaryotic repertoire associated with human beings as commensals or pathogens is a major goal for the scientific and medical community. The use of bacterial culture techniques remains a crucial step to describe new prokaryotic species. The large number of officially acknowledged bacterial species described since 1980 and the recent increase in the number of recognised pathogenic species have highlighted the absence of an exhaustive compilation of species isolated in human beings. By means of a thorough investigation of several large culture databases and a search of the scientific literature, we built an online database containing all human-associated prokaryotic species described, whether or not they had been validated and have standing in nomenclature. We list 2172 species that have been isolated in human beings. They were classified in 12 different phyla, mostly in the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. Our online database is useful for both clinicians and microbiologists and forms part of the Human Microbiome Project, which aims to characterise the whole human microbiota and help improve our understanding of the human predisposition and susceptibility to infectious agents.

High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae

Here we report a summary classification and the features of five anaerobic oral bacteria from the family Peptostreptococcaceae. Bacterial strains were isolated from human subgingival plaque. Strains ACC19a, CM2, CM5, and OBRC8 represent the first known cultivable members of “yet uncultured” human oral taxon 081; strain AS15 belongs to “cultivable” human oral taxon 377. Based on 16S rRNA gene sequence comparisons, strains ACC19a, CM2, CM5, and OBRC8 are distantly related to Eubacteriumyurii subs. yurii and Filifactor alocis, with 93.2 – 94.4 % and 85.5 % of sequence identity, respectively. The genomes of strains ACC19a, CM2, CM5, OBRC8 and AS15 are 2,541,543; 2,312,592; 2,594,242; 2,553,276; and 2,654,638 bp long. The genomes are comprised of 2277, 1973, 2325, 2277, and 2308 protein-coding genes and 54, 57, 54, 36, and 28 RNA genes, respectively. Based on the distinct characteristics presented here, we suggest that strains ACC19a, CM2, CM5, and OBRC8 represent a novel genus and species within the family Peptostreptococcaceae, for which we propose the name Peptoanaerobacter stomatis gen. nov., sp. nov. The type strain is strain ACC19a^T (=HM-483^T; =DSM 28705^T; =ATCC BAA-2665^T).

The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota

Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.

TM7 detection in human microbiome: Are PCR primers and FISH probes specific enough?

TM7 appears important and omnipresent because it is repeatedly detected by molecular techniques in diverse environments. Here we report that most of primers and FISH probes thought to be TM7-specific do hybridize with multiple species from oral and vaginal cavity. This calls for re-examination of TM7 distribution and abundance.

Cancer and the microbiota

A host's microbiota may increase, diminish, or have no effect at all on cancer susceptibility. Assigning causal roles in cancer to specific microbes and microbiotas, unraveling host-microbiota interactions with environmental factors in carcinogenesis, and exploiting such knowledge for cancer diagnosis and treatment are areas of intensive interest. This Review considers how microbes and the microbiota may amplify or mitigate carcinogenesis, responsiveness to cancer therapeutics, and cancer-associated complications.

Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea

Phenazines represent a large group of nitrogen-containing heterocyclic compounds produced by the diverse group of bacteria including actinobacteria. In this study, a total of 197 actinobacterial strains were isolated from seven different marine sponge species in the South China Sea using five different culture media. Eighty-seven morphologically different actinobacterial strains were selected and grouped into 13 genera, including Actinoalloteichus, Kocuria, Micrococcus, Micromonospora, Mycobacterium, Nocardiopsis, Prauserella, Rhodococcus, Saccharopolyspora, Salinispora, Serinicoccus, and Streptomyces by the phylogenetic analysis of 16S rRNA gene. Based on the screening of phzE genes, ten strains, including five Streptomyces, two Nocardiopsis, one Salinispora, one Micrococcus, and one Serinicoccus were found to be potential for phenazine production. The level of phzE gene expression was highly expressed in Nocardiopsis sp. 13-33-15, 13-12-13, and Serinicoccus sp. 13-12-4 on the fifth day of fermentation. Finally, 1,6-dihydroxy phenazine (1) from Nocardiopsis sp. 13-33-15 and 13-12-13, and 1,6-dimethoxy phenazine (2) from Nocardiopsis sp. 13-33-15 were isolated and identified successfully based on ESI-MS and NMR analysis. The compounds 1 and 2 showed antibacterial activity against Bacillus mycoides SJ14, Staphylococcus aureus SJ51, Escherichia coli SJ42, and Micrococcus luteus SJ47. This study suggests that the integrated approach of gene screening and chemical analysis is an effective strategy to find the target compounds and lays the basis for the production of phenazine from the sponge-associated actinobacteria.