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bioRxiv2026

Curli Carrier Burden: a quantitative trait-level microbiome index for amyloidogenic bacterial signals in Parkinsons disease gut metagenomes

BackgroundParkinsons disease (PD) gut metagenomic studies have repeatedly reported disease-associated shifts in microbial taxa, genes, and pathways. However, the field still lacks transparent trait-level indices that summarize biologically coherent microbial exposures. Curli fibres are extracellular bacterial amyloids produced by several Enterobacteriaceae and related taxa, and they provide a plausible microbiological bridge between gut microbial ecology, epithelial/immune interfaces, and alpha-synuclein-centered gut-brain-axis hypotheses. We introduced Curli Carrier Burden (CCB), a mathematically explicit, taxon-informed index that estimates the aggregate abundance of curated curli-carrier bacterial taxa in processed metagenomic profiles. MethodsA curated curli-carrier candidate panel was converted into an evidence-weighted taxon set. For sample s, CCB was defined as [Formula], where ais is the processed relative abundance of matched curli-carrier taxon i and wi is an evidence weight reflecting curli-carrier confidence. We evaluated CCB in five main PD gut metagenomic evidence streams: Wallen 2022, Integrated-US, Mao Central China, Romano non-Wallen, and DuruIC 2024. Results were interpreted cohort-wise rather than as a formal meta-analysis. ResultsThe CCB framework generated a reproducible sample-level microbial trait variable and enabled cohort-wise comparison of amyloidogenic bacterial burden. Wallen showed discovery-stage PD-associated elevation (724 samples; 31 matched curli taxa; Mann-Whitney p = 0.0020). Integrated-US provided supportive independent evidence (244 samples; 18 matched taxa; p = 0.0079). Mao Central China and DuruIC 2024 showed the same PD-greater-than-control direction by mean and median CCB, although their individual comparisons were not nominally significant. Romano non-Wallen provided a large multi-study analysis (600 samples; 29 matched curli-associated mOTUs taxa), with higher PD mean and median CCB in pooled analysis (p = 0.0036, Cliffs{delta} = 0.137) and cohort-sensitive behavior under study-stratified permutation (p = 0.1974). Additional processed-cohort checks indicated that CCB interpretability depends on taxonomic representation and matched curli-candidate coverage, reinforcing the value of explicit compatibility reporting. ConclusionsCCB is a novel, extensible, microbiology-informed index for quantifying amyloidogenic curli-carrier bacterial burden in processed gut metagenomic profiles. The current results support CCB as a useful exploratory trait-level variable for PD microbiome research and provide a principled route toward future raw-read, csg-operon, strain-resolved, and phenotype-aware studies of the curli-vagal PD axis.

neuroscience↗

bioRxiv2015

Comparison Between Non-Catheterized And Catheter Associated Urinary Tract Infections Caused By Extended Spectrum Β-Lactamase Producing Escherichia Coli And Klebsiella Pneumoniae

AbstractCatheter associated urinary tract infections (CAUTI) account for more than 80% of all healthcare associated infections (HAIs) as compared to non-catheterized urinary tract infections. Catheter associated urinary tract infections occur on the third day after insertion of catheter in patients having urinary tract infection (UTI). In long term catheter use, bio-film form along the catheter which increases the risk of antibiotic resistant pathogens. Most common pathogens involved were Escherichia coli and Klebsiella pneumoniae which produce the enzymes Extended Spectrum {beta}-Lactamases (ESBLs).\n\nObjectiveTo compare the frequency of ESBLs in catheterized and non-catheterized UTI infections.\n\nMaterials and MethodsThis comparative study was conducted at the Microbiology Department, Allama Iqbal Medical College, Lahore, from June 2014 to January 2015. Urine samples were cultured according to WHO protocol and antimicrobial Susceptibility testing was performed by Modified Kirby-Bauer disc diffusion Method. Escherichia coli and Klebsiella pneumoniae were tested for ESBL production by phenotypic confirmatory method of disk diffusion synergy using a disc of amoxicillin-clavulonate (30g) and ceftrixone (30g), cefotaxime (30g) and aztreonam (30g) discs.\n\nResultsOut of 300 positive urinary isolates of Escherichia coli and Klebsiella pneumoniae from CAUTI, 65.33% were ESBL producing isolates whereas out of 300 positive urinary isolates of Escherichia coli and Klebsiella pneumoniae from non-catheterized UTI, 47.66% were ESBL producing isolates. The results were highly significant (p < 0.001).\n\nConclusionResults showed that frequency of ESBLs were higher in catheterized patients as compared to non-catheterized patients. This is suggestive of a need for regular screening and surveillance for ESBL producing organisms. Patients infected with these organisms should be nursed with contact precautions to avoid the spread of nosocomial infection.

Microbiology↗

bioRxiv2016

Divorcing strain classification from species names

Confusion about strain classification and nomenclature permeates modern microbiology. Although taxonomists have traditionally acted as gatekeepers of order, the numbers of and speed at which new strains are identified has outpaced the opportunity for professional classification for many lineages. Furthermore, the growth of bioinformatics and database fueled investigations have placed metadata curation in the hands of researchers with little taxonomic experience. Here I describe practical challenges facing modern microbial taxonomy, provide an overview of complexities of classification for environmentally ubiquitous taxa like Pseudomonas syringae, and emphasize that classification and nomenclature need not be the one in the same. A move toward implementation of relational classification schemes based on inherent properties of whole genomes could provide sorely needed continuity in how strains are referenced across manuscripts and data sets.

Microbiology↗

bioRxiv2016

THE PATTERN OF BACTERIA AND ITS RESISTANCE ON ADULT SEPSIS PATIENT AT Dr. MOEWARDI GENERAL HOSPITAL, INDONESIA

BackgroundSepsis incidence which related with morbidity and mortality, is globally increasing. Sepsis occurs because of severe infections. Sepsis has life-threatening potential with organ disfungction complication, septic shock, and death. Alteration of resistance pattern always change at certain period. The aim of the study is to investigate the bacteria pattern and its resistance from adult sepsis patient at Dr. Moewardi Regional General Hospital.\n\nMethodsIsolated bacteria from adult sepsis patients blood at Dr. Moewardi Regional General Hospital. 7 bacteria isolates were taken from blood of adult sepsis patient (September - October 2014) and 46 bacteria isolates of secondary data (January - March 2014) at Dr. Moewardi Regional General Hospital. Bacteria isolation was performed based on standard Laboratory of Microbiology of Dr. Moewardi Regional General Hospital. 7 bacteria isolates were tested by using disc diffusion antibiotic on Mueller Hinton and coupled by 46 secondary data.\n\nResultsThe bacteria pattern from adult sepsis patients were Staphylococcus haemolyticus (15,09%), Staphylococcus hominis (15,09%), Escherichia coli (13,21%), and Acinetobacter baumannii (11,32%). Resistance pattern of bacteria on adult sepsis with level of resistant more than 50% as Staphylococcus haemolyticus (ciprofloxacin, erythromycin, levofloxacin, moxifloxacin, and gentamicin), Escherichia coli (gentamicin, ciprofloxacin, and levofloxacin), and Acinetobacter baumannii (gentamicin, ciprofloxacin, levofloxacin, and ceftazidime)\n\nConclutionsBased on this research, revealed that the most common bacteria caused sepsis was Gram negative about 64,64% of all bacteria on sepsis patient. The most frequent cause of sepsis was Staphylococcus hominis, Staphylococcus haemolyticus, and Escherichia coli.

Microbiology↗

bioRxiv2016

Complex molecular mixtures under cycling gradients as basis for lifes origins

We consider life as a cyclic physicochemical process that makes heredity and Darwinian evolution observable through living cells. We elaborate four principles that constrain current speculations about lifes emergence to natural processes driven by diurnal physicochemical gradients, primarily of temperature, water activity and electromagnetic radiation. First, Earths prebiotic chemical evolution is historically continuous with Darwinian evolution; second, cycling energies of solar radiation are primary drivers of chemical evolution; third, environmental molecular complexity must be high at the origin of life; and fourth, non-covalent molecular forces determine molecular recognition and cellular organization. Under normal physiological conditions of high ionic strength and high macromolecular crowding, hydration interactions (hydrogen bonding), screened electrostatic forces and excluded volume repulsions act over a commensurate distance of about one nanometer. This intermolecular distance governs chemical coevolution of proto-biomacromolecular surfaces (nucleic acids, proteins and membranes) toward Darwinian thresholds and living states. The above physicochemical principles of lifes emergence are consistent with the second law of thermodynamics, and with the current facts of molecular microbiology and planetary sciences. New kinds of experimentation with crowded molecular mixtures under oscillating temperature gradients - a PCR-like mechanism of lifes origins - can further illuminate how living states come about.\n\nGraphical abstractLifes emergence follows from chemical and Darwinian evolution, a high degree of molecular complexity and a high crowdedness, and non-covalent molecular forces that determine molecular recognition and cellular organization. The macromolecules divide the cytoplasm into dynamically crowded macromolecular regions and topologically complementary electrolyte pools. Small ions and ionic metabolites are transported vectorially between the electrolyte pools and through the (semi-conducting) electrolyte pathways of the crowded macromolecular regions.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC=\"FIGDIR/small/050740_fig1.gif\" ALT=\"Figure 1\">\nView larger version (36K):\norg.highwire.dtl.DTLVardef@1963682org.highwire.dtl.DTLVardef@d49be0org.highwire.dtl.DTLVardef@45ac46org.highwire.dtl.DTLVardef@312efc_HPS_FORMAT_FIGEXP M_FIG C_FIG

Microbiology↗

bioRxiv2016

Millions of Boreal Shield Lakes can be used to Probe the Evolution of Archaean Ocean Life

Life originated in Archaean oceans, almost 4 billion years ago, in the absence of oxygen and the presence of high dissolved iron concentrations. Early Earth oxidation is marked globally by extensive banded iron formations but the contributing processes and timing remain controversial. Very few aquatic habitats have been discovered that match key physico-chemical parameters of the early Archaean Ocean. All previous whole ecosystem Archaean analogue studies have been confined to rare, low sulfur, and permanently stratified lakes. Here we provide first evidence that millions of Boreal Shield lakes with natural anoxia offer the opportunity to constrain biogeochemical and microbiological aspects of early Archaean life. Specifically, we combined novel isotopic signatures and nucleic acid sequence data to examine processes in the anoxic zone of stratified boreal lakes that are naturally low in sulfur and rich in ferrous iron, hallmark characteristics predicted for the Archaean Ocean. Anoxygenic photosynthesis was prominent in total water column biogeochemistry, marked by distinctive patterns in natural abundance isotopes of carbon, nitrogen, and iron. These processes are robust, returning reproducibly after water column re-oxygenation following lake turnover. Evidence of coupled iron oxidation, iron reduction, and methane oxidation affect current paradigms of both early Earth and modern aquatic ecosystems.

Microbiology↗

bioRxiv2016

A dormant microbial component in the development of pre-eclampsia

Pre-eclampsia (PE) is a complex, multi-system disorder that remains a leading cause of morbidity and mortality in pregnancy. Four main classes of dysregulation accompany PE, and are widely considered to contribute to its severity. These are abnormal trophoblast invasion of the placenta, anti-angiogenic responses, oxidative stress, and inflammation. What is lacking, however, is an explanation of how these themselves are caused.\n\nWe here develop the unifying idea, and the considerable evidence for it, that the originating cause of PE (and of the four classes of dysregulation) is in fact microbial infection, that most such microbes are dormant and hence resist detection by conventional (replication-dependent) microbiology, and that by occasional resuscitation and growth it is they that are responsible for all the observable sequelae, including the continuing, chronic inflammation. In particular, bacterial products such as lipopolysaccharide (LPS), also known as endotoxin, are well known as highly inflammagenic and stimulate an innate (and possibly trained) immune response that exacerbates the inflammation further. The known need of microbes for free iron can explain the iron dysregulation that accompanies PE. We describe the main routes of infection (gut, oral, urinary tract infection) and the regularly observed presence of microbes in placental and other tissues in PE. Every known proteomic biomarker of \"pre-eclampsia\" that we assessed has in fact also been shown to be raised in response to infection. An infectious component to PE fulfils the Bradford Hill criteria for ascribing a disease to an environmental cause, and suggests a number of treatments, some of which have in fact been shown to be successful.\n\nPE was classically referred to as endotoxaemia or toxaemia of pregnancy, and it is ironic that it seems that LPS and other microbial endotoxins really are involved. Overall, the recognition of an infectious component in the aetiology of PE mirrors that for ulcers and other diseases that were previously considered to lack one.\n\nInsight, innovation, integrationMany descriptors of pre-eclampsia are widely accepted (e.g. abnormal trophoblast invasion, oxidative stress, inflammation and altered immune response, and anti-angiogenic responses). However, without knowing what causes them, they do not explain the syndrome. The Biological Insight of this manuscript is that there is considerable evidence to the effect that each of these phenomena (hence PE) are caused by the resuscitation of dormant bacteria that shed (known and potent) inflammagens such as LPS, often as a consequence of iron availability. PE is thus seen as a milder form of sepsis. The Technological Innovations come from the use of molecular markers (of microbes and omics more generally, as well as novel markers of coagulopathies) to measure this. The Benefit of Integration comes from bringing together a huge number of disparate observations into a unifying theme.

Microbiology↗

bioRxiv2016

Genomic dissection of an Icelandic epidemic of equine respiratory disease

The native horse population of Iceland has remained free of major infectious diseases. Between May and July 2010 an epidemic of respiratory disease swept through the population. Initial microbiological investigations ruled out known equine viral agents as the cause of the infections, but identified the opportunistic pathogen Streptococcus zooepidemicus as being frequently isolated from diseased animals. This diverse bacterial species has a broad host range and is usually regarded as a commensal of horses. By genome sequencing S. zooepidemicus recovered from horses during the epidemic we show that although multiple clones of S. zooepidemicus were present in the population, one particular clone, ST209, was responsible for the epidemic. Concurrent with the epidemic, ST209 caused zoonotic infections, highlighting the pathogenic potential of this clone. Phylogenetic analysis suggests that the original ST209 strain entered Iceland in late 2008 or early 2009. Epidemiological investigation revealed that the incursion of this strain into a training yard that utilized a submerged treadmill between the 5th and 19th of February 2010 was a critical trigger for the ensuing epidemic of disease, provided a nidus for the infection of multiple horses, and subsequent distribution of these animals to multiple sites in Iceland.

Microbiology↗

bioRxiv2016

General calibration of microbial growth in microplate readers

Optical density (OD) measurements of microbial growth are one of the most common techniques used in microbiology, with applications ranging from antibiotic efficacy studies, studies of growth under different nutritional or stress environments, to studies of different mutant strains, including those harbouring synthetic circuits. OD measurements are performed under the assumption that the OD value obtained is proportional to the cell number, i.e. the concentration of the sample. However, the assumption holds true in a limited range of conditions and calibration techniques that determine that range are currently missing. Here we present a set of calibration procedures and considerations that are necessary to successfully estimate the cell concentration from OD measurements.

Microbiology↗

bioRxiv2016

Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei With Increased Virulence or Fluoroquinolone Resistance

Shigella sonnei has caused unusually large outbreaks of shigellosis in California in 2014 - 2015. Preliminary data indicated the involvement of two distinct yet related bacterial populations, one from San Diego and San Joaquin (SD/SJ) and one from the San Francisco (SF) Bay area. Whole genome sequencing of sixty-eight outbreak and archival isolates of S. sonnei was performed to investigate the microbiological factors related to these outbreaks. Both SD/SJ and SF populations, as well as almost all of the archival S. sonnei isolates belonged to sequence type 152 (ST152). Genome-wide SNP analysis clustered the majority of California (CA) isolates to an earlier described global Lineage III, which has persisted in CA since 1986. Isolates in the SD/SJ population had a novel Shiga-toxin (STX)-encoding lambdoid bacteriophage, most closely related to that found in an Escherichia coli O104:H4 strain responsible for a large outbreak. However, the STX genes (stxla and stxlb) from this novel phage had sequences most similar to the phages from S. flexneri and S. dysenteriae. The isolates in the SF population yielded evidence of fluoroquinolone resistance acquired via the accumulation of point mutations in gyrA and parC genes. Thus, the CA S. sonnei lineage continues to evolve by the acquisition of increased virulence and antibiotic resistance, and enhanced monitoring is advocated for its early detection in future outbreaks.

Microbiology↗

bioRxiv2016

Extreme metagenomics using nanopore DNA sequencing: a field report from Svalbard, 78 N

In the field of observation, chance favours only the prepared mind (Pasteur). Impressive developments in genomics have led microbiology to its third \"Golden Age\". However, conventional metagenomics strategies necessitate retrograde transfer of samples from extreme or remote environments for later analysis, rendering the powerful insights gained retrospective in nature, striking a contrast with Pasteurs dictum. Here we implement highly portable USB-based nanopore DNA sequencing platforms coupled with field-adapted environmental DNA extraction, rapid sequence library generation and off-line analyses of shotgun metagenome and 16S ribosomal RNA gene amplicon profiles to characterize microbiota dwelling within cryoconite holes upon Svalbard glaciers, the Greenland Ice Sheet and the Austrian Alps. We show in-field nanopore sequencing of metagenomes captures taxonomic composition of supraglacial microbiota, while 16S rRNA Furthermore, comparison of nanopore data with prior 16S rRNA gene V1-V3 pyrosequencing from the same samples, demonstrates strong correlations between profiles obtained from nanopore sequencing and laboratory based sequencing approaches. gene amplicon sequencing resolves bacterial community responses to habitat changes. Finally, we demonstrate the fidelity and sensitivity of in-field sequencing by analysis of mock communities using field protocols. Ultimately, in-field sequencing potentiated by nanopore devices raises the prospect of enhanced agility in exploring Earths most remote microbiomes.

Microbiology↗

bioRxiv2016

16S rRNA Gene Sequencing as a Clinical Diagnostic Aid for Gastrointestinal-related Conditions

Accurate detection of the microorganisms underlying gut dysbiosis in the patient is critical to initiate the appropriate treatment. However, most clinical microbiology techniques used to detect gut bacteria were developed over a century ago and rely on culture-based approaches that are often laborious, unreliable, and subjective. Further, culturing does not scale well for multiple targets and detects only a minority of the microorganisms in the human gastrointestinal tract. Here we present a clinical test for gut microorganisms based on targeted sequencing of the prokaryotic 16S rRNA gene. We tested 46 clinical prokaryotic targets in the human gut, 28 of which can be identified by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. Using microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay accurately quantified all 28 targets and correctly reflected 38/38 verification samples of real and synthetic stool material containing known pathogens. Thus, we have established a new test to interrogate microbiome composition and diversity, which will improve patient diagnosis, treatment and monitoring. More broadly, our test will facilitate epidemiological studies of the microbiome as it relates to overall human health and disease.

microbiology↗

bioRxiv2017

Identifying the abundant and active microorganisms common to full scale anaerobic digesters

Anaerobic digestion is widely applied to treat organic waste at wastewater treatment plants. Characterisation of the underlying microbiology represents a source of information to develop strategies for improved operation. To this end, we investigated the microbial community composition of thirty-two full-scale digesters over a six-year period using 16S rRNA gene amplicon sequencing. Sampling of the sludge fed into these systems revealed that several of the most abundant populations were likely inactive and immigrating with the influent. This observation indicates that a failure to consider immigration will interfere with correlation analysis and give an inaccurate picture of the active microbial community. Furthermore, several abundant OTUs could not be classified to genus level with commonly applied taxonomies, making inference of their function unreliable. As such, the existing MiDAS taxonomy was updated to include these abundant phylotypes. The communities of individual plants surveyed were remarkably similar - with only 300 OTUs representing 80% of the total reads across all plants, and 15% of these identified as likely inactive immigrating microbes. By identifying the abundant and active taxa in anaerobic digestion, this study paves the way for targeted characterisation of the process important organisms towards an in-depth understanding of the microbial ecology of these biotechnologically important systems.

microbiology↗

bioRxiv2017

Validation and Implementation of CLIA-Compliant Whole Genome Sequencing (WGS) in Public Health Laboratory

BackgroundPublic health microbiology laboratories (PHL) are at the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards.\n\nObjectives1) Establish the performance specifications of WGS applications used in PHL to conform with CLIA (Clinical Laboratory Improvements Act) guidelines for laboratory developed tests (LDT), 2) Develop quality assurance (QA) and quality control (QC) measures, 3) Establish reporting language for end users with or without WGS expertise, 4) Create a validation set of microorganisms to be used for future validations of WGS platforms and multi-laboratory comparisons and, 5) Create modular templates for the validation of different sequencing platforms.\n\nMethodsMiSeq Sequencer and Illumina chemistry (Illumina, Inc.) were used to generate genomes for 34 bacterial isolates with genome sizes from 1.8 to 4.7 Mb and wide range of GC content (32.1%-66.1%). A customized CLCbio Genomics Workbench - shell script bioinformatics pipeline was used for the data analysis.\n\nResultsWe developed a validation panel comprising ten Enterobacteriaceae isolates, five gram-positive cocci, five gram-negative non-fermenting species, nine Mycobacterium tuberculosis, and five miscellaneous bacteria; the set represented typical workflow in the PHL. The accuracy of MiSeq platform for individual base calling was >99.9% with similar results shown for reproducibility/repeatability of genome-wide base calling. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from MLST and genotyping tests were 100%. A test report format was developed for the end users with and without WGS knowledge.\n\nConclusionWGS was validated for routine use in PHL according to CLIA guidelines for LDTs. The validation panel, sequencing analytics, and raw sequences will be available for future multi-laboratory comparisons of WGS in PHL. Additionally, the WGS performance specifications and modular validation template are likely to be adaptable for the validation of other platforms and reagents kits.

microbiology↗

bioRxiv2017

Molecular diagnosis of orthopaedic device infection direct from sonication fluid by metagenomic sequencing

Culture of multiple periprosthetic tissue samples is the current gold-standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through sonication fluid culture of explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of complete bacterial DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI.\n\nWe compared metagenomic sequencing with standard aerobic and anaerobic culture in 97 sonication fluid samples from prosthetic joint and other orthopaedic device infections. Reads from Illumina MiSeq sequencing were taxonomically classified using Kraken. Using 50 samples (derivation set), we determined optimal thresholds for the number and proportion of bacterial reads required to identify an infection and validated our findings in 47 independent samples.\n\nCompared to sonication fluid culture, the species-level sensitivity of metagenomic sequencing was 61/69(88%,95%CI 77-94%) (derivation samples 35/38[92%,79-98%]; validation 26/31[84%,66-95%]), and genus-level sensitivity was 64/69(93%,84-98%). Species-level specificity, adjusting for plausible fastidious causes of infection, species found in concurrently obtained tissue samples, and prior antibiotics, was 85/97(88%,79-93%) (derivation 43/50[86%,73-94%], validation 42/47[89%,77-96%]). High levels of human DNA contamination were seen despite use of laboratory methods to remove it. Rigorous laboratory good practice was required to prevent bacterial DNA contamination.\n\nWe demonstrate metagenomic sequencing can provide accurate diagnostic information in PJI. Our findings combined with increasing availability of portable, random-access sequencing technology offers the potential to translate metagenomic sequencing into a rapid diagnostic tool in PJI.

microbiology↗

bioRxiv2017

Lysinibacillus fusiformis M5 induces increased complexity in Bacillus subtilis 168 colony biofilms via hypoxanthine

In recent years, biofilms have become a central subject of research in the fields of microbiology, medicine, agriculture, or systems biology amongst others. The sociomicrobiology of multispecies biofilms, however, is still poorly understood. Here, we report a screening system that allowed us to identify soil bacteria, which induce architectural changes in biofilm colonies when cocultured with B. subtilis. We identified the soil bacterium Lysinibacillus fusiformis M5 as inducer of wrinkle-formation in B. subtilis colonies mediated by a diffusible signaling molecule. This compound was isolated by bioassay-guided chromatographic fractionation. The elicitor was identified to be the purine hypoxanthine using mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy. We show that the induction of wrinkle formation by hypoxanthine is not dependent on signal recognition by the histidine kinases KinA, KinB, KinC, and KinD, which are generally involved in phosphorylation of the master regulator Spo0A. Likewise, we show that hypoxanthine signaling does not induce the expression of biofilm-matrix related operons epsA-O and tasA-sipW-tapA. Finally, we demonstrate that the purine permease PbuO, but not PbuG, is necessary for hypoxanthine to induce an increase in wrinkle formation of B. subtilis biofilm colonies. Our results suggest that hypoxanthine-stimulated wrinkle development is not due to a direct induction of biofilm-related gene expression, but rather caused by the excess of hypoxanthine within B. subtilis cells, which may lead to cell stress and death.\n\nIMPORTANCEBiofilms are a bacterial lifestyle with high relevance regarding diverse human activities. Biofilms can be favorable, for instance in crop protection. In nature, biofilms are commonly found as multispecies communities displaying complex social behaviors and characteristics. The study of interspecies interactions will thus lead to a better understanding and use of biofilms as they occur outside laboratory conditions. Here, we present a screening method suitable for the identification of multispecies interactions, and showcase L. fusiformis as a soil bacterium that is able to live alongside B. subtilis and modify the architecture of its biofilms.

microbiology↗

bioRxiv2017

Response Of Microbial Community Function To Fluctuating Geochemical Conditions Within A Legacy Radioactive Waste Trench Environment

During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in three-metre-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels impact upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse, to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically-diverse microbial community played in this transition. In particular, aerobes dominated in the first day followed by an increase of facultative anaerobes/denitrifiers at day four. Towards the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.\n\nImportanceThe role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility.\n\nResults demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solidiron-associated species immediately after the initial rainwater pulse, to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically-diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.

microbiology↗

bioRxiv2017

Microbial Metagenome Of Urinary Tract Infection

Urine culture and microscopy techniques are used to profile the bacterial species present in urinary tract infections. To gain insight into the urinary flora in infection and health, we analyzed clinical laboratory features and the microbial metagenome of 121 clean-catch urine samples. 16S rDNA gene signatures were successfully obtained for 116 participants, while whole genome shotgun sequencing data was successfully generated for samples from 49 participants. Analysis of these datasets supports the definition of the patterns of infection and colonization/contamination. Although 16S rDNA sequencing was more sensitive, whole genome shotgun sequencing allowed for a more comprehensive and unbiased representation of the microbial flora, including eukarya and viral pathogens, and of bacterial virulence factors. Urine samples positive by whole genome shotgun sequencing contained a plethora of bacterial (median 41 genera/sample), eukarya (median 2 species/sample) and viral sequences (median 3 viruses/sample). Genomic analyses revealed cases of infection with potential pathogens (e.g., Alloscardovia sp, Actinotignum sp, Ureaplasma sp) that are often missed during routine urine culture due to species specific growth requirements. We also observed gender differences in the microbial metagenome. While conventional microbiological methods are inadequate to identify a large diversity of microbial species that are present in urine, genomic approaches appear to comprehensively and quantitatively describe the urinary microbiome.

microbiology↗