Key Bacterial Species Research Articles

Gut Bacteria Seize Control of the Brain to Prevent Epilepsy

Why ketogenic diet (KD) effectively controls seizures in some people with epilepsy is unclear. In a recent issueof Cell, Olson etal. (2018) showed that KD prevents seizures by upregulating key bacterial species (Akkermansia muciniphila and Parabacteroides merdae). These bacteria synergize to decrease gammaglutamylation of amino acids, increase hippocampal GABA/Glutamate ratios, and, ultimately, prevent seizures.

Distinct consequences of amoxicillin and ertapenem exposure in the porcine gut microbiome

The gut microbiome influences many, if not all, aspects of human health. Antibiotics, while lifesaving, have the unintended consequence of killing commensal microbiota inhabiting the gastrointestinal (GI) tract, which can lead to overgrowth of opportunistic pathogens such as Clostridium difficile and emergence of antibiotic-resistant organisms. Here, porcine models were developed to evaluate changes to the gut microbiome caused by two distinct types of beta-lactam antibiotics delivered via common administration routes, oral amoxicillin and intravenous ertapenem. Amoxicillin is one of the most often used broad-spectrum antibiotics, frequently prescribed to young children. Ertapenem, a carbapenem considered a last resort antibiotic, is used sparingly in humans and prohibited for use in animals. Cohorts of normal pigs (n = 5) were treated with amoxicillin (20 mg/kg, PO, BID) or ertapenem (30 mg/kg, IV, SID) for seven days. Microbiomes were evaluated using whole genome shotgun metagenomics analyses of fecal DNA collected prior to, during, and after antibiotic treatment. Each antibiotic resulted in significant and distinct changes in the microbiome, causing elimination of key commensal bacterial species and overgrowth of other, potentially pathogenic taxa. In addition, amoxicillin promoted propagation of a broad range of antibiotic resistance genes, many encoding efflux pump components and beta-lactamases, while ertapenem triggered emergence of genes encoding vancomycin resistance, and beta-lactamases, including the carbapenemase, IMP-27. Notably, microbiota alterations and antibiotic resistance gene propagation displayed unique patterns following exposure to amoxicillin or ertapenem. These data underscore the importance of understanding consequences of individual antibiotic use to predict and potentially mitigate adverse outcomes. The porcine models developed here can facilitate evaluation of therapeutic interventions to prevent antibiotic-mediated microbiome disruption.

Microbial degradation of poly(ε-caprolactone) in a coastal environment

Biodegradable plastics may be a solution for eliminating large marine plastic debris, such as fishing gear, which causes environmental damage. The biodegradable polyester poly(ε-caprolactone) (PCL) is degraded in various environments; however, no reports have examined PCL-degrading microbes inhabiting coastal environments, despite the fact that marine plastic debris accumulates in this environment. Therefore, in this study, we isolated a PCL-degrading bacterium (strain TKCM 64) from marine plastic debris in coastal seawater (Okinoshima Park, Chiba, Japan) for the first time. Genetic and biochemical analyses showed that strain TKCM 64 was closely related to Pseudomonas pachastrellae JCM12285T. The maximum specific growth rate (0.4 h−1) of the isolate was observed in the absence of NaCl at 30 °C, and the strain was able to grow, even at 1.20 M NaCl, suggesting that the strain could belong to a marine species showing halotolerance. Strain TKCM 64 degraded PCL film at a rate of 1.39 ± 0.09 mg cm−2·day−1. The strain showed PCL hydrolytic activity, which was induced in the presence of PCL and its hydrolysate: 6-hydroxyhexanoic acid (6HH), in addition to a major component of cutin, 16-hydroxyhexadecanoic acid. Thus, we concluded that the PCL hydrolysate 6HH, as an analog of cutin hydrolysate, functioned as an inducer of a PCL hydrolase that is a kind of cutinase in strain TKCM 64. In addition, Pseudomonas pachastrellae was found to be a key bacterial species involved in PCL degradation in coastal environments.

Microbial Complexes and Caries in 17-Year-Olds with and without Streptococcus mutans

Streptococcus mutans is a key bacterial species in the caries process, which affects >90% of the population worldwide. However, other acidogenic and aciduric/acidophilic species may contribute to disease development. In Sweden, a country with low prevalences of caries and S. mutans, a significant portion of caries-affected adolescents lack detectable levels of S. mutans. The objectives of the present study were 1) to characterize the tooth biofilm and saliva microbiota of adolescents with caries disease, with or without detectable S. mutans, from tooth biofilm and saliva samples and 2) to assess taxa clustering in the tooth biofilm and saliva samples and relate this information to caries status. For 17-y-old participants (N = 154), enamel and dentin caries (the total number of present carious surfaces in the enamel and dentin) and caries experience (the number of decayed and filled tooth surfaces) were recorded, dental biofilm and saliva samples obtained, and information on medical and lifestyle habits collected. Multiplex 16S rDNA (V3-V4) sequencing of bacterial DNA was performed with the Illumina MiSeq platform. The Human Oral Microbiome Database and the ProbeSeq pipeline were used in the HOMINGS procedure. In subjects with caries experience, high levels of S. mutans were associated with a few species and low levels with a panel of saccharolytic species. Present caries was similarly associated with a panel of saccharolytic species in subjects without S. mutans. Furthermore, tooth biofilm microbiota could be used to establish 4 clusters of subjects with different caries experiences. In particular, high levels of S. mutans were associated with the presence of a few influential species in multivariate modeling, including Scardovia wiggsiae. By contrast, a panel of less avid lactic acid–producing species was influential in patients with undetectable or low S. mutans levels in such modeling. These findings support a prominent role of S. mutans in infected adolescents but also the ecologic concept, especially in S. mutans–free subjects.

Effect of Soy Isoflavones on Growth of Representative Bacterial Species from the Human Gut.

The present work aimed to assess the susceptibility of dominant and representative bacterial populations from the human gut to isoflavones and their metabolites. To do so, the minimum inhibitory concentration (MIC) of isoflavone glycosides, isoflavone aglycones, and equol to 37 bacterial strains was determined by broth microdilution. Additionally, for 10 representative strains, growth curves, growth rate (μ), and optical density (OD600 nm) of the cultures at 24 h were also determined. MICs of daidzin, genistin, daidzein, and genistein were >2048 μg mL−1 for all strains assayed, while that of equol ranged from 16 μg mL−1 for Bifidobacterium animalis subsp. animalis to >2048 μg mL−1 for Enterobacteriaceae strains. Changes in growth curves, μ, and final OD were observed among the species in the presence of all tested compounds. Genistein reduced μ of Bacteroides fragilis, Lactococcus lactis subsp. lactis, and Slackia equolifaciens, while both genistein and equol increased that of Lactobacillus rhamnosus and Faecalibacterium prausnitzii. Compared to controls, lower final OD in the presence of aglycones and equol were recorded for some strains but were higher for others. Altogether, the results suggest that isoflavone-derived compounds could modify numbers of key bacterial species in the gut, which might be associated with their beneficial properties.

Qualitative Analysis of Microbial Dynamics during Anaerobic Digestion of Microalgal Biomass in a UASB Reactor.

Anaerobic digestion (AD) is a microbiologically coordinated process with dynamic relationships between bacterial players. Current understanding of dynamic changes in the bacterial composition during the AD process is incomplete. The objective of this research was to assess changes in bacterial community composition that coordinates with anaerobic codigestion of microalgal biomass cultivated on municipal wastewater. An upflow anaerobic sludge blanket reactor was used to achieve high rates of microalgae decomposition and biogas production. Samples of the sludge were collected throughout AD and extracted DNA was subjected to next-generation sequencing using methanogen mcrA gene specific and universal bacterial primers. Analysis of the data revealed that samples taken at different stages of AD had varying bacterial composition. A group consisting of Bacteroidales, Pseudomonadales, and Enterobacteriales was identified to be putatively responsible for the hydrolysis of microalgal biomass. The methanogenesis phase was dominated by Methanosarcina mazei. Results of observed changes in the composition of microbial communities during AD can be used as a road map to stimulate key bacterial species identified at each phase of AD to increase yield of biogas and rate of substrate decomposition. This research demonstrates a successful exploitation of methane production from microalgae without any biomass pretreatment.

Informativeness of NGS Analysis for Vaginal Fluid Identification.

The identification of vaginal fluids in forensic examinations plays an important role in crime scene reconstruction. Molecular detection of vaginal bacterial communities can lead to the correct discrimination of body fluids. These kinds of studies can be performed through multiplex real-time PCR using primers for a specific selection of bacteria. The availability of next-generation sequencing (NGS) protocols provided for the extension of the analysis to evaluate the prokaryotes present in specimens. In this study, DNA was extracted from 18 samples (vaginal, oral, fecal, yoghurt) and analyzed by real-time PCR and NGS. The comparison between the two approaches has demonstrated that the information developed through NGS can augment the more conventional real-time PCR detection of a few key bacterial species to provide a more probative result and the correct identification of vaginal fluid from samples that are more forensically challenged.

Permuting the PGF Signature Motif Blocks both Archaeosortase-Dependent C-Terminal Cleavage and Prenyl Lipid Attachment for the Haloferax volcanii S-Layer Glycoprotein.

For years, the S-layer glycoprotein (SLG), the sole component of many archaeal cell walls, was thought to be anchored to the cell surface by a C-terminal transmembrane segment. Recently, however, we demonstrated that the Haloferax volcanii SLG C terminus is removed by an archaeosortase (ArtA), a novel peptidase. SLG, which was previously shown to be lipid modified, contains a C-terminal tripartite structure, including a highly conserved proline-glycine-phenylalanine (PGF) motif. Here, we demonstrate that ArtA does not process an SLG variant where the PGF motif is replaced with a PFG motif (slg(G796F,F797G)). Furthermore, using radiolabeling, we show that SLG lipid modification requires the PGF motif and is ArtA dependent, lending confirmation to the use of a novel C-terminal lipid-mediated protein-anchoring mechanism by prokaryotes. Similar to the case for the ΔartA strain, the growth, cellular morphology, and cell wall of the slg(G796F,F797G) strain, in which modifications of additional H. volcanii ArtA substrates should not be altered, are adversely affected, demonstrating the importance of these posttranslational SLG modifications. Our data suggest that ArtA is either directly or indirectly involved in a novel proteolysis-coupled, covalent lipid-mediated anchoring mechanism. Given that archaeosortase homologs are encoded by a broad range of prokaryotes, it is likely that this anchoring mechanism is widely conserved. Prokaryotic proteins bound to cell surfaces through intercalation, covalent attachment, or protein-protein interactions play critical roles in essential cellular processes. Unfortunately, the molecular mechanisms that anchor proteins to archaeal cell surfaces remain poorly characterized. Here, using the archaeon H. volcanii as a model system, we report the first in vivo studies of a novel protein-anchoring pathway involving lipid modification of a peptidase-processed C terminus. Our findings not only yield important insights into poorly understood aspects of archaeal biology but also have important implications for key bacterial species, including those of the human microbiome. Additionally, insights may facilitate industrial applications, given that photosynthetic cyanobacteria encode uncharacterized homologs of this evolutionarily conserved enzyme, or may spur development of unique drug delivery systems.

Bacterial interactions in pathogenic subgingival plaque

Chronic periodontitis has a polymicrobial biofilm aetiology. Polymicrobial biofilms are complex, dynamic microbial communities formed by two or more bacterial species that are important for the persistence and proliferation of participating microbes in the environment. Interspecies adherence, which often involves bacterial surface-associated molecules, and communications are essential in the spatial and temporal development of a polymicrobial biofilm, which in turn is necessary for the overall fitness of a well-organized multispecies biofilm community. In the oral cavity, interactions between key oral bacterial species, including Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia, are essential for the progression of chronic periodontitis. In vivo, P. gingivalis and T. denticola are frequently found to co-exist in deep periodontal pockets and have been co-localized to the superficial layers of subgingival plaque as microcolony blooms adjacent to the pocket epithelium, suggesting possible interbacterial interactions that contribute towards disease. The motility and chemotactic ability of T. denticola, although not considered as classic virulence factors, are likely to be important in the synergistic biofilm formation with P. gingivalis. In vitro, P. gingivalis and T. denticola display a symbiotic relationship in nutrient utilization and growth promotion. Together these data suggest there is an intimate relationship between these two species that has evolved to enhance their survival and virulence.

Rapid and Profound Shifts in the Vaginal Microbiota Following Antibiotic Treatment for Bacterial Vaginosis

Bacterial vaginosis (BV) is a common polymicrobial disease associated with numerous negative reproductive health outcomes, including an increased risk of human immunodeficiency virus acquisition. BV is treatable with antibiotics, but relapse is common. A more detailed understanding of bacterial dynamics during antibiotic therapy for BV could identify conditions that favor establishment, maintenance, and eradication of BV-associated bacterial species, thereby improving treatment outcomes. We used mathematical models to analyze daily quantitative measurements of 11 key bacterial species during metronidazole treatment for 15 cases of BV. We identified complete reorganization of vaginal bacterial composition within a day of initiating therapy. Although baseline bacterial levels predicted a longer time to clearance, all anaerobic species were eliminated rapidly within a median of 3 days. However, reemergence of BV-associated species was common following treatment cessation. Gardnerella vaginalis, a facultative anaerobe, was cleared more slowly than anaerobic BV-associated species, and levels of G. vaginalis often rebounded during treatment. We observed gradual Lactobacillus species growth, indicating that untargeted microbes fill the transient vacuum formed during treatment. Under antibiotic pressure, the human microbiome can undergo rapid shifts on a scale of hours. When treatment is stopped, BV-associated bacteria quickly reemerge, suggesting a possible role for intermittent prophylactic treatment.

Current roles of specific bacteria in the pathogenesis of inflammatory bowel disease

The relevance of alterations in gut microbiota in the pathogenesis of inflammatory bowel disease (IBD) remains unclear. Currently there is conflicting evidence with regards to the roles of specific bacterial species. <em>Escherichia coli </em>(particularly the adherent invasive strain) are more prevalent in those with IBD and are associated with higher risk of IBD. However, the organisms are also present in healthy individuals and colonisation does not correlate with the degree of inflammation in IBD. <em>Campylobacter concisus</em> is more prevalent in those with IBD and higher levels of <em>C. concisus</em> specific IgG antibodies are found in the serum of those with IBD compared to healthy controls. Further, <em>C. concisus</em> has immunogenic properties that stimulate an antibody response suggesting the bacteria might trigger or exacerbate disease. Conversely most mycobacteria are unlikely to be causative as they are not presentin microbial stool cultures early in disease. In various studies,<em>Mycobacterium aviumparatuberculosis</em>has been detected both more frequently and not at all in individuals with Crohn's disease. Similar conflict exists with respect to <em>Yersinia enterocolitica,Bacteroidesvulgatus</em> and <em>Helicobacter hepaticus</em>, which are also more prevalent in IBD. However, these organisms appear more likely to contribute to disease persistence than initial disease development. This review aims to summarise the current understanding of key bacterial species implicated in the pathogenesis of IBD.

Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome

Coral diseases are characterized by microbial community shifts in coral mucus and tissue, but causes and consequences of these changes are vaguely understood due to the complexity and dynamics of coral-associated bacteria. We used 16S rRNA gene microarrays to assay differences in bacterial assemblages of healthy and diseased colonies displaying White Plague Disease (WPD) signs from two closely related Caribbean coral species, Orbicella faveolata and Orbicella franksi. Analysis of differentially abundant operational taxonomic units (OTUs) revealed strong differences between healthy and diseased specimens, but not between coral species. A subsequent comparison to data from two Indo-Pacific coral species (Pavona duerdeni and Porites lutea) revealed distinct microbial community patterns associated with ocean basin, coral species and health state. Coral species were clearly separated by site, but also, the relatedness of the underlying bacterial community structures resembled the phylogenetic relationship of the coral hosts. In diseased samples, bacterial richness increased and putatively opportunistic bacteria were consistently more abundant highlighting the role of opportunistic conditions in structuring microbial community patterns during disease. Our comparative analysis shows that it is possible to derive conserved bacterial footprints of diseased coral holobionts that might help in identifying key bacterial species related to the underlying etiopathology. Furthermore, our data demonstrate that similar-appearing disease phenotypes produce microbial community patterns that are consistent over coral species and oceans, irrespective of the putative underlying pathogen. Consequently, profiling coral diseases by microbial community structure over multiple coral species might allow the development of a comparative disease framework that can inform on cause and relatedness of coral diseases.

Porphyromonas gingivalis and Treponema denticola Synergistic Polymicrobial Biofilm Development

Chronic periodontitis has a polymicrobial biofilm aetiology and interactions between key bacterial species are strongly implicated as contributing to disease progression. Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia have all been implicated as playing roles in disease progression. P. gingivalis cell-surface-located protease/adhesins, the gingipains, have been suggested to be involved in its interactions with several other bacterial species. The aims of this study were to determine polymicrobial biofilm formation by P. gingivalis, T. denticola and T. forsythia, as well as the role of P. gingivalis gingipains in biofilm formation by using a gingipain null triple mutant. To determine homotypic and polymicrobial biofilm formation a flow cell system was employed and the biofilms imaged and quantified by fluorescent in situ hybridization using DNA species-specific probes and confocal scanning laser microscopy imaging. Of the three species, only P. gingivalis and T. denticola formed mature, homotypic biofilms, and a strong synergy was observed between P. gingivalis and T. denticola in polymicrobial biofilm formation. This synergy was demonstrated by significant increases in biovolume, average biofilm thickness and maximum biofilm thickness of both species. In addition there was a morphological change of T. denticola in polymicrobial biofilms when compared with homotypic biofilms, suggesting reduced motility in homotypic biofilms. P. gingivalis gingipains were shown to play an essential role in synergistic polymicrobial biofilm formation with T. denticola.

Appraisal of the tire derived rubber (TDR) medium for wastewater treatment under aerobic and anaerobic conditions

AbstractBACKGROUNDThe present study evaluated the effectiveness and durability of tire derived rubber (TDR) for biofilm development and related long term use in fixed biofilm reactors for wastewater treatment.RESULTSTDR incubated (30 ± 2°C) with activated sludge showed comparatively higher biofilm development (0.51 g) under aerobic than under anaerobic (0. 42 g) conditions after 7 weeks. During biofilm succession, a significant shift in bacterial community was observed from pathogenic to autotrophic after 4 weeks. The decreasing bacterial count (MPN index) (≈80%) (Escheria coli and feacal coliforms) and chemical oxygen demand (COD), and biological oxygen demand (BOD) (70% approx.) depicted diminishing organic load in sludge. Changes in pH and nutrients like NO2‐, NO3‐, PO43‐ and SO32‐ indicated presence of other key bacterial species with efficient nutrient consuming abilities in biofilm. Scanning electron microscopy showed few aberration and rich bacterial growth on treated TDR. Furthermore, detailed analysis through Fourier transform infrared (FTIR) spectroscopy confirmed minor transformation in TDR under anaerobic conditions.CONCLUSIONTDR proved to be a durable and cost effective support material that can be used in aerobic fixed biofilm reactors for wastewater treatment. However, operational conditions of the reactor should be optimized to keep the biofilm structure intact and to achieve the desired wastewater treatment efficiency. © 2013 Society of Chemical Industry

Structural characteristics of genomic islands associated with GMP synthases as integration hotspot among sequenced microbial genomes

tRNA, tmRNA and some small RNA genes are recognized as general integration hotspots of genomic islands (GIs). The GMP synthase gene (guaA) has been firstly identified as one insertion hotspot of foreign DNA fragments. Thirty four islands integrated into the guaA genes were identified in the 987 completely sequenced archaeal and bacterial genomes. These alien islands were widely distributed within the host strains belonging to Proteobacteria, Firmicutes and Actinobacteria. The analysis of structural characteristics of these GIs is important for further determination of the island mobility and transference into suitable hosts. The putative functional integrases encoded by guaA-associated islands were mainly composed of phage P4 integrases, and followed by phage PhiLC3 integrases. Interestingly, island-encoding AlpA is close to P4 integrase and is deduced to be the positive transcriptional regulatory factor of P4 integrase while the XRE protein is close to PhiLC3 integrase and may be the negative transcriptional regulatory factor of PhiLC3 integrase. An 8-bp consensus sequence (5′-GAGTGGGA-3′) within the direct repeats of these GIs is the cutting site of the P4 integrases encoding by guaA-associated islands, in which the third nucleotide (G) is the key site. The large-scale investigation of the content of GMP synthase gene hotspots may be useful to find important functional islands within members of many key bacterial species and to transfer useful islands into more suitable hosts.

Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species

Butyrate is the preferred energy source for colonocytes and has an important role in gut health; in contrast, accumulation of high concentrations of lactate is detrimental to gut health. The major butyrate-producing bacterial species in the human colon belong to the Firmicutes. Eubacterium hallii and a new species, Anaerostipes coli SS2/1, members of clostridial cluster XIVa, are able to utilize lactate and acetate via the butyryl CoA : acetate CoA transferase route, the main metabolic pathway for butyrate synthesis in the human colon. Here we provide a mathematical model to analyse the production of butyrate by lactate-utilizing bacteria from the human colon. The model is an aggregated representation of the fermentation pathway. The parameters of the model were estimated using total least squares and maximum likelihood, based on in vitro experimental data with E. hallii L2-7 and A. coli SS2/1. The findings of the mathematical model adequately match those from the bacterial batch culture experiments. Such an in silico approach should provide insight into carbohydrate fermentation and short-chain fatty acid cross-feeding by dominant species of the human colonic microbiota.

Influence of Antimicrobial Feed Additives on Broiler Commensal Posthatch Gut Microbiota Development and Performance

The effects of avilamycin, zinc bacitracin, and flavophospholipol on broiler gut microbial community colonization and bird performance in the first 17 days posthatch were investigated. Significant differences in gut microbiota associated with gut section, dietary treatment, and age were identified by terminal restriction fragment length polymorphism (T-RFLP), although no performance-related differences between dietary treatments were detected. Similar age-related shifts in the gut microbiota were identified regardless of diet but varied between the ilea and ceca. Interbird variabilities in ileal bacterial communities were reduced (3 to 7 days posthatch) in chicks fed with feed containing antimicrobial agents. Avilamycin and flavophospholipol had the most consistent effect on gut microbial communities. Operational taxonomic units (OTU) linked to changes in gut microbiota in birds on antimicrobial-supplemented diets were characterized and identified. Some OTUs could be identified to the species level; however, the majority could be only tentatively classified to the genus, family, order, or domain level. OTUs 140 to 146 (Lachnospiraceae), OTU 186/188 (Lactobacillus johnsonii), OTU 220 (Lachnospiraceae), OTUs 284 to 288 (unclassified bacterial spp. or Ruminococcaceae), OTU 296/298 (unclassified bacterium or Clostridiales), and OTU 480/482 (Oxalobacteraceae) were less prevalent in the guts of chicks fed antimicrobial-supplemented diets. OTU 178/180 (Lactobacillus crispatus), OTU 152 (Lactobacillus reuteri or unclassified Clostridiales), OTU 198/200 (Subdoligranulum spp.), and OTU 490/492 (unclassified bacterium or Enterobacteriaceae) were less prevalent in the gut of chicks raised on the antimicrobial-free diet. The identification of key bacterial species influenced by antimicrobial-supplemented feed immediately posthatch may assist in the formulation of diets that facilitate beneficial gut microbial colonization and, hence, the development of alternatives to current antimicrobial agents in feed for sustainable poultry production.

Expansion of the known Klebsiella pneumoniae species gene pool by characterization of novel alien DNA islands integrated into tmRNA gene sites

Klebsiella pneumoniae is an important bacterial pathogen of man that is commonly associated with opportunistic and hospital-associated infections. Increasing levels of multiple-antibiotic resistance associated with this species pose a major emerging clinical problem. This organism also occurs naturally in other diverse environments, including the soil. Consistent with its varied lifestyle and membership of the Enterobacteriaceae family, K. pneumoniae genomes exhibit highly plastic architecture comprising a core genome backbone interspersed with numerous and varied alien genomic islands. In this study the size of the presently known K. pneumoniae pan-genome gene pool was estimated through analysis of complete sequences of three chromosomes and 31 plasmids belonging to K. pneumoniae strains. In addition, using a PCR-based strategy the genomic content of eight tRNA/ tmRNA gene sites that serve as DNA insertion hotspots were investigated in 28 diverse environmental and clinical strains of K. pneumoniae. Sequencing and characterization of five newly identified horizontally-acquired tmRNA-associated islands further expanded the archived K. pneumoniae gene pool to a total of 7648 unique gene members. Large-scale investigation of the content of tRNA/ tmRNA hotspots will be useful to identify and/or survey accessory sequences dispersed amongst hundreds to thousands of members of many key bacterial species.

An investigation into the effects of silver nanoparticles on antibiotic resistance of naturally occurring bacteria in an estuarine sediment

The aim of this study was to test whether silver nanoparticles (Ag-NPs) released into estuarine environments result in increased antibiotic resistance amongst the natural bacterial population in estuarine sediments. A 50-day microcosm exposure experiment was carried out to investigate the effects of Ag-NPs (50 nm average diameter) on the antibiotic resistance of bacteria in sediments from an estuary in southwest England. Experimental microcosms were constructed using 3.5 kg sediment cores with 20 l of overlaying seawater treated with (final) Ag-NPs concentrations of 0, 50 or 2000 μg l −1 ( n = 3). Sediment samples were screened at the end of the exposure period for the presence of bacteria resistant to eight different antibiotics. Multivariate statistical analyses showed that there was no increase in antibiotic resistance amongst the bacterial population in the sediment due to the dosing of the microcosms with Ag-NPs. This study indicates that, under the tested conditions, Ag-NPs released into the coastal marine environment do not increase antibiotic resistance among naturally occurring bacteria in estuarine sediments. These results contrast previous findings where antimicrobial effects of Ag-NPs on key bacterial species in laboratory experiments have been demonstrated, and reasons for this are discussed. The negligible effects demonstrated on bacterial populations under the selected estuarine conditions, provide important information on no observed effect concentrations (NOECs) for environmental regulation.

Analysis of bacterial populations in the gut of developing cod larvae and identification of Vibrio logei, Vibrio anguillarum and Vibrio splendidus as pathogens of cod larvae

Poor larval survival rates currently limit production in aquaculture and a better understanding of the bacterial flora in the larval digestive tract is essential to improving survival in hatchery reared larval fish. Identification of bacteria alone is insufficient, as the concentrations of key bacterial species may be important in determining survival. Here, we analysed bacteria, principally vibrios, in developing cod larvae from a Scottish hatchery. Six tanks of larvae were sampled weekly in parallel to monitor the microbial populations in larvae successively fed on rotifers and Artemia before weaning onto dry feed. When cod larvae were fed on rotifers the digestive tract microbiota was dominated by Ruegeria/Roseobacter, Pseudoalteromonas, and Microbacterium but when the diet was changed to Artemia over 90% of the microbiota consisted of vibrios. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) analysis was used to identify the vibrios present and this showed that the microbiota was affected by changes in larval diet. Whilst feeding on Artemia, the larval digestive tract microbiota was dominated by Vibrio alginolyticus, but the population rapidly switched to one dominated by V. splendidus when larvae were weaned onto dry feed. Other Vibrio species were detected at lower levels at various times. During the survey, one tank experienced heavy mortalities associated with an elevated level of Vibrio anguillarum. The V. anguillarum isolates differed from those typically associated with mortalities in gadoid fish. Apparently healthy larvae from the tank experiencing heavy mortalities had a culturable microbiota almost equally represented by V. anguillarum and V. logei. Both species, as well as a V. splendidus strain isolated from turbot larvae, were pathogenic to cod larvae in laboratory experiments, and these vibrios could be targets for intervention to control the microbial flora of the larval digestive tract.