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PubMed2006

Resource availability controls fungal diversity across a plant diversity gradient.

Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales.

Biodiversity↗

PubMed2003

Leitbakteria of microbial biofilm communities causing occlusion of biliary stents.

Biliary stents inserted to relieve obstructive jaundice caused by biliary or pancreatic malignancies inevitably become occluded by microbial growth in the form of diverse microbial community biofilms. The scarce information available on these communities is based on cultivation methods, but such methods usually provide distorted overviews of community composition, so commonalities and differences in biliary stent communities are uncertain. We extracted DNA and RNA from the microbial communities of 11 biliary stents explanted from nine patients in hospitals from two different countries, amplified 16S rRNA and rDNA sequences, analysed the amplicons by the single-strand conformation polymorphism (SSCP) method, and sequenced and deduced phylogenetic assignments of the major amplicons representing the major biofilm community members. We used a Modified Robbins Device (MRD) to study de novo development of a stent biofilm from a patient stent microbial community. Single-strand conformation polymorphism fingerprinting revealed the same six abundant bacterial species, here designated Leitbakteria, namely Klebsiella pneumoniae, Enterococcus faecalis, Pseudomonas aeruginosa, Enterobacter aerogenes, and two unculturable bacteria distantly related to E. coli and Shigella sonnei, in all of the stent biofilm communities. In the experimental biliary stent system, a sequential colonization of the stent surface was observed, with P. aeruginosa being the pioneer colonizer, followed by K. pneumoniae and one of the unculturable Leitbakteria, followed by the remainder of the community. The overview of microbial biofilm communities of biliary stents gained by the use of culture-independent methods revealed new unculturable bacteria as major members of biliary stent biofilms, and the diversity of the abundant members of the stent biofilms is considerably lower than suggested from earlier studies based on cultivation methods, and that communities from different stents from different patients in different countries are remarkably similar and have similar major members, the stent Leitbakteria.

Aged↗

PubMed2001

Biogeochemical characterisation of a coal tar distillate plume.

The distillation of acidified coal tars for up to 50 years has given rise to a phenol plume approximately 500 m long, 50 m deep and containing up to 15 g l(-1) dissolved organic carbon (DOC) in the Triassic Sandstones aquifer. A conceptual biogeochemical model based on chemical and microbiological analysis of groundwater samples has been developed as a preliminary to more detailed studies of the controls on natural attenuation. While the development of redox zones and the production of methane and carbon dioxide provide evidence of natural attenuation, it appears that degradation is slow. The existence of sulphate in the plume indicates that this electron acceptor has not been depleted and that consequently methanogenesis is probably limited. Based on a simple estimate of sulphate input concentration, a half-life of about 15 years has been estimated for sulphate reduction. Geochemical modelling predicts that increased alkalinity within the plume has not led to carbonate precipitation, and thus within the limits of accuracy of the measurement, alkalinity may reflect the degree of biodegradation. This implies a loss of around 18% of the DOC over a 30-year period. Despite limited degradation, microbial studies show that there are diverse microbial communities in the aquifer with the potential for both anaerobic and aerobic biodegradation. Microbial activity was found to be greatest at the leading edge of the plume where DOC concentrations are 60 mg l(-1) or less, but activity could still be observed in more contaminated samples even though cells could not be cultured. The study suggests that degradation may be limited by the high phenol concentrations within the core of the plume, but that once diluted by dispersion, natural attenuation may proceed. More detailed studies to confirm these initial findings are identified and form the basis of associated papers.

Biodegradation, Environmental↗

PubMed2006

Genetic profiling of the oral microbiota associated with severe early-childhood caries.

The determination of the composition of the microbial community in the oral cavity is usually based on cultivation methods; however, nearly half of the bacteria in the saliva and the dental plaque are not cultivable. In this study, we evaluated the difference in oral microbial diversity between children with severe early-childhood caries (S-ECC) and caries-free (CF) controls by means of a cultivation-independent approach called denaturing gradient gel electrophoresis (DGGE). Pooled dental plaque samples were collected from 20 children aged 2 to 8 years. Total microbial genomic DNA was isolated from those subjects, and a portion of the 16S rRNA gene locus was PCR amplified by using universal primers. We observed that the mean species richness of the bacterial population was greater in the CF children (n = 12) (42 +/- 3.7) than in the S-ECC children (n = 8) (35 +/- 4.3); the difference was statistically significant (P = 0.005). The overall diversity of plaque samples as measured by the Shannon index was 3.5 for the S-ECC group and 3.7 for the CF group (P = 0.004). Differences in DGGE profiles were distinguished on the basis of a cluster analysis. Sequence analysis of excised DGGE bands consisted of 2.7 phylotypes, on average. After adjusting for the number of observed bands, we estimated that the S-ECC group exhibited 94.5 total phylotypes and that the CF group exhibited 113.4. These results suggest that the microbial diversity and complexity of the microbial biota in dental plaque are significantly less in S-ECC children than in CF children.

Bacterial Typing Techniques↗

PubMed2005

Estimating and comparing the diversity of marine actinobacteria.

This paper reviews the application of species richness estimators to microbial diversity data and describes phylogenetic approaches to comparing microbial communities. The techniques are demonstrated using a community of marine actinobacteria. Results demonstrate that marine environments harbour massive actinobacterial diversity. Furthermore, these predictions are likely to be severe underestimates due to the use of arbitrary OTU definitions.

Actinobacteria↗

PubMed2003

High 16S rDNA bacterial diversity in glacial meltwater lake sediment, Bratina Island, Antarctica.

The microbial diversity in maritime meltwater pond sediments from Bratina Island, Ross Sea, Antarctica was investigated by 16S rDNA-dependent molecular phylogeny. Investigations of the vertical distribution, phylogenetic composition, and spatial variability of Bacteria and Archaea in the sediment were carried out. Results revealed the presence of a highly diverse bacterial population and a significantly depth-related composition. Assessment of 173 partial 16S rDNA clones analyzed by amplified rDNA restriction analysis (ARDRA) using tetrameric restriction enzymes (HinP1I 5'G/CGC3'and Msp I. 5'C/CGG3', BioLabs) revealed 153 different bacterial OTUs (operational taxonomic units). However, only seven archaeal OTUs were detected, indicating low archaeal diversity. Based on ARDRA results, 30 bacterial clones were selected for sequencing and the sequenced clones fell into seven major lineages of the domain Bacteria; the alpha, gamma, and delta subdivisions of Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides, the Spirochaetaceae, and the Actinobacteria. All of the archaeal clones sequenced belonged to the group Crenarchaeota and phylogenetic analysis revealed close relationships with members of the deep-branching Group 1 Marine Archaea.

Actinobacteria↗

PubMed1980

Aspects of diversity measurement for microbial communities.

A useful measure of diversity was calculated for microbial communities collected from lake water and sediment samples using the Shannon index (H') and rarefaction [E(S)]. Isolates were clustered by a numerical taxonomy approach in which limited (<20) tests were used so that the groups obtained represented a level of resolution other than species. The numerical value of diversity for each sample was affected by the number of tests used; however, the relative diversity compared among several sampling locations was the same whether 11 or 19 characters were examined. The number of isolates (i.e., sample size) strongly influenced the value of H' so that unequal sized samples could not be compared. Rarefaction accounts for differences in sample size inherently so that such comparisons are made simple. Due to the type of sampling carried out by microbiologists, H' is estimated and not determined and therefore requires a statement of error associated with it. Failure to report error provided potentially misleading results. Calculation of the variance of H' is not a simple matter and may be impossible when handling a large number of samples. With rarefaction, the variance of E(S) is readily determined, facilitating the comparison of many samples.

Journal Article↗

PubMedDate not supplied

Impact of genetically modified crops on soil- and plant-associated microbial communities.

Transgenic or genetically modified plants possess novel genes that impart beneficial characteristics such as herbicide resistance. One of the least understood areas in the environmental risk assessment of genetically modified crops is their impact on soil- and plant-associated microbial communities. The potential for interaction between transgenic plants and plant residues and the soil microbial community is not well understood. The recognition that these interactions could change microbial biodiversity and affect ecosystem functioning has initiated a limited number of studies in the area. At this time, studies have shown the possibility that transgenes can be transferred to native soil microorganisms through horizontal gene transfer, although there is not evidence of this occurring in the soil. Furthermore, novel proteins have been shown to be released from transgenic plants into the soil ecosystem, and their presence can influence the biodiversity of the microbial community by selectively stimulating the growth of organisms that can use them. Microbial diversity can be altered when associated with transgenic plants; however, these effects are both variable and transient. Soil- and plant-associated microbial communities are influenced not only by plant species and transgene insertion but also by environmental factors such as field site and sampling date. Minor alterations in the diversity of the microbial community could affect soil health and ecosystem functioning, and therefore, the impact that plant variety may have on the dynamics of the rhizosphere microbial populations and in turn plant growth and health and ecosystem sustainability, requires further study.

Bacteria↗

PubMed2025

Clinical and Microbiological Insights into Caseous Lymphadenitis in Sheep and Goats in Khorasan Razavi, Iran.

INTRODUCTION: Caseous lymphadenitis (CLA), a chronic bacterial disease caused by Corynebacterium pseudotuberculosis, significantly impacts small-ruminant health and productivity worldwide, causing economic losses through reduced wool and milk yields, reproductive issues, and carcass condemnation. Despite its importance, CLA prevalence and microbial dynamics remain under explored in Iran, where small ruminants are vital to rural economies. This study assessed the prevalence, clinical manifestations, and bacteriological profile of CLA in Khorasan Razavi Province, northeast Iran, to inform regional control strategies and address potential zoonotic risks. MATERIALS & METHODS: We examined 15 flocks totaling 4,733 animals (4,640 sheep, 93 goats) through clinical inspections and microbiological analysis of pus samples from affected lymph nodes. RESULTS: The results revealed a lymphadenitis prevalence of 11.59% (95% CI, 10.58%, 12.66%), with 8.62% of sheep (400/4640) and 8.60% of goats (8/93) affected, varying across flocks from 0% to 28.57%. Submandibular lymph nodes were most commonly affected (51.35%), followed by retropharyngeal (18.02%) and parotid (15.32%) nodes, with peak incidence in the 2-3-year age group (38.24%), likely linked to shearing practices. Bacteriological analysis of 102 pus samples identified C. pseudotuberculosis in 19.6% (20/102) of cases, characterized by small, dry, white colonies with β-hemolysis on Columbia blood agar. A diverse microbial profile included Actinobacillus spp. (7.8%), Trueperella pyogenes (3.9%), and novel isolates like Acinetobacter spp. and Yersinia spp. (1.0% each), with 43.14% of samples sterile, suggesting chronicity or sampling challenges. CONCLUSION: These findings indicate CLA etiology is complex, extending beyond a single pathogen and influenced by local husbandry practices. The study underscores CLA's economic burden and zoonotic potential, given rare but documented human cases. Integrated control measures-enhanced molecular diagnostics, recombinant phospholipase D (PLD) vaccine trials, and improved biosecurity-are urgently needed. Future research should prioritize genomic strain typing and environmental reservoir analysis to refine CLA management in Northeast Iran, offering insights applicable to similar agroecosystems globally.

Animals↗

PubMed1977

Nose, throat, and fecal flora of beagle dogs housed in "locked" or "open" environments.

The microbial flora of the nose, throat, and feces of male beagle dogs housed in a "locked environment" (i.e. confined to germfree-style isolators and supplied with sterile food, air, and water) or an open environment were assessed between 26 and 30 months into the study. Forty-five genera and 170 different species or types of microorganisms were cultured from the nose, throat, and feces of the beagles. Clostridia, eubacteria, corynebacteria, bacteroides, lactobacilli, and anaerobic, gram-positive cocci accounted for most of the microbial diversity in the flora. Some of the facultative anaerobes, especially streptococci and lactobacilli (in feces), occurred in numbers that were comparable to the most numerous anaerobic species. Confinement to the locked environment resulted in an increased diversity of microorganisms in the flora, but the total microbial counts did not increase to any great extent. Even with the increased diversity of bacteria in the flora of confined dogs, some bacteria seemed to favor certain areas of the gastrointestinal tract over others. The increased diversity of bacteria observed in these confined dogs may pose some infectious disease problems for other mammals (including humans) that may be confined to a locked, ultra-clean environment for a prolonged period of time.

Aerobiosis↗

PubMed1994

Metabolic cooperation in oral microbial communities during growth on mucin.

Hog gastric mucin has been used as a model glycoprotein to determine the role of particular glycosidases produced by different oral bacteria in the development of stable, diverse microbial communities. The patterns of glycosidase and protease activity were determined in pure cultures of ten representative species of oral bacteria using synthetic substrates. A five-member mixed culture was established in a chemostat, comprising species with minimal glycosidase and protease activity, in which hog gastric mucin was the major carbon and energy source. Introduction of additional species with novel enzyme activities (e.g. sialidase, alpha-fucosidase and endopeptidase) led to their establishment within the community to make communities with seven, eight, nine and ten members and resulted in an increase in the total viable counts of the microbial consortium. This increase in viable count was made up of the numbers of the newly added species as well as from a rise in the numbers of the existing community members. This result suggested that glycoprotein catabolism involved the synergistic and concerted action of several species with overlapping patterns of enzyme activity. Such metabolic cooperation results in the liberation of additional nutrients, and this may help to maintain the characteristic diversity of resident microbial communities found in many natural habitats.

Animals↗

PubMed2005

A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates.

A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750-800 base pairs (bp) encompassing hypervariable regions in the 5' portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram + high GC content, Gram + low GC content). The 2273 microorganisms surveyed encompass 834 alpha-Proteobacteria (representing 60 different phylotypes), 25 beta-Proteobacteria (3 phylotypes), 767 gamma-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram + high GC content (43 phylotypes), and 198 Gram + low GC content isolates (24 phylotypes). Notably, 11 phylotypes were < or =93% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (approximately 1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported "uncultured" microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr_hbmmd.html).

Alphaproteobacteria↗

PubMed2006

Beyond diversity: functional microbiomics of the human colon.

Molecular tools have revealed wide microbial diversity in the human alimentary tract. Most intestinal microorganisms have not been cultured and the in situ functions of distinct groups of the intestinal microbiota are largely unknown but pivotal to understanding the role of these microorganisms in health and disease. Promising strategies to gain more insight into the functionality of the complex microbial communities in the human alimentary tract, including fermentation processes in the colon, are discussed. These research approaches could provide a basis for the definition of a healthy gut based on key properties of microbial functionality. This will also enable the development of direct nutritional strategies for intestinal disease prevention and health promotion.

Biodiversity↗

PubMed2005

Bacterial evasion of innate defense at epithelial linings.

The evolution of multicellular organisms has been, and continues to be, paralleled by the evolution of the surrounding microbial flora. This intimate coexistence between higher host organisms and microbes has generated a myriad of adaptation strategies at both sides to cope with, or even benefit from the given conditions. On the host side, the development of an effective immune defence system allowed the maintenance of an astonishingly stable homeostasis on many body sites, and even the establishment of sterile surfaces at vulnerable anatomical sites. On the other hand, microbial diversity has led to the establishment of a large number of microbial life styles that allow persistence and proliferation in the presence of host defense mechanisms. The following review describes bacterial strategies to circumvent or modify host defenses that operate at the epithelial lining. It illustrates the enormous diversity of mechanisms that are part of the complex interplay between microbial organisms and the host. It also reflects the dramatic progress made in the understanding of the mammalian immune defense system which many times has been initiated by the surprising results from the study of microbial pathogenesis.

Animals↗

PubMed2004

Evaluating putative chimeric sequences from PCR-amplified products.

MOTIVATION: PCR amplification of highly homologous genes from complex DNA mixtures is known to generate a significant proportion of chimeric sequences. Ribosomal RNA genes are used for microbial species detection and identification in natural environments, and current assessments of microbial diversity are based on these sequences. Thus, chimeric sequences could lead to the discovery of non-existent microbial species and false diversity estimates. METHODS: In essence, our only source of information to decide if a sequence is chimeric or not is to compare it with known, non-chimeric sequences. Putative chimeric sequences were analyzed from sequence fragments of selected length (referred to as words) by comparing nucleotides at corresponding positions. Distances for each word between reference sequences (closely related to the tested sequence) were compared to the differences introduced by the tested sequence. The proposed strategy considers the actual variability existing in different regions throughout the analyzed sequences. The result is an efficient strategy for the evaluation of putative chimeric sequences. AVAILABILITY: A program computing the above procedure, Chimera and Cross-Over Detection and Evaluation (Ccode), is available at http://www.irnase.csic.es/users/jmgrau/index.html and http://www.rtphc.csic.es/download.html.

Algorithms↗

PubMed1994

Antibiotic susceptibility testing by flow cytometry.

The first significant development in antibiotic susceptibility testing in recent years may be the flow cytofluorometric susceptibility test (FCST). The advanced analytical capability of the flow cytometer has provided the means to measure microbial diversity in culture. Membrane integrity and other indicators of microbial viability can be evaluated on a cell-by-cell basis. The FCST measures subtle dosage-response effects as well as the conventional minimum inhibitory and minimum bactericidal concentrations, simultaneously, in rapid tests which have the potential to supersede conventional techniques in terms of sensitivity and reproducibility.

Bacteria↗

PubMed2005

Molecular analysis of microbial community in a groundwater sample polluted by landfill leachate and seawater.

Seashore landfill aquifers are environments of special physicochemical conditions (high organic load and high salinity), and microbes in leachate-polluted aquifers play a significant role for intrinsic bioremediation. In order to characterize microbial diversity and look for clues on the relationship between microbial community structure and hydrochemistry, a culture-independent examination of a typical groundwater sample obtained from a seashore landfill was conducted by sequence analysis of 16S rDNA clone library. Two sets of universal 16S rDNA primers were used to amplify DNA extracted from the groundwater so that problems arising from primer efficiency and specificity could be reduced. Of 74 clones randomly selected from the libraries, 30 contained unique sequences whose analysis showed that the majority of them belonged to bacteria (95.9%), with Proteobacteria (63.5%) being the dominant division. One archaeal sequence and one eukaryotic sequence were found as well. Bacterial sequences belonging to the following phylogenic groups were identified: Bacteroidetes (20.3%), beta, gamma, delta and epsilon-subdivisions of Proteobacteria (47.3%, 9.5%, 5.4% and 1.3%, respectively), Firmicutes (1.4%), Actinobacteria (2.7%), Cyanobacteria (2.7%). The percentages of Proteobacteria and Bacteroides in seawater were greater than those in the groundwater from a non-seashore landfill, indicating a possible influence of seawater. Quite a few sequences had close relatives in marine or hypersaline environments. Many sequences showed affiliations with microbes involved in anaerobic fermentation. The remarkable abundance of sequences related to (per)chlorate-reducing bacteria (ClRB) in the groundwater was significant and worthy of further study.

Bacteria↗

PubMed2026

Metagenomic insights into antibiotic resistance genes and virulence factors in sediments of river Yamuna.

Riverine sediments serve as critical reservoirs of microbial diversity and functional genes, reflecting both natural ecological processes and anthropogenic impacts. In the present study, we employed a shotgun metagenomic approach to investigate microbial community composition, antimicrobial resistance (AMR) genes, and virulence factors in sediments collected from three environmentally distinct locations of the Yamuna River near Agra, India, representing BSA, TGY, and YEA. The sediment DNA was subjected to high-throughput Illumina sequencing, followed by quality control, assembly, and open reading frame prediction. Taxonomic classification and diversity analyses were performed using MEGAN6 and R-based statistical tools, while AMR genes were identified from predicted metagenomic proteins using the Resistance Gene Identifier (RGI) against the CARD database, with high-confidence perfect and strict hits retained; ARGs were interpreted independently of species-level host assignment. Virulence factors were assessed through presence-absence profiling of functionally relevant gene categories. The results revealed pronounced spatial heterogeneity in microbial communities, with increasing taxonomic diversity, functional complexity, and evenness from BSA to TGY and YEA. TGY and YEA composite samples showed greater observed representation of high-confidence AMR gene predictions spanning multiple drug classes and resistance mechanisms, alongside a diverse repertoire of virulence-associated genes linked to motility, adhesion, and secretion systems. In contrast, the BSA site harbored a comparatively simpler resistome and virulome. Overall, this study highlights Yamuna River sediments as important reservoirs of resistance and virulence determinants and underscores the need for long-term genomic surveillance to inform risk assessment, pollution control, and sustainable river management strategies.

AMR↗