Individual variation in the avian gut microbiota: The influence of host state and environmental heterogeneity.

The gut microbiota have important consequences for host biological processes and there is some evidence that they also affect fitness. However, the complex, interactive nature of ecological factors that influence the gut microbiota has scarcely been investigated in natural populations. We sampled the gut microbiota of wild great tits (Parus major) at different life stages allowing us to evaluate how microbiota varied with respect to a diverse range of key ecological factors of two broad types: (1) host state, namely age and sex, and the life history variables, timing of breeding, fecundity and reproductive success; and (2) the environment, including habitat type, the distance of the nest to the woodland edge, and the general nest and woodland site environments. The gut microbiota varied with life history and the environment in many ways that were largely dependent on age. Nestlings were far more sensitive to environmental variation than adults, pointing to a high degree of flexibility at an important time in development. As nestlings developed their microbiota from one to two weeks of life, they retained consistent (i.e., repeatable) among-individual differences. However these apparent individual differences were driven entirely by the effect of sharing the same nest. Our findings point to important early windows during development in which the gut microbiota are most sensitive to a variety of environmental drivers at multiple scales, and suggest reproductive timing, and hence potentially parental quality or food availability, are linked with the microbiota. Identifying and explicating the various ecological sources that shape an individual's gut bacteria is of vital importance for understanding the gut microbiota's role in animal fitness.

Winogradskyella bathintestinalis sp. nov., isolated from the intestine of the deep-sea loosejaw dragonfish, Malacosteus niger.

A novel bacterial strain, APC 3343T, was isolated from the intestine of a deep-sea loosejaw dragon fish, Malacosteus niger, caught at a depth of 1000 m in the Northwest Atlantic Ocean. Cells were aerobic, rod-shaped, yellow/orange-pigmented, non-motile and Gram-negative. Growth of strain APC 3343T was observed at 4-30 °C (optimum, 21-25 °C), pH 5.5-10 (optimum, pH 7-8) and 0.5-8 % (w/v) NaCl (optimum, 2-4 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain APC 3343T was most closely related to members of the genus Winogradskyella, with the most closely related type strains being Winogradskyella algae Kr9-9T (98.46 % identity), Winogradskyella damuponensis F081-2T (98.07 %), Winogradskyella eximia CECT 7946T (97.93 %), Winogradskyella litoriviva KMM 6491T (97.79 %) and Winogradskyella endarachnes HL2-2T (97.79 %). Major fatty acids (>10 % of total) were iso-C16 : 0 3-OH, iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone-6 (MK-6). Polar lipids were phosphatidylethanolamine, three unknown aminolipids and eight unknown lipids. The draft genome sequence was 3.8 Mb in length with a G+C content of 33.43 mol%. Based on the phenotypic characteristics and phylogenetic analysis, strain APC 3343T is deemed to be a novel species of the genus Winogradskyella, and for which the name Winogradskyella bathintestinalis sp. nov. is proposed. The type strain of this species is APC 3343T (=DSM 115832T=NCIMB 15464T).

A time-lagged association between the gut microbiome, nestling weight and nestling survival in wild great tits.

Natal body mass is a key predictor of viability and fitness in many animals. While variation in body mass and therefore juvenile viability may be explained by genetic and environmental factors, emerging evidence points to the gut microbiota as an important factor influencing host health. The gut microbiota is known to change during development, but it remains unclear whether the microbiome predicts fitness, and if it does, at which developmental stage it affects fitness traits. We collected data on two traits associated with fitness in wild nestling great tits Parus major: weight and survival to fledging. We characterised the gut microbiome using 16S rRNA sequencing from nestling faeces and investigated temporal associations between the gut microbiome and fitness traits across development at Day-8 (D8) and Day-15 (D15) post-hatching. We also explored whether particular microbial taxa were 'indicator species' that reflected whether nestlings survived or not. There was no link between mass and microbial diversity on D8 or D15. However, we detected a time-lagged relationship where weight at D15 was negatively associated with the microbial diversity at D8, controlling for weight at D8, therefore reflecting relative weight gain over the intervening period. Indicator species analysis revealed that specificity values were high and fidelity values were low, suggesting that indicator taxa were primarily detected within either the survived or not survived groups, but not always detected in birds that either survived or died. Therefore these indicator taxa may be sufficient, but not necessary for determining either survival or mortality, perhaps owing to functional overlap in microbiota. We highlight that measuring microbiome-fitness relationships at just one time point may be misleading, especially early in life. Instead, microbial-host fitness effects may be best investigated longitudinally to detect critical development windows for key microbiota and host traits associated with neonatal weight. Our findings should inform future hypothesis testing to pinpoint which features of the gut microbial community impact on host fitness, and when during development this occurs. Such confirmatory research will shed light on population level processes and could have the potential to support conservation.

Gut microbiome of a porcine model of metabolic syndrome and HF-pEF.

Metabolic syndrome (MetS) is a composite of cardiometabolic risk factors, including obesity, dyslipidemia, hypertension, and insulin resistance, with a range of secondary sequelae such as nonalcoholic fatty liver disease and diastolic heart failure. This syndrome has been identified as one of the greatest global health challenges of the 21st century. Herein, we examine whether a porcine model of diet- and mineralocorticoid-induced MetS closely mimics the cardiovascular, metabolic, gut microbiota, and functional metataxonomic phenotype observed in human studies. Landrace pigs with deoxycorticosterone acetate-induced hypertension fed a diet high in fat, salt, and sugar over 12 wk were assessed for hyperlipidemia, hyperinsulinemia, and immunohistologic, echocardiographic, and hemodynamic parameters, as well as assessed for microbiome phenotype and function through 16S rRNA metataxonomic and metabolomic analysis, respectively. All MetS animals developed obesity, hyperlipidemia, insulin resistance, hypertension, fatty liver, structural cardiovascular changes including left ventricular hypertrophy and left atrial enlargement, and increased circulating saturated fatty acid levels, all in keeping with the human phenotype. A reduction in α-diversity and specific microbiota changes at phylum, family, and genus levels were also observed in this model. Specifically, this porcine model of MetS displayed increased abundances of proinflammatory bacteria coupled with increased circulating tumor necrosis factor-α and increased secondary bile acid-producing bacteria, which substantially impacted fibroblast growth factor-19 expression. Finally, a significant decrease in enteroprotective bacteria and a reduction in short-chain fatty acid-producing bacteria were also noted. Together, these data suggest that diet and mineralocorticoid-mediated development of biochemical and cardiovascular stigmata of metabolic syndrome in pigs leads to temporal gut microbiome changes that mimic key gut microbial population signatures in human cardiometabolic disease.NEW & NOTEWORTHY This study extends a prior porcine model of cardiometabolic syndrome to include systemic inflammation, fatty liver, and insulin sensitivity. Gut microbiome changes during evolution of porcine cardiometabolic disease recapitulate those in human subjects with alterations in gut taxa associated with proinflammatory bacteria, bile acid, and fatty acid pathways. This clinical scale model may facilitate design of future interventional trials to test causal relationships between gut dysbiosis and cardiometabolic syndrome at a systemic and organ level.

Pathogenic Enteric Viruses and Microbial Indicators during Secondary Treatment of Municipal Wastewater.

Pathogenic enteric viruses are responsible for a wide range of infections in humans, with diverse symptoms. Raw and partially treated wastewaters are major sources of environmental contamination with enteric viruses. We monitored a municipal secondary wastewater treatment plant (New Orleans, LA) on a monthly basis for norovirus (NoV) GI and GII and enterovirus serotypes using multiplex reverse transcription-quantitative PCR (RT-qPCR) and microbial indicators of fecal contamination using standard plating methods. Densities of indicator bacteria (enterococci, fecal coliforms, and Escherichia coli) did not show monthly or seasonal patterns. Norovirus GII was more abundant than GI and, along with enterovirus serotypes, increased in influent during fall and spring. The highest NoV GI density in influent was in the fall, reaching an average of 4.0 log10 genomic copies/100 ml. Norovirus GI removal (0.95 log10) was lower than that for GII, enterovirus serotypes, and male-specific coliphages (1.48 log10) or for indicator bacteria (4.36 log10), suggesting higher resistance of viruses to treatment. Male-specific coliphages correlated with NoV GII densities in influent and effluent (r = 0.48 and 0.76, respectively) and monthly removal, indicating that male-specific coliphages can be more reliable than indicator bacteria to monitor norovirus GII load and microbial removal. Dominant norovirus genotypes were classified into three GI genotypes (GI.1, GI.3, and GI.4) and four GII genotypes (GII.3, GII.4, GII.13, and GII.21), dominated by GI.1 and GII.4 strains. Some of the seasonal and temporal patterns we observed in the pathogenic enteric viruses were different from those of epidemiological observations.

Fodinicurvata halophila sp. nov., a moderately halophilic bacterium from a marine saltern.

A Gram-stain-negative, rod-shaped, facultatively anaerobic, moderately halophilic bacterium, designated strain BA45AL(T), was isolated from water of a saltern located in Santa Pola, Alicante, Spain. Cells were motile, and catalase- and oxidase-positive. Strain BA45AL(T) grew at temperatures in the range 14-45 °C (optimally at 37 °C), at pH 5.0-9.0 (optimally at pH 7.5), and in media containing 5-20 % (w/v) salts [optimally in media containing 10 % (w/v) salts]. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain BA45AL(T) is a member of the genus Fodinicurvata. The closest relatives to the novel strain were Fodinicurvata fenggangensis YIM D812(T) and Fodinicurvata sediminis YIM D82(T) with sequence similarities of 98.2 % and 97.4 %, respectively. DNA-DNA hybridization between the novel isolate and these phylogenetically related species revealed relatedness values of 30 % and 15 %, respectively, with respect to the aforementioned species. The major cellular fatty acids of strain BA45AL(T) were C18 : 1ω7c, C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA of strain BA45AL(T) was 58.0 mol%, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine and a number of unknown phospholipids and lipids. Based on phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain BA45AL(T) constituted a novel species of the genus Fodinicurvata, for which the name Fodinicurvata halophila sp. nov. is suggested. The type strain is BA45AL(T) ( = CCM 8504(T) = CECT 8472(T) = JCM 19075(T) = LMG 27945(T)).

Savagea faecisuis gen. nov., sp. nov., a tylosin- and tetracycline-resistant bacterium isolated from a swine-manure storage pit.

A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular methods was performed on three strains of a Gram-stain positive, non-sporeforming, motile aerobic rod-shaped bacterium resistant to tylosin and tetracycline isolated from a swine-manure storage pit. On the basis of 16S rRNA gene sequence analyses, it was confirmed that these isolates are highly related to each other and form a hitherto unknown lineage within the Planococcaceae. In particular, pairwise analysis of the 16S rRNA gene sequence demonstrated that the novel organism is closely related to members of the genus Sporosarcina (92.8-94.5 %), Pyschrobacillus (93.5-93.9 %) and Paenisporosarcina (93.3-94.5 %). The predominant fatty acids were found to consist of iso-C15:0 and iso-C17:1 ω10c and the G+C mol% was determined to be 41.8. Based on biochemical, chemotaxonomic, and phylogenetic evidence, it is proposed that these novel strains be classified as a novel genus and species, Savagea faecisuis gen nov., sp. nov. The type strain is Con12(T) (=CCUG 63563(T) = NRRL B-59945(T) = NBRC 109956(T)).

Peptoniphilus stercorisuis sp. nov., isolated from a swine manure storage tank and description of Peptoniphilaceae fam. nov.

A species of a previously unknown Gram-positive-staining, anaerobic, coccus-shaped bacterium recovered from a swine manure storage tank was characterized using phenotypic, chemotaxonomic, and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies and biochemical characteristics demonstrated that this organism is genotypically and phenotypically distinct, and represents a previously unknown sub-line within the order Clostridiales, within the phylum Firmicutes. Pairwise sequence analysis demonstrated that the novel organism clustered within the genus Peptoniphilus, most closely related to Peptoniphilus methioninivorax sharing a 16S rRNA gene sequence similarity of 95.5%. The major long-chain fatty acids were found to be C14:0 (22.4%), C16:0 (15.6%), C16:1ω7c (11.3%) and C16 : 0 ALDE (10.1%) and the DNA G +C content was 31.8 mol%. Based upon the phenotypic and phylogenetic findings presented, a novel species Peptoniphilus stercorisuis sp. nov. is proposed. The type strain is SF-S1(T) ( = DSM 27563(T) = NBRC 109839(T)). In addition, it is proposed to accommodate the genera Peptoniphilus, Anaerococcus, Anaerosphaera, Finegoldia, Gallicola, Helcococcus, Murdochiella and Parvimonas in a new family of the order Clostridiales, for which the name Peptoniphilaceae fam. nov. is proposed; the type genus of the family is Peptoniphilus.

Youngiibacter fragilis gen. nov., sp. nov., isolated from natural gas production-water and reclassification of Acetivibrio multivorans as Youngiibacter multivorans comb. nov.

A taxonomic study employing a polyphasic approach was performed on a novel anaerobic bacterium isolated from natural gas production-water. The bacterium stained Gram-negative and consisted of non-motile, non-spore-forming, rod-shaped cells. Products of glucose or starch fermentation were ethanol, CO2, formate, acetate and H2. The predominant fatty acids were C16 : 0 ALDE and summed feature 3 comprising C16 : 1ω7c and/or C16 : 1ω6c. The DNA G+C content was 45.5 mol%. 16S rRNA gene sequence analysis demonstrated that the nearest phylogenetic neighbours of the novel strain were Acetivibrio multivorans DSM 6139(T) (98.5 %) and Proteiniclasticum ruminis JCM 14817(T) (95.4 %). The DNA-DNA hybridization value between the novel organism and Acetivibrio multivorans PeC1 DSM 6139(T) was determined to be only 30.2 %, demonstrating the separateness of the two species. Based on phylogenetic, phenotypic and chemotaxonomic evidence that clearly distinguished strain 232.1(T) from Proteiniclasticum ruminis and other close relatives, it is proposed that the novel isolate be classified as representing a novel species of a new genus within the family Clostridiaceae, Youngiibacter fragilis gen. nov., sp. nov. The type strain of the type species is 232.1(T) ( = ATCC BAA-2257(T) = DSM 24749(T)). In addition, Acetivibrio multivorans is proposed to be reclassified as Youngiibacter multivorans comb. nov.

Autotransplantation of culture-positive islet product: is dirty always bad?

BACKGROUND: In selected patients, total pancreatectomy with islet autotransplantation (TPIAT) effectively relieves pain caused by chronic pancreatitis and ameliorates the brittle diabetes of the apancreatic state. Patients often undergo multiple endoscopic and surgical interventions prior to TPIAT, increasing the risk for pancreas colonization with enteric microorganisms. Little is known of the safety of transplanting islet cells with microbial contamination. METHODS: A prospectively collected database of 80 patients submitted to TPIAT at the Medical University of South Carolina from March 2009 to February 2012 was retrospectively reviewed. Patient charts were reviewed for postoperative infectious complications and organisms identified were compared with those identified in pre-transplant islet cultures. RESULTS: A total of 35 patients (43.8%) had a positive pre-transplant islet cell Gram stain or islet cell culture from the final islet preparation solution. Of these 35 patients, 33 (94.3%) were given antibiotics prophylactically post-transplant for a positive islet Gram stain or culture. Twenty patients (57.1%) receiving Gram stain- or culture-positive islets developed postoperative infectious complications, but only four patients (11.4%) developed infections that concorded with their pre-transplant islet product. CONCLUSIONS: Islet transplant solutions are frequently culture-positive, presumably as a result of prior pancreas intervention. Microbial contamination of islet preparations should not preclude autotransplantation.

Fitness factors in vibrios: a mini-review.

Vibrios are Gram-negative curved bacilli that occur naturally in marine, estuarine, and freshwater systems. Some species include human and animal pathogens, and some vibrios are necessary for natural systems, including the carbon cycle and osmoregulation. Countless in vivo and in vitro studies have examined the interactions between vibrios and their environment, including molecules, cells, whole animals, and abiotic substrates. Many studies have characterized virulence factors, attachment factors, regulatory factors, and antimicrobial resistance factors, and most of these factors impact the organism's fitness regardless of its external environment. This review aims to identify common attributes among factors that increase fitness in various environments, regardless of whether the environment is an oyster, a rabbit, a flask of immortalized mammalian cells, or a planktonic chitin particle. This review aims to summarize findings published thus far to encapsulate some of the basic similarities among the many vibrio fitness factors and how they frame our understanding of vibrio ecology. Factors representing these similarities include hemolysins, capsular polysaccharides, flagella, proteases, attachment factors, type III secretion systems, chitin binding proteins, iron acquisition systems, and colonization factors.

Evaluation of Alternative Colony Hybridization Methods for Pathogenic Vibrios.

Vibrios, such as Vibrio parahaemolyticus, are naturally occurring halophilic bacteria that are a major cause of foodborne illness. Because of their autochthonous nature, managing vibrio levels in marine and estuarine environments is impossible. Instead, it is crucial to reliably enumerate their abundance to minimize human exposure. One method of achieving this is the direct plating/colony hybridization (DP/CH) method, which has been used to efficiently quantify pathogenic vibrios in oysters and other seafood products. Although successful, the method relies on proprietary resources. We examined alternative approaches, assessed the influence of the reagent suppliers' source on enumeration accuracy, and made experimental adjustments that maximized efficiency, sensitivity, and specificity. We report here that in-house conjugation via Cell Mosaic is a viable alternative to the previously available sole-source distributor of the alkaline phosphatase-conjugated probes used to enumerate vibrios in oysters. We also report that milk was a viable alternative as a blocking reagent, pH must be eight, an orbital shaker was a viable alternative to a water bath, and narrow polypropylene containers were a viable alternative to Whirl-Pak bags. These modifications will be crucial to scientists enumerating vibrios and other pathogens in food products.

Ecology of Vibrio parahaemolyticus and Vibrio vulnificus in the coastal and estuarine waters of Louisiana, Maryland, Mississippi, and Washington (United States).

Vibrio parahaemolyticus and Vibrio vulnificus, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of Vibrio spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and V. parahaemolyticus and V. vulnificus populations in water, oysters, and sediment in three coastal areas of the United States. Because ecologically unique sites were included in the study, it was possible to analyze individual parameters over wide ranges. Molecular methods were used to detect genes for thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) as indicators of V. parahaemolyticus and the hemolysin gene vvhA for V. vulnificus. SST and suspended particulate matter were found to be strong predictors of total and potentially pathogenic V. parahaemolyticus and V. vulnificus. Other predictors included chlorophyll a, salinity, and dissolved organic carbon. For the ecologically unique sites included in the study, SST was confirmed as an effective predictor of annual variation in vibrio abundance, with other parameters explaining a portion of the variation not attributable to SST.

Peptostreptococcus canis sp. nov., isolated from subgingival plaque from canine oral cavity.

A polyphasic taxonomic study was performed on two strains of an unknown Gram-positive, asaccharolytic, nonspore-forming, obligately anaerobic coccus-shaped bacterium isolated from oral subgingival plaque of Labrador retriever dogs. Comparative 16S rRNA gene sequencing confirmed that these isolates were highly related to each other and formed a hitherto unknown linage within the clostridial rRNA XI cluster of organisms. Pairwise analysis demonstrated that the novel organism to be most closely related to members of the genus Peptostreptococcus with 16S rDNA gene sequence similarity values between 92.8% and 96.7%, respectively. The G + C DNA base composition was 30.8 mol% and the major cellular fatty acids included iso-C(14:0,) iso-C(16:0), and iso-C(16:0 DMA). Based on biochemical, chemotaxonomic, and phylogenetic evidence it is proposed that the unknown bacterium be classified as a new species, Peptostreptococcus canis sp. nov. The type strain is CCUG 57081(T).

Substrate and low intensity fires influence bacterial communities in longleaf pine savanna.

Bacterial communities associated with vegetation-soil interfaces have important roles in terrestrial ecosystems. These bacterial communities, studied almost exclusively in unburnt ecosystems or those affected by rare, high-intensity wildfires, have been understudied in fire-frequented grasslands and savannas. The composition of ground-level bacterial communities was explored in an old-growth pine savanna with a centuries-long management history of prescribed fires every 1-2 years. Using 16S metabarcoding, hypotheses were tested regarding differences in bacterial families of litter and soil surface substrates in patches of ground layer vegetation that were naturally burnt or unburnt during landscape-level prescribed fires. Litter/soil substrates and fire/no fire treatments explained 67.5% of bacterial community variation and differences, driven by relative abundance shifts of specific bacterial families. Fires did not strongly affect plant or soil variables, which were not linked to bacterial community differences. Litter/soil substrates and the naturally patchy frequent fires appear to generate microhabitat heterogeneity in this pine savanna, driving responses of bacterial families. Prescribed fire management may benefit from considering how fire-altered substrate heterogeneity influences and maintains microbial diversity and function, especially in these fiery ecosystems. Frequent, low-intensity fires appear ecologically important in maintaining the diverse microbial foundation that underlie ecosystem processes and services in fire-frequented habitats.

Hoeflea anabaenae sp. nov., an epiphytic symbiont that attaches to the heterocysts of a strain of Anabaena.

The heterotrophic, epiphytic, symbiotic bacterial strain WH2K(T) was previously isolated from a two-member culture in which it was attached to the heterocysts of a strain of Anabaena (SSM-00). Analysis of its 16S rRNA gene sequence demonstrated that the symbiont was most closely related to the type strain of Hoeflea marina (96.9 % similarity), which belongs to the family Phyllobacteriaceae within the order Rhizobiales of the class Alphaproteobacteria. A polyphasic taxonomic study was performed on strain WH2K(T), which consisted of irregular rods (2-5 µm long, 0.2 µm wide) that appeared to be narrower at one pole. Optimal growth was obtained in complex media with 15 g sea salts l(-1), at 18-34 °C (30 °C optimum) and at pH 6.0-8.0 (optimum pH 6.5). Unknown growth requirements were provided by small amounts of yeast extract but not by standard vitamin and trace metal solutions. Of the substrates tested, WH2K(T) was able to utilize only acetate, pyruvate, malate and fumarate. Growth was observed only under aerobic and microaerobic conditions, and nitrate was not reduced. No photosynthetic pigments were detected under any of the growth conditions tested. The predominant fatty acids were a summed feature that comprises C(18 : 1)ω7c, C(18 : 1)ω9t, C(18 : 1)ω12t or any combination of these (64.0 %) and an unidentified fatty acid of equivalent chain length 17.603 (13.5 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphoglycolipid, unknown lipids and an unidentified aminolipid. The only respiratory ubiquinone detected was Q-10. The DNA G+C content of the strain was 58.1 mol%. The organism can form a site-specific attached symbiotic relationship with a species of Anabaena. Based on phylogenetic and phenotypic evidence, it is proposed that strain WH2K(T) be classified within a novel species of the genus Hoeflea, for which the name Hoeflea anabaenae sp. nov. is proposed. The type strain is WH2K(T) ( = CCUG 56626(T)  = NRRL B-59520(T)).

Efficacy of Phage- and Bacteriocin-Based Therapies in Combatting Nosocomial MRSA Infections.

Staphylococcus aureus is a pathogen commonly found in nosocomial environments where infections can easily spread - especially given the reduced immune response of patients and large overlap between personnel in charge of their care. Although antibiotics are available to treat nosocomial infections, the increased occurrence of antibiotic resistance has rendered many treatments ineffective. Such is the case for methicillin resistant S. aureus (MRSA), which has continued to be a threat to public health since its emergence. For this reason, alternative treatment technologies utilizing antimicrobials such as bacteriocins, bacteriophages (phages) and phage endolysins are being developed. These antimicrobials provide an advantage over antibiotics in that many have narrow inhibition spectra, enabling treatments to be selected based on the target (pathogenic) bacterium while allowing for survival of commensal bacteria and thus avoiding collateral damage to the microbiome. Bacterial resistance to these treatments occurs less frequently than with antibiotics, particularly in circumstances where combinatory antimicrobial therapies are used. Phage therapy has been well established in Eastern Europe as an effective treatment against bacterial infections. While there are no Randomized Clinical Trials (RCTs) to our knowledge examining phage treatment of S. aureus infections that have completed all trial phases, numerous clinical trials are underway, and several commercial phage preparations are currently available to treat S. aureus infections. Bacteriocins have primarily been used in the food industry for bio-preservation applications. However, the idea of repurposing bacteriocins for human health is an attractive one considering their efficacy against many bacterial pathogens. There are concerns about the ability of bacteriocins to survive the gastrointestinal tract given their proteinaceous nature, however, this obstacle may be overcome by altering the administration route of the therapy through encapsulation, or by bioengineering protease-resistant variants. Obstacles such as enzymatic digestion are less of an issue for topical/local administration, for example, application to the surface of the skin. Bacteriocins have also shown impressive synergistic effects when used in conjunction with other antimicrobials, including antibiotics, which may allow antibiotic-based therapies to be used more sparingly with less resistance development. This review provides an updated account of known bacteriocins, phages and phage endolysins which have demonstrated an impressive ability to kill S. aureus strains. In particular, examples of antimicrobials with the ability to target MRSA strains and their subsequent use in a clinical setting are outlined.

Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird.

The microbial community in the gut is influenced by environmental factors, especially diet, which can moderate host behaviour through the microbiome-gut-brain axis. However, the ecological relevance of microbiome-mediated behavioural plasticity in wild animals is unknown. We presented wild-caught great tits (Parus major) with a problem-solving task and showed that performance was weakly associated with variation in the gut microbiome. We then manipulated the gut microbiome by feeding birds one of two diets that differed in their relative levels of fat, protein and fibre content: an insect diet (low content), or a seed diet (high content). Microbial communities were less diverse among individuals given the insect compared to those on the seed diet. Individuals were less likely to problem-solve after being given the insect diet, and the same microbiota metrics that were altered as a consequence of diet were also those that correlated with variation in problem solving performance. Although the effect on problem-solving behaviour could have been caused by motivational or nutritional differences between our treatments, our results nevertheless raise the possibility that dietary induced changes in the gut microbiota could be an important mechanism underlying individual behavioural plasticity in wild populations.

What genomic sequence information has revealed about Vibrio ecology in the ocean--a review.

To date, the genomes of eight Vibrio strains representing six species and three human pathogens have been fully sequenced and reported. This review compares genomic information revealed from these sequencing efforts and what we can infer about Vibrio biology and ecology from this and related genomic information. The focus of the review is on those attributes that allow the Vibrios to survive and even proliferate in their ocean habitats, which include seawater, plankton, invertebrates, fish, marine mammals, plants, man-made structures (surfaces), and particulate matter. Areas covered include general information about the eight genomes, each of which is distributed over two chromosomes; a discussion of expected and unusual genes found; attachment sites and mechanisms; utilization of particulate and dissolved organic matter; and conclusions.

The gut microbiome as a driver of individual variation in cognition and functional behaviour.

Research into proximate and ultimate mechanisms of individual cognitive variation in animal populations is a rapidly growing field that incorporates physiological, behavioural and evolutionary investigations. Recent studies in humans and laboratory animals have shown that the enteric microbial community plays a central role in brain function and development. The 'gut-brain axis' represents a multi-directional signalling system that encompasses neurological, immunological and hormonal pathways. In particular it is tightly linked with the hypothalamic-pituitary-adrenal axis (HPA), a system that regulates stress hormone release and influences brain development and function. Experimental examination of the microbiome through manipulation of diet, infection, stress and exercise, suggests direct effects on cognition, including learning and memory. However, our understanding of these processes in natural populations is extremely limited. Here, we outline how recent advances in predominantly laboratory-based microbiome research can be applied to understanding individual differences in cognition. Experimental manipulation of the microbiome across natal and adult environments will help to unravel the interplay between cognitive variation and the gut microbial community. Focus on individual variation in the gut microbiome and cognition in natural populations will reveal new insight into the environmental and evolutionary constraints that drive individual cognitive variation.This article is part of the theme issue 'Causes and consequences of individual differences in cognitive abilities'.