Incorporating prior knowledge improves detection of differences in bacterial growth rate

BACKGROUND: Robust statistical detection of differences in the bacterial growth rate can be challenging, particularly when dealing with small differences or noisy data. The Bayesian approach provides a consistent framework for inferring model parameters and comparing hypotheses. The method captures the full uncertainty of parameter values, whilst making effective use of prior knowledge about a given system to improve estimation. RESULTS: We demonstrated the application of Bayesian analysis to bacterial growth curve comparison. Following extensive testing of the method, the analysis was applied to the large dataset of bacterial responses which are freely available at the web-resource, ComBase. Detection was found to be improved by using prior knowledge from clusters of previously analysed experimental results at similar environmental conditions. A comparison was also made to a more traditional statistical testing method, the F-test, and Bayesian analysis was found to perform more conclusively and to be capable of attributing significance to more subtle differences in growth rate. CONCLUSIONS: We have demonstrated that by making use of existing experimental knowledge, it is possible to significantly improve detection of differences in bacterial growth rate

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics.

UnlabelledRegionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroirImportanceWine production is a multi-billion-dollar global industry for which microbial control and wine chemical composition are crucial aspects of quality. Terroir is an important feature of consumer appreciation and wine culture, but the many factors that contribute to terroir are nebulous. We show that grape and wine microbiota exhibit regional patterns that correlate with wine chemical composition, suggesting that the grape microbiome may influence terroir In addition to enriching our understanding of how growing region and wine properties interact, this may provide further economic incentive for agricultural and enological practices that maintain regional microbial biodiversity

The Origin, Succession, and Predicted Metabolism of Bacterial Communities Associated with Leaf Decomposition.

Intraspecific variation in plant nutrient and defensive traits can regulate ecosystem-level processes, such as decomposition and transformation of plant carbon and nutrients. Understanding the regulatory mechanisms of ecosystem functions at local scales may facilitate predictions of the resistance and resilience of these functions to change. We evaluated how riverine bacterial community assembly and predicted gene content corresponded to decomposition rates of green leaf inputs from red alder trees into rivers of Washington State, USA. Previously, we documented accelerated decomposition rates for leaves originating from trees growing adjacent to the site of decomposition versus more distant locales, suggesting that microbes have a "home-field advantage" in decomposing local leaves. Here, we identified repeatable stages of bacterial succession, each defined by dominant taxa with predicted gene content associated with metabolic pathways relevant to the leaf characteristics and course of decomposition. "Home" leaves contained bacterial communities with distinct functional capacities to degrade aromatic compounds. Given known spatial variation of alder aromatics, this finding helps explain locally accelerated decomposition. Bacterial decomposer communities adjust to intraspecific variation in leaves at spatial scales of less than a kilometer, providing a mechanism for rapid response to changes in resources such as range shifts among plant genotypes. Such rapid responses among bacterial communities in turn may maintain high rates of carbon and nutrient cycling through aquatic ecosystems.IMPORTANCE Community ecologists have traditionally treated individuals within a species as uniform, with individual-level biodiversity rarely considered as a regulator of community and ecosystem function. In our study system, we have documented clear evidence of within-species variation causing local ecosystem adaptation to fluxes across ecosystem boundaries. In this striking pattern of a "home-field advantage," leaves from individual trees tend to decompose most rapidly when immediately adjacent to their parent tree. Here, we merge community ecology experiments with microbiome approaches to describe how bacterial communities adjust to within-species variation in leaves over spatial scales of less than a kilometer. The results show that bacterial community compositional changes facilitate rapid ecosystem responses to environmental change, effectively maintaining high rates of carbon and nutrient cycling through ecosystems

A keystone Methylobacterium strain in biofilm formation in drinking water

The structure of biofilms in drinking water systems is influenced by the interplay between biological and physical processes. Bacterial aggregates in bulk fluid are important in seeding biofilm formation on surfaces. In simple pure and co-cultures, certain bacteria, including Methylobacterium, are implicated in the formation of aggregates. However, it is unclear whether they help to form aggregates in complex mixed bacterial communities. Furthermore, different flow regimes could affect the formation and destination of aggregates. In this study, real drinking water mixed microbial communities were inoculated with the Methylobacterium strain DSM 18358. The propensity of Methylobacterium to promote aggregation was monitored under both stagnant and flow conditions. Under stagnant conditions, Methylobacterium enhanced bacterial aggregation even when it was inoculated in drinking water at 1% relative abundance. Laminar and turbulent flows were developed in a rotating annular reactor. Methylobacterium was found to promote a higher degree of aggregation in turbulent than laminar flow. Finally, fluorescence in situ hybridisation images revealed that Methylobacterium aggregates had distinct spatial structures under the different flow conditions. Overall, Methylobacterium was found to be a key strain in the formation of aggregates in bulk water and subsequently in the formation of biofilms on surfaces

Impact of Age and Body Site on Adult Female Skin Surface pH

Background: pH is known as an important parameter in epidermal barrier function and homeostasis. Aim: The impact of age and body site on skin surface pH (pH(SS)) of women was evaluated in vivo. Methods: Time domain dual lifetime referencing with luminescent sensor foils was used for pH(SS) measurements. pH(SS) was measured on the forehead, the temple, and the volar forearm of adult females (n = 97, 52.87 +/- 18.58 years, 20-97 years). Every single measurement contained 2,500 pH values due to the luminescence imaging technique used. Results: pH(SS) slightly increases with age on all three investigated body sites. There are no significant differences in pH(SS) between the three investigated body sites. Conclusion: Adult pH(SS) on the forehead, the temple and the volar forearm increases slightly with age. This knowledge is crucial for adapting medical skin care products. Copyright (C) 2012 S. Karger AG, Base

Aquaculture Asia, Vol. 7, No. 3, pp.1-60, July - September 2002

CONTENTS: Sustainable Aquaculture - Peter Edwards writes on rural aquaculture: Aquaculture for Poverty Alleviation and Food Security - Part II. Shrimp pond waste management by U Win Latt. The role of rural extension in the sustainable development of Chinese aquaculture by Min Kuanhong. Farmers as Scientists: Diversity enhances profitability and sustainability by M.C. Nandeesha. Properties of Liming Materials by Claude E. Boyd, Mali Boonyaratpalin & Taworn Thunjai. Seed Production of Mud Crab Scylla spp. by Emilia T. Quinitio, Fe Delores Parado-Estepa and Eduard Rodriguez Genes and Fish: The dilemmas of strain selection by Graham Mair. Seed Production of the Crucifix Crab Charybdis feriatus by Fe Delores Parado-Estepa, Eduard Rodriguez and Emilia T. Quinitio. Aquaculture Fundamentals: A general approach to disease treatment & control by Simon Wilkinson. Marine Finfish Aquaculture Network meets in Vietnam. New APEC Project: Improving Coastal Livelihoods Through Sustainable Aquaculture Practices. Breeding and Seed Production of the Mangrove Red Snapper by Arnil C. Emata. APEC, FAO, NACA, and OIE enhance Capacity on Risk Analysis (IRA)in Aquatic Animal Movement in Asia-Pacific region by Melba Reantaso. Advice on Aquatic Animal Health: Questions & answers on drugs and chemicals by Pornlerd Chanratchakool. Responsible use of antibiotics in shrimp farming by Sara Graslund, Karin Karlsson and Janenuj Wongtavatchai. Molecular methods for rapid and specific detection of pathogens in seafood by Iddya Karunasagar, Indrani Karunasagar and H. Samath Kumar. Practical approaches to health management for cage cultured marine fishes by Leong Tak Seng

PRImary care Streptococcal Management (PRISM) study:In vitro study, diagnostic cohorts and a pragmatic adaptive randomised controlled trial with nested qualitative study and cost-effectiveness study

Background: Antibiotics are still prescribed to most patients attending primary care with acute sore throat, despite evidence that there is modest benefit overall from antibiotics. Targeting antibiotics using either clinical scoring methods or rapid antigen detection tests (RADTs) could help. However, there is debate about which groups of streptococci are important (particularly Lancefield groups C and G), and uncertainty about the variables that most clearly predict the presence of streptococci. Objective: This study aimed to compare clinical scores or RADTs with delayed antibiotic prescribing. Design: The study comprised a RADT in vitro study; two diagnostic cohorts to develop streptococcal scores (score 1; score 2); and, finally, an open pragmatic randomised controlled trial with nested qualitative and cost-effectiveness studies. Setting: The setting was UK primary care general practices. Participants: Participants were patients aged ≥ 3 years with acute sore throat. Interventions: An internet program randomised patients to targeted antibiotic use according to (1) delayed antibiotics (control group), (2) clinical score or (3) RADT used according to clinical score. Main outcome measures: The main outcome measures were self-reported antibiotic use and symptom duration and severity on seven-point Likert scales (primary outcome: mean sore throat/difficulty swallowing score in the first 2-4 days). Results: The IMI TestPack Plus Strep A (Inverness Medical, Bedford, UK) was sensitive, specific and easy to use. Lancefield group A/C/G streptococci were found in 40% of cohort 2 and 34% of cohort 1. A five-point score predicting the presence of A/C/G streptococci [FeverPAIN: Fever; Purulence; Attend rapidly (≤ 3 days); severe Inflammation; and No cough or coryza] had moderate predictive value (bootstrapped estimates of area under receiver operating characteristic curve: 0.73 cohort 1, 0.71 cohort 2) and identified a substantial number of participants at low risk of streptococcal infection. In total, 38% of cohort 1 and 36% of cohort 2 scored ≤ 1 for FeverPAIN, associated with streptococcal percentages of 13% and 18%, respectively. In an adaptive trial design, the preliminary score (score 1; n = 1129) was replaced by FeverPAIN (n = 631). For score 1, there were no significant differences between groups. For FeverPAIN, symptom severity was documented in 80% of patients, and was lower in the clinical score group than in the delayed prescribing group (-0.33; 95% confidence interval -0.64 to -0.02; p = 0.039; equivalent to one in three rating sore throat a slight rather than moderately bad problem), and a similar reduction was observed for the RADT group (-0.30; -0.61 to 0.00; p = 0.053). Moderately bad or worse symptoms resolved significantly faster (30%) in the clinical score group (hazard ratio 1.30; 1.03 to 1.63) but not the RADT group (1.11; 0.88 to 1.40). In the delayed group, 75/164 (46%) used antibiotics, and 29% fewer used antibiotics in the clinical score group (risk ratio 0.71; 0.50 to 0.95; p = 0.018) and 27% fewer in the RADT group (0.73; 0.52 to 0.98; p = 0.033). No significant differences in complications or reconsultations were found. The clinical score group dominated both other groups for both the cost/quality-adjusted life-years and cost/change in symptom severity analyses, being both less costly and more effective, and cost-effectiveness acceptability curves indicated the clinical score to be the most likely to be cost-effective from an NHS perspective. Patients were positive about RADTs. Health professionals' concerns about test validity, the time the test took and medicalising self-limiting illness lessened after using the tests. For both RADTs and clinical scores, there were tensions with established clinical experience. Conclusions: Targeting antibiotics using a clinical score (FeverPAIN) efficiently improves symptoms and reduces antibiotic use. RADTs used in combination with FeverPAIN provide no clear advantages over FeverPAIN alone, and RADTs are unlikely to be incorporated into practice until health professionals' concerns are met and they have experience of using them. Clinical scores also face barriers related to clinicians' perceptions of their utility in the face of experience. This study has demonstrated the limitation of using one data set to develop a clinical score. FeverPAIN, derived from two data sets, appears to be valid and its use improves outcomes, but diagnostic studies to confirm the validity of FeverPAIN in other data sets and settings are needed. Experienced clinicians need to identify barriers to the use of clinical scoring methods. Implementation studies that address perceived barriers in the use of FeverPAIN are needed

Incorporation of Bifidobacterium animalis subspecies lactis BB-12® and Akkermansia muciniphila in chocolate matrices

Currently, consumers are seeking healthier food options, prioritizing goods with improved organoleptic and health properties. Consequently, the food industry has been focusing on developing functional foods, which are characterized by the incorporation of bioactive ingredients, which complement essential nutrition (food supplement) or have a pharmacological activity (nutraceutical). Probiotics, defined as "live microorganisms that, when administered in adequate amounts, confer benefits to human health", are a good example. These have been incorporated into different types of food matrices, particularly dairy matrices, and more recently into cereal or fruit and vegetable matrices. In an attempt to increase the portfolio of attractive food vectors for the delivery of probiotic bacteria to the consumer, chocolate was selected and studied due to its extreme popularity among consumers. Thus, the main objective of this thesis was to study the incorporation of two probiotic strains, namely Bifidobacterium animalis subsp. lactis BB-12® (classical probiotic strain) and Akkermansia muciniphila DSM 22959 (candidate strain for new probiotic generation) in three chocolate matrices with different cocoa percentages (33. 6%; 54.5% and 70.5%) and evaluate their viability and stability over 28 days of aerobic storage and in simulated gastrointestinal tract (GIT) passage. Simultaneously, the content of total phenolic compounds was quantified, and the following biological activities were determined: antioxidant, antidiabetic, and antihypertensive. For the probiotic B. animalis BB-12®, the most suitable matrix was the chocolate containing 70.5% cocoa content, as it assured cell concentration levels of 108 CFU/g after 28 days of aerobic storage and presented viable cell numbers of 107 CFU/g during in vitro GIT simulation. Furthermore, the chocolates with 70.5% cocoa presented greater total phenolic compounds content and higher bioactivities (antioxidant, antidiabetic and antihypertensive). Regarding A. muciniphila DSM 22959, the most appropriate chocolate matrix was the one with 54.5% cocoa content, as cell viability was kept at 106 CFU/g, after 28-day aerobic storage. Though, A. muciniphila survived during aerobic storage in the chocolate matrix, this bacterium was unable to endure the simulated GIT conditions, when incorporated into chocolate. Regarding parameters such as overall quality aspect and texture, results indicated that the addition of probiotics modifies the chocolate’s surface and increases its hardness. Moreover, the results of a performed sensory analysis test (triangular test) with 70.5% cocoa content chocolate incorporated with A. muciniphila demonstrated that more than 50% of the testers could not distinguish between a plain chocolate (control) and a probiotic-incorporated chocolate. Although the addition of probiotics leads to changes in the organoleptic properties of the chocolate matrix, the supplementary benefits of a probiotic chocolate overweigh these differences, being therefore more attractive to the consumer. In conclusion, a chocolate matrix with high cocoa content (dark chocolate) is a suitable carrier for Bifidobacterium animalis subsp. lactis BB-12® and Akkermansia muciniphila.Atualmente, os consumidores procuram alternativas mais saudáveis para a sua alimentação, priorizando assim alimentos com melhores propriedades organoléticas e com maiores benefícios a nível da saúde. Consequentemente, a indústria alimentar teve de se adaptar a esta procura, concentrando-se assim no desenvolvimento de alimentos funcionais. Estes produtos alimentares caracterizam-se pela incorporação de ingredientes bioativos, que complementam a nutrição essencial (suplemento alimentar) ou que apresentam uma atividade farmacológica (nutracêutica). Os probióticos, definidos como "microrganismos vivos que, quando administrados em quantidades adequadas, conferem um benefício para a saúde humana”, são um bom exemplo. Estes têm sido incorporados em diferentes tipologias de matrizes alimentares particularmente matrizes lácteas, e mais recentemente em matrizes cerealíferas ou hortofrutícolas. Numa abordagem de aumentar o portefólio de vetores alimentares atrativos para o fornecimento de bactérias probióticas ao consumidor, foi selecionado e estudado o chocolate por ser um produto com extrema popularidade entre os consumidores. Assim, o objetivo principal da presente tese foi estudar a incorporação de duas estirpes probióticas, nomeadamente Bifidobacterium animalis subsp. lactis BB-12® (estirpe probiótica clássica) e Akkermansia muciniphila DSM 22959 (estirpe candidata a nova geração de probióticos) em três matrizes de chocolate com diferentes percentagens de cacau (33.6%; 54.5% e 70.5%) e avaliar a sua viabilidade e estabilidade ao longo de 28 dias de armazenamento aeróbico e na simulação da passagem do trato gastrointestinal (TGI). Simultaneamente foram quantificados o teor de compostos fenólicos totais e determinadas as seguintes atividades biológicas: antioxidante, antidiabética e anti-hipertensiva. Para o probiótico B. animalis BB-12®, a matriz mais adequada foi o chocolate contendo 70.5% de cacau, uma vez que assegurou níveis de concentração celular de 108 UFC/g, após 28 dias de armazenamento aeróbico e assegurou níveis de 107 UFC/g durante a simulação in vitro do trato gastrointestinal. Além disso, os chocolates com 70.5% de cacau exibiram maior conteúdo de compostos fenólicos totais e bioatividades superiores (antioxidante, antidiabética e anti-hipertensiva). Relativamente a A. muciniphila DSM 22959, a matriz de chocolate mais apropriada foi a de 54.5% de cacau, uma vez que a viabilidade celular foi mantida a 106 UFC/g, após 28 dias de armazenamento aeróbio. Apesar de A. muciniphila ter sobrevivido durante o armazenamento na matriz de chocolate, o probiótico foi incapaz de suportar as condições do TGI, quando incorporada no chocolate. Relativamente a parâmetros como o aspeto e textura, os resultados indicaram que a adição de probióticos modifica a superfície do chocolate e aumenta simultaneamente a dureza destes. Adicionalmente, os resultados de uma prova de análise sensorial (prova triangular) com chocolate com 70.5% de cacau incorporados com A. muciniphila demonstraram como mais de 50% dos provadores não consegue distinguir entre um chocolate sem bactéria e o chocolate incorporado com probiótico. Embora a adição de probióticos leve a alterações nas propriedades organoléticas da matriz do chocolate, os benefícios suplementares de um chocolate probiótico compensam estas diferenças, sendo por consequente o chocolate funcional mais atrativo para o consumidor. Em conclusão, uma matriz de chocolate com elevado teor de cacau (chocolate preto) é um método adequado para a incorporação dos probióticos Bifidobacterium animalis subsp. lactis BB-12® e Akkermansia muciniphila

Evaluating the role of the bovine vaginal microbiome in neonatal and maternal health outcomes

The dam vaginal microbiota is the first major microbial inoculating community within the neonate. The composition of the dam vaginal microbiota has implications in calf commensal microbiota development. Alterations of the dam microbial community prior to parturition could alter inoculating communities and immune responses in both the dam and calf. Thus, authors aimed to elucidate the microbial community composition of the bovine dam vaginal and calf nasal microbiota post-partum after utilizing betadine lavages (BL). The dam vaginal and calf nasal microbial communities and immune responses were evaluated at 0-, 15-, 30- and 60-day post-partum. Microbiota composition of the dam haircoat, udder, and IgG in the colostrum/calf sera were also evaluated at day 0. Serial BLG prior to parturition did not alter the alpha diversity of the dam-vaginal microbiota but did alter the calf-nasal microbiota at parturition (P = 0.03). Dams receiving BLG prior to calving had increased colostrum IgG concentrations compared to CON dams (P =0.04). These results suggest physiological insults (BLG) prior to parturition led to an increased immune response which altering dam colostrum IgG. Thus, neonatal colostrum consumption could drive immune responses against inoculating bacteria resulting in differing nasal microbial communities between treatment groups. The beta diversity of the calf nasal microbiota was significantly different at day 0 compared to all other timepoints (P = 0.006). The calf nasal beta diversity at day 15 was similar to day 30 (P = 0.38) but significantly different compared to day 60 (P = 0.006). There was no effect of time on altering the alpha (P = 0.60) or beta (P = 0.06) diversity of the dam vaginal microbiota. The calf nasal microbiota was different from the dam vaginal microbiota at all timepoints post-partum, regardless of treatment. At day 15, the alpha and beta diversity of calves was altered compared to day 0, suggestive of a reinoculation timepoint between 0 and 14 days of age. Together, this data contributes to the paucity within beef cattle dam-calf post-partum microbiota literature and provides directionality for future research objectives within this field