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Abstract Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40–60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.

Osteocutaneous flap (OCF) mandible reconstruction is at high risk for surgical site infection. This study aimed to describe diagnosis, management, and outcome of OCF-related osteomyelitis. All patients managed at our institution for an OCF-related osteomyelitis following mandible reconstruction were included in a retrospective cohort study (2012–2019). Microbiology was described according to gold-standard surgical samples, considering all virulent pathogens, and potential contaminants if present on at least two samples. Determinants of treatment failure were assessed by logistic regression and Kaplan–Meier curve analysis. The 48 included patients (median age 60.5 (IQR, 52.4–66.6) years) benefited from OCF mandible reconstruction mostly for carcinoma (n=27/48; 56.3 %) or osteoradionecrosis (n=12/48; 25.0 %). OCF-related osteomyelitis was mostly early (≤3 months post-surgery; n=43/48; 89.6 %), presenting with local inflammation (n=28/47; 59.6 %), nonunion (wound dehiscence) or sinus tract (n=28/47; 59.6 %), and/or bone or device exposure (n=21/47; 44.7 %). Main implicated pathogens were Enterobacteriaceae (n=25/41; 61.0 %), streptococci (n=22/41; 53.7 %), Staphylococcus aureus (n=10/41; 24.4 %), enterococci (n=9/41; 22.0 %), non-fermenting Gram-negative bacilli (n=8/41; 19.5 %), and anaerobes (n=8/41; 19.5 %). Thirty-nine patients (81.3 %) benefited from surgery, consisting of debridement with implant retention (DAIR) in 25/39 (64.1 %) cases, associated with 93 (IQR, 64–128) days of antimicrobial therapy. After a follow-up of 18 (IQR, 11–31) months, 24/48 (50.0 %) treatment failures were observed. Determinants of treatment outcomes were DAIR (OR, 3.333; 95 % CI, 1.020–10.898) and an early infectious disease specialist referral (OR, 0.236 if ≤2 weeks; 95 % CI, 0.062–0.933). OCF-related osteomyelitis following mandibular reconstruction represents difficult-to-treat infections. Our results advocate for a multidisciplinary management, including an early infectious-disease-specialist referral to manage the antimicrobial therapy driven by complex microbiological documentation.

No abstract.

Agroscope Culture Collection was screened to identify bacterial strains effective in production of dairy flavor inducing lactones using grapeseed oil as a substrate. Lentilactobacillus parafarraginis FAM-1079, Lactococcus lactis subsp. lactis FAM-17918, and L. lactis subsp. lactis biovar diacetylactis FAM-22003 showed the most efficient formation of targeted δ-lactones. The application of sublethal heat stress significantly increased target lactone production. The most profound improvement was for L. lactis subsp. lactis biovar diacetylactis where δ-octadecalactone generation was improved by factor of 9. The pre-fermentation step as well as growth phase in which bacteria are harvested did not have a significant impact on lactones yield. The lactone production process from vegetable oil developed in this study offers a new way of developing a natural flavor ingredient for incorporation into plant-based products.

The identification of molecular biomarkers that can be used to quantitatively link dietary intake to phenotypic traits in humans is a key theme in modern nutritional research. Although dairy products (with and without fermentation) represent a major food group, the identification of markers of their intake lags behind that of other food groups. Here, we report the results from an analysis of the metabolites in postprandial serum and urine samples from a randomized crossover study with 14 healthy men who ingested acidified milk, yogurt, and a non-dairy meal. Our study confirms the potential of lactose and its metabolites as markers of lactose-containing dairy foods and the dependence of their combined profiles on the fermentation status of the consumed products. Furthermore, indole-3-lactic acid and 3-phenyllactic acid are two products of fermentation whose postprandial behaviour strongly discriminates yogurt from milk intake. Our study also provides evidence of the ability of milk fermentation to increase the acute delivery of free amino acids to humans. Notably, 3,5-dimethyloctan-2-one also proves to be a specific marker for milk and yogurt consumption, as well as for cheese consumption (previously published data). These molecules deserve future characterisation in human interventional and observational studies.

A method based on dynamic headspace vacuum transfer in trap extraction, followed by gas chromatography coupled with a mass spectrometer (DHS-VTT-GC-MS), was validated for the fast quantitation of 1,4-dichlorobenzene (p-dichlorobenzene; PDCB) and thymol residues in beeswax. The quantitation limits (LOQ) were 0.05 mg/kg (PDCB) and 0.25 mg/kg (thymol). Recoveries above 80% were obtained for PDCB concentrations between 0.05 and 10 mg/kg and for thymol concentrations between 0.25 and 200 mg/kg. Analysis of beeswax samples showed a good correlation between the results obtained by DHS-VTT-GC-MS analysis and those of a previous method based on SPE extraction followed by gas chromatography and triple- quadrupole mass spectrometry (GC-MS/MS) (R2 = 0.9770 for PDCB and 0.9666 for thymol). However, the sample preparation and chromatography were much shorter using the DHS-VTT-GC-MS method. Forty comb foundations samples produced in Switzerland in 2019 and 2021 were analysed using DHS-VTT-GC-MS. Fourteen samples contained PDCB above the LOQ of 0.05 mg/kg, ranging up to a maximum of 1.53 mg/kg. The mean concentration of the positive samples was 0.22 mg/kg. All samples contained thymol residues ranging between 3.9 and 84.4 mg/kg with mean and median concentrations of 22.7 mg/kg and 17.4 mg/kg. Residue levels of PCDB and thymol in Swiss beeswax were substantially below those measured 20 (PDCB) and 10 (thymol) years ago, respectively.

Bacterial volatiles play important roles in mediating beneficial interactions between plants and their associated microbiota. Despite their relevance, bacterial volatiles are mostly studied under laboratory conditions, although these strongly differ from the natural environment bacteria encounter when colonizing plant roots or shoots. In this work, we ask the question whether plant-associated bacteria also emit bioactive volatiles when growing on plant leaves rather than on artificial media. Using four potato-associated Pseudomonas, we demonstrate that potato leaves offer sufficient nutrients for the four strains to grow and emit volatiles, among which 1-undecene and Sulfur compounds have previously demonstrated the ability to inhibit the development of the oomycete Phytophthora infestans, the causative agent of potato late blight. Our results bring the proof of concept that bacterial volatiles with known plant health-promoting properties can be emitted on the surface of leaves and warrant further studies to test the bacterial emission of bioactive volatiles in greenhouse and field-grown plants.

Aim: Wine quality is influenced by the nitrogen nutrition of grapevines in the vineyard. A deficiency of this nutrient will affect grape quality, decrease yeast available nitrogen (YAN) and influence alcoholic fermentation. Chasselas wines from nitrogen-deficient grapes (YAN < 140 mg N/L) are systematically more astringent and bitter and less fruity than those from grapes with higher YAN content (Spring et al., 2014). The aim of this study was to identify chemical markers in wine linked to nitrogen deficiencies in the vineyard. Methods and results: Wine samples produced from grapes growing in nitrogen-deficient vineyards with nitrogen treatment (HN) and without it (LN) were used over four consecutive years (2006–2009). They were all analysed at the same time (2012) with electronic-nose, GC-MS and UHPLC-TOFMS techniques. A metabolomics approach was used for a comprehensive survey of volatile and nonvolatile compounds in order to identify markers related to nitrogen nutrition. Volatile markers with alcohol and ester functions and nitrogen-containing compounds were found and tentatively identified by GC-MS. Additionally, 16 nonvolatile markers were putatively identified by UHPLC-TOFMS, including compounds from diverse chemical classes, namely, amino acids, vitamins, hormones, organic acids, phenolic compounds and polysaccharides. Conclusion: The nitrogen nutrition of grapevines has a clear but complex effect on the chemical composition of wine. Several markers were tentatively identified and their role in wine composition discussed according to the actual knowledge reported in the literature. Significance of the study: This study is an important starting point for selecting the most relevant chemical markers in wine, and for determining whether organoleptic problems are related to nitrogen nutrition deficiency in the vineyard and changes in vineyard management are needed.

Clémence Guenne,1 Jérôme Fayette,2 Alain Cosmidis,1 Carine Fuchsmann,1 Sophie Tartas,3 Véronique Favrel,4 Philippe Céruse1 1Head and Neck Surgery Department, Lyon-I University, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France; 2Medicine Department, Lyon-I University, Centre Léon Bérard, Lyon, France; 3Medical Oncology Department, Lyon-I University, Hospices Civils de Lyon, Lyon Sud Hospital, 4Radiotherapy Department, Lyon-I University, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France Background: No specific study has focused on patients with metastatic squamous cell carcinoma of the head and neck (SCCHN) at diagnosis. Due to high response rates of induction chemotherapy in chemo-naïve patients with localized disease, their prognosis should be better than patients with recurrent disease.Methods: From January 1, 2008 to July 1, 2012, we retrospectively collected all patients’ records with SCCHN diagnosed as metastatic. Patients, disease, treatment and its results were analyzed. Survival was calculated using the Kaplan–Meier method.Results: Of the 749 new patients treated for SCCHN in our institution, 16 (2.1%) were metastatic at diagnosis, of whom five had cytological results to prove it. Six patients died before treatment or had palliative care and ten received initial chemotherapy and then surgery and/or radiotherapy according to the primary response. Four patients treated with first-line chemotherapy with docetaxel-5FU-cisplatin (TPF) showed a complete response of metastatic lesions allowing locoregional treatment. The overall survival at 1 year and 3 years was 50% and 24%, respectively. The median survival was 7 months (1–72 months). Seven patients (43.7%) had a higher survival at 12 months, including five (31.5%) who are still alive without recurrence with a mean follow-up of 30 months. There was a significant difference in overall survival (P