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PubMed2003

Rains, drains and active strains: towards online assessment of wastewater bacterial communities.

Wastewater treatment is one of the largest scale and arguably the most commercially important biotechnological process in the world. Bacterial breakdown of waste materials facilitates the safe disposal of effluents into receiving water bodies. Given this significance, research has focused on identifying the keystone species on which efficient treatment is based. However, unravelling the microbial diversity within such systems has proven difficult. This is highlighted by our lack of detailed knowledge of the microbial interactions within these complex populations, limiting our ability to fully exploit bacterial degradative abilities. Even with the incorporation of new emerging molecular techniques, there have been no investigations linking genetic sequence to microbial function and successful treatment operation. To reach this goal, researchers need the ability to identify, enumerate and monitor the metabolic functions of subpopulations within these complex bacterial communities. Flow cytometry (FCM) combined with fluorescence-based molecular identification techniques provides a method for such studies. Moreover, single-cell sorting provides a unique opportunity to identify and remove individual cells of interest. Laboratory culture of sorted cells is often possible and permits the use of more traditional microbiological techniques to backup molecular investigations. Utilising this approach will advance our understanding of wastewater treatment processes and help maintain and enhance plant operation to improve efficiency.

Environmental Monitoring↗

PubMed2004

13CO2 pulse labelling of plants in tandem with stable isotope probing: methodological considerations for examining microbial function in the rhizosphere.

Recently developed 13CO2 pulse labelling and stable isotope probing (SIP) methods offer the potential to track 13C-labelled plant photosynthate into phylogenetic groups of microbial taxa in the rhizosphere, permitting an examination of the link between soil microbial diversity and carbon flow in situ. We tested the feasibility of this approach to detect functional differences in microbial communities utilising recently fixed plant photosynthate in moisture perturbed grassland turfs. Specifically, we addressed two questions: (1) How does moisture perturbation (three treatments; continual wetting, drying, and drying followed by rewetting) affect the assimilation of 13C-labelled exudates carbon into the soil microbial community?; (2) Can 13C deposited in soil from pulse-labelled plants be used to identify microbes utilising plant exudates using SIP methodologies? Net CO2 fluxes showed that prior to 13CO2 pulse labelling, all treatments were photosynthetically active, but differences were observed in night time respiration, indicating moisture treatments had impacted on net CO2 efflux. Measurements of pulse-derived 13C incorporated into soil RNA over 2 months showed that there was only evidence of 13C enrichment in the continuously wetted treatments. However, isotopic values represented only a 0.1-0.2 13C at.% increase over natural abundance levels and were found to be insufficient for the application of RNA-SIP. These findings reveal that in this experimental system, the microbial uptake of labelled carbon from plant exudates is low, and further optimisation of methodologies may be required for application of SIP to natural plant-soil systems where 13C tracer dilution is a consideration.

Carbon Dioxide↗

PubMed2005

Cultivating the uncultivated: a community genomics perspective.

Current isolation methods access only a small subset of the total microbial diversity. Although an isolate traditionally has been required for genomic characterization, the advent of sequencing of entire natural microbial communities enables culture-independent genomic analysis. Information about the genetic potential of uncultivated organisms can be used to predict the form of metabolic interdependencies and nutritional requirements. We believe that this could provide the information necessary to bypass bottlenecks that have inhibited cultivation of many microorganisms. However, it might not be practical or possible to isolate all of the vast number of microbial species and strains for laboratory-based characterization. Ultimately, cultivation-independent genomic and genomically enabled approaches could provide a way to directly analyze microbial activity in its geochemical and ecological context.

Bacteria↗

PubMed2025

Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.

Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes directly from metagenomic samples, also known as metagenome-assembled genomes (MAGs). However, accurately characterizing these genomes remains a significant challenge due to the presence of sequencing errors, incomplete assembly, and contamination. Here we present MetaSBT, a new tool for organizing, indexing, and characterizing microbial reference genomes and MAGs. It is able to identify clusters of genomes at all seven taxonomic levels, from the kingdom all the way down to the species level, using the Sequence Bloom Tree (SBT) data structure that relies on Bloom Filters (BFs) to index massive amounts of genomes based on their k-mers composition. We have built an initial set of databases composed of over 190 thousand viral genomes from NCBI GenBank and public sources grouped into sequence consistent clusters at different taxonomic levels, making it the first software solution for the classification of viruses at different ranks, including still unknown ones. This results in the definition of over 40 thousand species clusters where ~80% do not match with any known viral species in reference databases to date. Furthermore, we show how our databases can be used as a new basis for existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. Finally, the framework is released open-source and, along with its public databases, is fully integrated into the Galaxy Platform enabling broad accessibility.

metagenome-assembled genomes↗

PubMed2003

Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea).

Present knowledge of microbial diversity is decidedly incomplete (S. J. Giovannoni and M. S. Rappé, p. 47-84, in D. Kirchman, ed., Microbial Ecology of the Oceans, 2000; E. Stackebrandt and T. M. Embley, p. 57-75, in R. R. Colwell and D. J. Grimes, ed., Nonculturable Microorganisms in the Environment, 2000). Protistan phylogenies are particularly deficient and undoubtedly exclude clades of principal ecological and evolutionary importance (S. L. Baldauf, Science 300:1703-1706, 2003). The rRNA approach has been extraordinarily successful in expanding the global prokaryotic record (S. J. Giovannoni and M. S. Rappé, p. 47-84, in D. Kirchman, ed., Microbial Ecology of the Oceans, 2000; E. Stackebrandt and T. M. Embley, p. 57-75, in R. R. Colwell and D. J. Grimes, ed., Nonculturable Microorganisms in the Environment, 2000) but has rarely been used in protistan discovery. Here we report the first application of the 18S rRNA approach to a permanently anoxic environment, the Cariaco Basin off the Venezuelan coast. On the basis of rRNA sequences, we uncovered a substantial number of novel protistan lineages. These included new clades of the highest taxonomic level unrelated to any known eukaryote as well as deep branches within established protistan groups. Three novel lineages branch at the base of the eukaryotic evolutionary tree preceding, contemporary with, or immediately following the earliest eukaryotic branches. These newly discovered protists may retain traits reminiscent of an early eukaryotic ancestor(s).

Animals↗

PubMed2006

Dental plaque as a biofilm and a microbial community - implications for health and disease.

Dental plaque is a structurally- and functionally-organized biofilm. Plaque forms in an ordered way and has a diverse microbial composition that, in health, remains relatively stable over time (microbial homeostasis). The predominant species from diseased sites are different from those found in healthy sites, although the putative pathogens can often be detected in low numbers at normal sites. In dental caries, there is a shift toward community dominance by acidogenic and acid-tolerating species such as mutans streptococci and lactobacilli, although other species with relevant traits may be involved. Strategies to control caries could include inhibition of biofilm development (e.g. prevention of attachment of cariogenic bacteria, manipulation of cell signaling mechanisms, delivery of effective antimicrobials, etc.), or enhancement of the host defenses. Additionally, these more conventional approaches could be augmented by interference with the factors that enable the cariogenic bacteria to escape from the normal homeostatic mechanisms that restrict their growth in plaque and out compete the organisms associated with health. Evidence suggests that regular conditions of low pH in plaque select for mutans streptococci and lactobacilli. Therefore, the suppression of sugar catabolism and acid production by the use of metabolic inhibitors and non-fermentable artificial sweeteners in snacks, or the stimulation of saliva flow, could assist in the maintenance of homeostasis in plaque. Arguments will be presented that an appreciation of ecological principles will enable a more holistic approach to be taken in caries control.

Journal Article↗

PubMed2005

Genetic diversity of bacterial strains isolated from soils, contaminated with polycyclic aromatic hydrocarbons, by 16S rRNA gene sequencing and amplified fragment length polymorphism fingerprinting.

In order to study microbial diversity in a polycyclic aromatic hydrocarbon-impacted soil, 14 bacterial strains were analyzed by 16S rRNA gene sequencing and amplified fragment length polymorphism (AFLP) analysis. Bacterial strains isolated from two different hydrocarbon-polluted sites were identified to the species level by 16S rRNA full-gene sequencing using MicroSeq 16S rRNA gene sequencing. Their genome was subsequently analyzed by high-resolution genotyping with AFLP analysis, in order to monitor species variability and to differentiate closely related strains. Cluster analysis based on AFLP fingerprinting showed intra-specific polymorphism, even among strains with 100% 16S rRNA gene sequence identity. The results show that AFLP is a powerful, highly reproducible and discriminatory tool for revealing genetic relationships in bacterial populations. The ability to differentiate and track related closely microbes is fundamental for studying structure and dynamics of microbial communities in contaminated ecosystems.

Bacteria↗

PubMed2006

Intervention of Toll-like receptor-mediated human innate immunity and inflammation by synthetic compounds and naturally occurring products.

Human innate immunity plays a pivotal role in host defense against various microbial challenges. Mediated by a family of Toll-like-receptors (TLR) and associated intracellular downstream signaling molecules, human innate immunity can specifically recognize diverse microbial products and many other non-microbial environmental cues. Beyond its role of providing first line of defense, activation of innate immunity signaling can lead to expression of diverse pro- and anti- inflammatory mediators, which are critical for regulating various cell and tissue metabolism. Alteration in innate immunity signaling may therefore lead to infection and inflammatory diseases such as atherosclerosis, diabetes, and cancer. TLR receptors as well as intracellular signaling proteins can serve as therapeutic targets for treating various inflammatory diseases. Several synthetic ligands of TLR receptors such as lipid A analogs, poly(I:C), loxoribine, oligodeoxynucleotides have been shown to be effective in regulating innate immune response. This review discusses the potential, challenge, and recent progress of developing synthetic as well as naturally occurring TLR ligands in regulating innate immunity and treating inflammatory diseases.

Biological Products↗

PubMed2007

Bacterial community structure associated with the Antarctic soft coral, Alcyonium antarcticum.

The structure and composition of microbial communities inhabiting the soft coral Alcyonium antarcticum were investigated across three differentially contaminated sites within McMurdo Sound, Antarctica. Diverse microbial communities were revealed at all sites using culture-based analysis, denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene clone-library analysis, and FISH. Phylogenetic analysis of isolates and retrieved sequences demonstrated close affiliation with known psychrophiles from the Antarctic environment and high similarity to Gammaproteobacteria clades of sponge-associated microorganisms. The majority of bacteria detected with all techniques reside within the Gammaproteobacteria, although other phylogenetic groups including Alpha- and Betaproteobacteria, Bacteroidetes, Firmicutes, Actinomycetales, Planctomycetes, and Chlorobi and bacteria from the functional group of sulfate-reducing bacteria were also present. Multivariate (nMDS) analysis of DGGE banding patterns and principal component analysis of quantitative FISH data revealed no distinct differences in community composition between differentially contaminated sites. Rather, conserved coral-associated bacterial groups were observed within and between sites, providing evidence to support specific coral-microbial interactions. This is the first investigation of microbial communities associated with Antarctic soft corals, and the results suggest that spatially stable microbial associations exist across an environmental impact gradient.

Animals↗

PubMed2006

Small molecules: the lexicon of biodiversity.

The extent of microbial diversity in the Biosphere is not known (and probably never will be!). One aspect of this diversity is the production of biologically active small molecules; within the Streptomycetes alone this may be millions of compounds with an extraordinary diversity and complexity of structure. First recognised as pigments and later, in the 1950s, as antibiotics, it is now clear that the small molecules produced by microbes have many different functions in nature. This huge collection of biologically active compounds with various properties has been used as pharmaceuticals and agriculturals. They also interact with proteins and RNA with high specificity and have been shown to be regulators and effectors of diverse biochemical reactions. The use of small molecules (other than as pharmaceuticals) deserves to be explored in order to exploit microbial biotechnology to the full.

Biodiversity↗

PubMed2026

Lactobacillus iners at the nexus of microbiota, immunity, and pregnancy.

Pregnancy induces a dynamic reconfiguration of the vaginal microbiome, typically marked by increased dominance of Lactobacillus species and reduced microbial diversity. Among these bacteria, Lactobacillus iners stands out for its unique genomic traits, controversial associations with vaginal health, and frequent presence across all stages of gestation. This review synthesizes current literature on the maternal microbiome with a focus on L. iners, exploring its strain-level diversity, metabolic idiosyncrasies, and inflammatory potential. We discuss how host factors such as ethnicity, sexual activity, maternal age, and especially obesity, influence microbial composition, and evaluate conflicting data surrounding L. iners in contexts like in vitro fertilization, preterm birth, and postpartum recovery. Emerging evidence suggests that L. iners may act as a transitional species, whose effect on pregnancy outcomes depends on its abundance, genetic features, and interactions with the host immune system. We also assess limitations of current animal models and propose future directions for understanding this enigmatic bacterium. Unraveling the role of L. iners will be essential to predicting, preventing, and managing adverse pregnancy outcomes in diverse populations.

Humans↗

PubMed2005

Diversity of phage integrases in Enterobacteriaceae: development of markers for environmental analysis of temperate phages.

Viruses are the most abundant biological entities in aquatic systems. Temperate bacteriophages have enormous influences on microbial diversity, genetic exchange and bacterial population dynamics. However, development of molecular tools for their detection in the environment has been problematic. The integrase gene is used here as a molecular marker to analyse the diversity of temperate bacteriophages in a population of freshwater bacteria. Interrogation of the GenBank database revealed 32 non-cryptic enteric phage integrase sequences, leading to the development of a suite of 11 degenerate primer sets specific to the extant sequences elucidated. Application of these primer sets to enterobacterial isolates recovered from a freshwater pond and the temperate phages induced from them revealed a number of diverse integrase genes, including novel integrase-like sequences not represented in the databases. This highlights the potential of utilizing the integrase gene family as a marker for phage diversity.

Bacteriophages↗

PubMed2026

Soil management practices shape the abundance, diversity, and spread of antimicrobial resistance.

Agricultural soils are critical hotspots of antimicrobial resistance genes (ARGs). Yet, the environmental factors shaping these reservoirs and the hazards they pose to humans and livestock remain poorly understood. Because management practices introduce antibiotics, heavy metals, and nonantibiotic biocides, they can rapidly select for resistance. Most studies have examined components of management practices in isolation, overlooking the multiple stressors of modern industrial agriculture. Here, we used a large-scale field experiment to examine how multiple stressors from soil and crop management interact to shape antimicrobial resistance. We combined shotgun metagenomics, phylogenomics, and risk-score analyses to quantify the diversity of ARGs, mobile genetic elements (MGEs), and the transmission potential of drug-resistant pathogens. Relative to other management systems, intensive, chemically reliant monoculture systems, typical of the US Corn Belt, create strong selective pressures promoting more abundant and diverse ARGs and MGEs. These systems therefore carry greater potential to transmit ARGs, including those with relevance to both livestock and public health such as tetA and blaPAM, likely mediated by integration and excision. In contrast, less-intensive, lower-input systems with diverse crop rotations maintained resistomes with lower abundance, diversity, and transmission potential. Our results suggest that these patterns could arise due to the divergent effects of management practices on overall soil microbial diversity, an ecological barrier that can suppress ARGs. This study highlights the need to understand the combined stressors of agricultural practices, beyond antimicrobial use, to design effective strategies to mitigate antimicrobial resistance.

Soil Microbiology↗

PubMed2026

Multi-omics analysis reveals stage-associated differences in gut immunity and microbiota between juvenile and adult common carp (Cyprinus carpio).

In vertebrates, the development of intestinal immunity is closely associated with dynamic changes in the gut microbiota. However, stage-associated differences in intestinal immunity and gut microbial communities remain poorly characterized in teleost fish. In this study, transcriptomic analysis combined with 16S rRNA gene sequencing was employed to characterize intestinal immunity and gut microbial communities in juvenile and adult common carp (Cyprinus carpio). Transcriptomic profiling revealed marked developmental differences in intestinal immune function. Juvenile carp exhibited a predominantly innate immune phenotype, characterized by elevated expression of pro-inflammatory cytokines, antimicrobial peptides, and lysozyme-related genes. This immune profile was accompanied by enhanced mucosal barrier function and a relatively pro-inflammatory intestinal environment. In contrast, adult carp displayed increased expression of genes associated with adaptive immunity, suggesting that adult common carp exhibit relatively stronger adaptive immune characteristics than juvenile fish. Gut microbiota analysis demonstrated significant stage-dependent differences in microbial diversity and community composition. Juvenile fish were enriched with bacterial taxa potentially associated with innate immune activation, whereas adult fish harbored distinct microbial communities linked to intestinal homeostasis and barrier maintenance. Furthermore, correlation analyses identified significant associations between specific microbial taxa and innate immune-related gene expression, suggesting a close association between gut microbiota composition and intestinal immune characteristics in juvenile and adult common carp. Collectively, these findings reveal stage-associated differences in intestinal immunity and gut microbial communities between juvenile and adult common carp, thereby providing insights into intestinal immune characteristics at different developmental stages in teleost fish.

Animals↗

PubMed1999

16S rDNA methods in soil microbiology

With the introduction of molecular methods, the past decade has seen renewed interest in soil microbiology. New and exciting molecular technologies and the promise of finally opening the microbial black box in soil drive much of this interest. Although these pioneering studies have added much to our knowledge of microbial diversity in soils, it is debatable whether they have as yet advanced our understanding of the relationship between this diversity and soil processes. Hopefully, over the next few years, the knowledge gained from molecular studies will provide a better understanding of microbial communities in soils and lead ultimately to improvements in land management and to the exploitation of the genetic resources of soil.

Journal Article↗

PubMed1999

Changes in quinone profiles of hot spring microbial mats with a thermal gradient

The respiratory and photosynthetic quinones of microbial mats which occurred in Japanese sulfide-containing neutral-pH hot springs at different temperatures were analyzed by spectrochromatography and mass spectrometry. All of the microbial mats that developed at high temperatures (temperatures above 68 degreesC) were so-called sulfur-turf bacterial mats and produced methionaquinones (MTKs) as the major quinones. A 78 degreesC hot spring sediment had a similar quinone profile. Chloroflexus-mixed mats occurred at temperatures of 61 to 65 degreesC and contained menaquinone 10 (MK-10) as the major component together with significant amounts of either MTKs or plastoquinone 9 (PQ-9). The sunlight-exposed biomats growing at temperatures of 45 to 56 degreesC were all cyanobacterial mats, in which the photosynthetic quinones (PQ-9 and phylloquinone) predominated and MK-10 was the next most abundant component in most cases. Ubiquinones (UQs) were not found or were detected in only small amounts in the biomats growing at temperatures of 50 degreesC and above, whereas the majority of the quinones of a purple photosynthetic mat growing at 34 degreesC were UQs. A numerical analysis of the quinone profiles was performed by using the following three parameters: dissimilarity index (D), microbial divergence index (MDq), and bioenergetic divergence index (BDq). A D matrix tree analysis showed that the hot spring mats consisting of the sulfur-turf bacteria, Chloroflexus spp., cyanobacteria, and purple phototrophic bacteria formed distinct clusters. Analyses of MDq and BDq values indicated that the microbial diversity of hot spring mats decreased as the temperature of the environment increased. The changes in quinone profiles and physiological types of microbial mats in hot springs with thermal gradients are discussed from evolutionary viewpoints.

Journal Article↗

PubMed1992

Identification of uncultured microorganisms: expanding the spectrum of characterized microbial pathogens.

The combination of enzymatic nucleic acid amplification techniques with 16S rRNA-based molecular phylogeny has brought about a new approach to the identification of microbial pathogens that can not be cultivated in the laboratory. The applications of this experimental approach to bacillary angiomatosis and to Whipple's disease have revealed the presence of two previously uncharacterized organisms. These results suggest the existence of a far greater microbial diversity among human pathogens than has been so far appreciated with culture-dependent methods. PCR-based studies of aquatic environmental microbial communities have already reached similar conclusions. As a result, new and provocative questions are raised concerning the association of amplified 16S rRNA sequences with diseased tissue. The answers must await the results of further investigations and the expansion of sequence data bases.

Animals↗

PubMed2004

Nitrogen removal characteristics analyzed with gas and microbial community in thermophilic aerobic digestion for piggery waste treatment.

In order to characterize the nitrogen conversion characteristics in a thermophilic aerobic digestion (TAD) system, a laboratory study has been conducted with the analysis of effluent gas and microbial community in the sludge samples. The lab TAD system was operated with HRT of 3 days and 60 degrees C. Based on the nitrogen mass balance, it has been found that about 2/3 of the daily load of nitrogen was converted to the gaseous form of nitrogen whereas cellular transformation and unmetabolized nitrogen accounted for about 1/3. Among the gaseous nitrogen transformation, significant amount of influent nitrogen had been converted to N2 gas (29% of influent N) and N2O (9% of influent N). Ammonia conversion was only 28% of influent N. The detection of N2O gas is a clear indication of the biological nitrogen reduction process in the thermophilic aerobic digester. No conclusive evidence for the existence of aerobic deammonification has been found. The microbial community analysis showed that thermophilic bacteria such as Bacillus thermocloacae, Bacillus sp. and Clostridial groups dominated in this TAD reactor. The diverse microbial community in TAD sludge may play an important role in removing both strong organics and nitrogen from piggery waste.

Agriculture↗