Catabolism of leucine to branched-chain fatty acids in Staphylococcus xylosus

Mechanism underlying effects of cellulose-degrading microbial inoculation on amino acid degradation and biosynthesis during composting

Amino acids are essential organic compounds in composting products. However, the mechanism underlying the amino acid metabolism during composting remains unclear. This study aims at exploring the impacts of inoculating cellulose-degrading microbes on amino acid metabolism during composting with mulberry branches and silkworm excrements. Cellulose-degrading microbial inoculation enhanced amino acid degradation by 18%-43% by increasing protease and sucrase activities and stimulating eight amino acid degradation pathways from the initial to thermophilic phases, with Enterococcus, Saccharomonospora, Corynebacterium being the dominant bacterial genera, but stimulated amino acid production by 54% by increasing sucrase and urease activities, decreasing β-glucosidase activities, and stimulating twenty-two amino acid synthesis pathways at the mature phase, with Thermobifida, Devosia, and Cellulosimicrobium being the dominant bacterial genera. The results suggest that cellulose-degrading microbial inoculation enhances amino acid degradation from the initial to thermophilic phases and biosynthesis at the mature phase, thereby improving the quality of organic fertilizer.

Effect of Limosilactobacillus fermentum 332 on physicochemical characteristics, volatile flavor components, and Quorum sensing in fermented sausage

The effects of Limosilactobacillus fermentum 332 on quality characteristics in fermented sausage were explored in terms of physicochemical characteristics, volatile flavor components, and Quorum sensing (QS). The results showed that the pH of fermented sausage decreased from 5.20 to 4.54 within 24 h with the inoculation of L. fermentum 332. Lightness and redness were significantly improved, and hardness and chewiness were significantly increased after the addition of L. fermentum 332. With the inoculation of L. fermentum 332, the thiobarbituric acid reactive substance content decreased from 0.26 to 0.19 mg/100 g and total volatile basic nitrogen content decreased from 2.16 to 1.61 mg/100 g. In total, 95 and 104 types of volatile flavor components were detected in the control and fermented sausage inoculated with starter culture, respectively. The AI-2 activity of fermented sausage inoculated with L. fermentum 332 was significantly higher than that of the control and positively correlated with viable count and quality characteristics. These results provide support for further research on the effect of microorganisms on the quality of fermented food.

Effects of the addition of leucine on flavor and quality of sausage fermented by Lactobacillus fermentum YZU-06 and Staphylococcus saprophyticus CGMCC 3475

Methyl-branched aldehydes, especially 3-methylbutanal, have been reported to be perceived either as a malty or as a nutty/chocolate-like aroma and were considered an important flavor contributor in fermented meat products. Decomposition of leucine (Leu) by branched-chain amino acid transaminase (BACT) is a crucial step in the metabolism of Leu to 3-methylbutanal. This study was conducted to explore the effects of mixed-starter culture (Lactobacillus fermentum YZU-06 and Staphylococcus saprophyticus CGMCC 3475) and addition of Leu (0, 1, and 3 mM) on the flavor and quality of fermented sausages. The pH, water activity, texture profile analysis, color, counts of lactic acid bacteria (LAB) and staphylococci, peptide, and flavor compounds were detected during fermentation. The results showed that the starter culture group increased hardness, elasticity, the counts of LAB and staphylococci, peptide content, volatile flavor compounds, as well as the sensorial scores of sausage, while decreasing pH, a _w , and L* and b* values compared with the non-inoculation group. The mixed starter of adding with 3 mM Leu enhanced the content of 3-methylbutanal and overall flavor of fermented sausages. It is applicable to directionally produce methyl-branched aldehydes and improve the overall quality of fermented sausage by the addition of Leu and using starter of L. fermentum YZU-06 and S. saprophyticus CGMCC 3475.

The Effect of the Improvement Technology on the Quality of Midu Pork Roll

Midu pork roll (MPR), produced in Midu County, Dali Bai Autonomous Prefecture, Yunnan, China, is a traditional fermented meat product with a long history. This study aims to enhance the physical and flavor profile of MPR by improving its process, fermentation conditions and formulations. There were three different formulations, including traditional craft (control group: C), optimization process of Sichuan spicy flavor formula (Test group 1: T1) and optimization process of halogen flavor formula (Test group 2: T2). Higher moisture content, L*, a* and b* values and lower hardness, chewiness and shear force were observed in T1 and T2 compared to C (p < 0.05). A total of 15 free amino acids were detected throughout the fermentation process, during which the content of umami amino acids, sweet amino acids and bitter amino acids underwent significant changes. A total of 88, 85 and 75 volatile compounds were detected in C, T1 and T2, respectively, in which the relative content of alkanes and ketones in T1 and T2 were higher than those in C (p < 0.05). The process and formulas have improved the color, texture characteristics and tenderness of MPR to a certain extent, meanwhile, they have enhanced the flavor of MPR.

The Effects of Carbon Source and Growth Temperature on the Fatty Acid Profiles of Thermobifida fusca

The aerobic, thermophilic Actinobacterium, Thermobifida fusca has been proposed as an organism to be used for the efficient conversion of plant biomass to fatty acid-derived precursors of biofuels or biorenewable chemicals. Despite the potential of T. fusca to catabolize plant biomass, there is remarkably little data available concerning the natural ability of this organism to produce fatty acids. Therefore, we determined the fatty acids that T. fusca produces when it is grown on different carbon sources (i.e., glucose, cellobiose, cellulose and avicel) and at two different growth temperatures, namely at the optimal growth temperature of 50°C and at a suboptimal temperature of 37°C. These analyses establish that T. fusca produces a combination of linear and branched chain fatty acids (BCFAs), including iso-, anteiso-, and 10-methyl BCFAs that range between 14- and 18-carbons in length. Although different carbon sources and growth temperatures both quantitatively and qualitatively affect the fatty acid profiles produced by T. fusca, growth temperature is the greater modifier of these traits. Additionally, genome scanning enabled the identification of many of the fatty acid biosynthetic genes encoded by T. fusca.

Regulation of microbial metabolism on the formation of characteristic flavor and quality formation in the traditional fish sauce during fermentation: a review

Fish sauce is a special flavored condiment formed by traditional fermentation of low-value fish in coastal areas, which are consumed and produced in many parts of the world, especially in Southeast Asia. In the process of fish sauce fermentation, the diversity of microbial flora and the complex metabolic reactions of microorganisms, especially lipid oxidation, carbohydrate fermentation and protein degradation, are accompanied by the formation of flavor substances. However, the precise reaction of microorganisms during the fersmentation process is difficult to accurately control in modern industrial production, which leads to the loss of traditional characteristic flavors in fermented fish sauces. This paper reviews the manufacturing processes, core microorganisms, metabolic characteristics and flavor formation mechanisms of fermented fish sauces at home and abroad. Various methods have been utilized to analyze and characterize the composition and function of microorganisms. Additionally, the potential safety issues of fermented fish sauces and their health benefits are also reviewed. Furthermore, some future directions and prospects of fermented fish sauces are also reviewed in this paper. By comprehensive understanding of this review, it is expected to address the challenges in the modern production of fish sauce thereby expanding its application in food or diet.

Effect of a rice bran extract-based active packaging, high pressure processing and storage temperature on the volatile compounds of sliced dry-cured high quality (Montanera) Iberian ham

The purpose of this study was to evaluate for the first time the effect of a rice bran extract based-active packaging with antioxidant and antimicrobial activity, high pressure processing (HPP) (600 MPa, 7 min), storage time (1, 90, and 180 days) and temperature (4 vs 20 °C) on the volatile compounds of sliced "Montanera" Iberian ham. The active packaging affected a quarter of the compounds, with a trend similar (although to a greater extent) to the one resulting from the HPP. The active packaging provided no clear advantages or serious drawbacks. The slight effect of the high pressure processing indicates that "Montanera" products might be more resistant to HPP-induced changes than other dry-cured hams. Regarding storage, despite the marked effect of time (30 out of 38 compounds), the temperature only influenced two compounds. This weak effect raises the possibility of storing and distributing this vacuum-packaged sliced product at room temperature.

The relationship between flavor formation, lipid metabolism, and microorganisms in fermented fish products

Traditional fermented fish products are favored due to their unique flavors. The fermentation process of fish is accompanied by the formation of flavor substances through a complex metabolic reaction of microorganisms, especially lipolysis and lipid oxidation. However, it is difficult to precisely control the reaction of microorganisms during the fermentation process in modern industrial production, and fermented fish products have lost their traditional characteristic flavors. The purpose of this review is to summarize the different kinds of fermented fish, core microorganisms in it, and flavor formation mechanisms, providing guidance for industrial cultural starters. Future research on the flavor formation mechanism is necessary to confirm the relationship between flavor formation, lipid metabolism, and microorganisms to ensure stable flavor and safety, and to elucidate the mechanism directly toward industrial application.

Potential genes associated with survival of Acinetobacter baumannii under ciprofloxacin stress

Acinetobacter baumannii is an opportunistic pathogen that has acquired resistance to all available drugs. The rise in multi-drug resistance in A. baumannii has been exacerbated by its ability to tolerate antibiotics due to the persister cells, which are phenotypic variants of normal cells that can survive various stress conditions, resulting in chronicity of infection. In the present study we observed that A. baumannii formed persister cells against lethal concentration of ciprofloxacin in exponential phase. The transcriptome of A. baumannii was analyzed after exposure to high concentration of ciprofloxacin (50X MIC) to determine the possible mechanisms of survival. Transcriptome analysis showed differential expression of 146 genes, of which 101 were up-regulated and 45 were down-regulated under ciprofloxacin stress. Differentially expressed genes that might be important for persistence against ciprofloxacin were involved in DNA repair, phenylacetic acid degradation, leucine catabolism, HicAB toxin-antitoxin system and ROS response (iron-sulfur clusters, hemerythrin-like metal binding and Kdp). recA, umuD and ddrR genes involved in SOS response were also up-regulated. Knockout of umuD showed significant decrease in persister cells formation while they were completely eradicated in recA mutant strain. The differentially expressed genes highlighted in the study merit further investigation as therapeutic targets for effective control of A. baumannii infections.

Contribution of S. xylosus and L. sakei ssp. carnosus Fermentation to the Aroma of Lupin Protein Isolates

Aroma-active compounds of lupin protein isolate and lupin protein isolate fermented with Staphylococcus xylosus and Lactobacillus sakei ssp. carnosus were investigated. The changes in aroma-active compounds were determined by application of aroma extract dilution analysis in combination with gas chromatography-mass spectrometry/olfactometry for identification, and by stable isotope dilution assays for quantification. A total of 30 aroma-active compounds for non-fermented and fermented samples were identified. The aroma profile of LPI fermented with Lactobacillus sakei ssp. carnosus was characterized as roasty and popcorn-like. Staphylococcus xylosus generated cheesy impressions, being in line with the fact that the main aroma compounds acetic acid, butanoic acid, and 2/3-methylbutanoic acid could be identified. Quantification of butanoic acid further confirmed these findings with the highest concentration of 140 mg/kg for LPI fermented with Staphylococcus xylosus. Our study provides insights into how fermentation utilizing different fermentative microbial strains, namely Staphylococcus xylosus and Lactobacillus sakei ssp. carnosus alters the aroma profile of lupin protein isolates. This demonstrates the potential of shaping fermented protein-based foods via targeted microbiological refinement.

Very Long-Chain Branched-Chain Fatty Acids in Chia Seeds: Implications for Human Use

Dairy and fermented foods are common sources of dietary branched-chain fatty acids (BCFA) of chain lengths C13-C18 serving a putative prebiotic role and a component of human integument. Few studies have reported on nonfermented plant-derived BCFA in human diets or cosmetics. A three-ion monitoring method was adapted to confirm branch position of ultratrace (<0.01%, w/w) BCFA. We identified chia as a new source of BCFA with C15-C35 chain lengths. Surprisingly, even-numbered very long-chain BCFA (VLC BCFA), anteiso-22:0, anteiso-24:0, and anteiso-26:0 were unequivocally identified in natural products for the first time. Plant-derived BCFA are predominantly anteiso, in contrast with similar iso and anteiso levels in ruminant and fermented foods. Chia seeds contain 0.4% BCFA, w/w of total fatty acids, or 32 mg BCFA in a food serving, surpassing other plant oils. Topical administration of chia seed oil containing VLC BCFA may have a role in skin and hair functionality.

Casing Contribution to Proteolytic Changes and Biogenic Amines Content in the Production of an Artisanal Naturally Fermented Dry Sausage

The effect of two kinds of casings on the production and characteristics of a dry fermented sausage was investigated. In detail, an Italian product, naturally fermented at low temperatures and normally wrapped in beef casing instead of the most diffused hog one, was selected. Two different productions (one traditionally in beef casing (MCB) and another in hog casing (MCH)) were investigated over time to determine the differences particularly regarding proteolytic changes during fermentation and ripening. First of all, the product in hog casing required a longer ripening time, up to 120 days, instead of 45–50 days, because of the lower drying rate, while the microbial dynamics were not significantly modified. Conversely, the proteolysis showed a different evolution, being more pronounced, together with the biogenic amines content up to 341 mg/Kg instead of 265 mg/Kg for the traditional products. The latter products were instead characterized by higher quantities of total free amino acids, 3-methyl butanoic acid, 3-Methyl-1-butanal, and 2-Methylpropanal, enriching the final taste and aroma. The traditional product MCB also showed lower hardness and chewiness than MCH. The results highlight how the choice of casing has a relevant impact on the development of the final characteristics of fermented sausages.

5-methyl Furfural Reduces the Production of Malodors by Inhibiting Sodium l-lactate Fermentation of Staphylococcus epidermidis: Implication for Deodorants Targeting the Fermenting Skin Microbiome

Staphylococcus epidermidis (S. epidermidis) is a common bacterial colonizer on the surface of human skin. Lactate is a natural constituent of skin. Here, we reveal that S. epidermidis used sodium l-lactate as a carbon source to undergo fermentation and yield malodors detected by gas colorimetric tubes. Several furan compounds such as furfural originating from the fermentation metabolites play a role in the negative feedback regulation of the fermentation process. The 5-methyl furfural (5MF), a furfural analog, was selected as an inhibitor of sodium l-lactate fermentation of S. epidermidis via inhibition of acetolactate synthase (ALS). S. epidermidis treated with 5MF lost its ability to produce malodors, demonstrating the feasibility of using 5MF as an ingredient in deodorants targeting malodor-causing bacteria in the skin microbiome.

Characterization and Transcriptome Studies of Autoinducer Synthase Gene from Multidrug Resistant Acinetobacter baumannii Strain 863

Quorum sensing (QS) is a cell-to-cell communication system that uses autoinducers as signaling molecules to enable inter-species and intra-species interactions in response to external stimuli according to the population density. QS allows bacteria such as Acinetobacter baumannii to react rapidly in response to environmental changes and hence, increase the chances of survival. A. baumannii is one of the causative agents in hospital-acquired infections and the number of cases has increased remarkably in the past decade. In this study, A. baumannii strain 863, a multidrug-resistant pathogen, was found to exhibit QS activity by producing N-acyl homoserine lactone. We identified the autoinducer synthase gene, which we named abaI, by performing whole genome sequencing analysis of A. baumannii strain 863. Using high resolution tandem triple quadrupole mass spectrometry, we reported that abaI of A. baumannii strain 863 produced 3-hydroxy-dodecanoyl-homoserine lactone. A gene deletion mutant was constructed, which confirmed the functionality of abaI. A growth defect was observed in the QS-deficient mutant strain. Transcriptome profiling was performed to determine the possible genes regulated by QS. Four groups of genes that showed differential expression were discovered, namely those involved in carbon source metabolism, energy production, stress response and the translation process.

Optimization of a headspace solid-phase micro-extraction method to quantify volatile compounds in plain sufu, and application of the method in sample discrimination

A rapid headspace solid-phase microextraction method was optimized to detect volatile components in three commercial plain sufu samples. The method was then used to qualify 14 aroma impact components that contribute significantly to the volatile profile in 12 commercial samples produced at three locations and laboratory-scale fermented samples aged for 3, 15, 30, and 90 days. Principal component analysis (PCA) was subsequently used to group the samples. The optimized method identified 148 volatile compounds in three commercial samples, and the concentrations of 14 aroma impact compounds varied significantly among commercial and laboratory samples. PCA confirmed that these samples could be discriminated according to their production location and aging time, thereby rendering this method a simple strategy for sample discrimination.

Microbiota of sliced cooked ham packaged in modified atmosphere throughout the shelf life: Microbiota of sliced cooked ham in MAP

Fourteen lots of cooked ham in modified atmosphere packaging (CH) were analyzed within a few days from packaging (S) and at the end of the shelf-life (E), after storage at 7 °C to simulate thermal abuse. Five more lots, rejected from the market because spoiled (R), were included in the study. Quality of the products was generally compromised during the shelf life, with only 4 lots remaining unaltered. Analysis of 16S rRNA gene amplicons resulted in 801 OTUs. S samples presented a higher diversity than E and R ones. At the beginning of the shelf life, Proteobacteria and Firmicutes dominated the microbiota, with Acinetobacter, Brochothrix, Carnobacterium, Lactobacillus, Prevotella, Pseudomonas, Psychrobacter, Weissella, Vibrio rumoiensis occurring frequently and/or abundantly. E and R samples were dominated by Firmicutes mostly ascribed to Lactobacillales. It is noteworthy the appearance of abundant Leuconostoc, negligible in S samples, in some E and R samples, while in other LAB were outnumbered by V. rumoiensis or Brochothrix thermosphacta. The microbiota of spoiled and R samples could not be clustered on the basis of specific defects (discoloration, presence of slime, sourness, and swollen packages) or supplemented additives. LAB population of S samples, averaging 2.9 log₁₀(cfu/g), increased to 7.7 log₁₀(cfu/g) in the E and R samples. Dominant cultivable LAB belonged to the species Lactobacillus sakei and Leuconostoc carnosum. The same biotypes ascribed to different species where often found in the corresponding S and R samples, and sometime in different batches provided from the same producer, suggesting a recurrent contamination from the plant of production. Consistently with growth of LAB, initial pH (6.26) dropped to 5.74 in E samples. Volatiles organic compound (VOCs) analysis revealed that ethanol was the major metabolite produced during the shelf life. The profile of volatile compounds got enriched with other molecules (e.g. 2-butanone, ethyl acetate, acetic acid, acetoin, butanoic acid, ethyl ester, butanoic acid, and 2,3-butanediol) mainly ascribed to microbial metabolism.

The overexpression of cucumber (Cucumis sativus L.) genes that encode the branched-chain amino acid transferase modulate flowering time in Arabidopsis thaliana

The overexpression of CsBCATs promotes flowering in Arabidopsis by regulating the expression of flowering time genes. The branched-chain amino acid transferases (BCATs) play an important role in the metabolism of branched-chain amino acids (BCAAs), such as isoleucine, leucine, and valine. They function in both the synthesis and the degradation of this class of amino acids. We identified and characterized the three BCAT genes in cucumber (Cucumis sativus L.). The tissue-specific expression profiling in cucumber plants revealed that CsBCAT2 and CsBCAT7 were highly expressed in the reproductive tissues, whereas CsBCAT3 expression was highly detected in the vegetative tissues. The subcellular localization patterns of three CsBCATs were observed in the mitochondria. The functional analyses of CsBCATs showed that CsBCAT2 and CsBCAT3 restored the growth of bat1Δ/bat2Δ double knockout yeast (Saccharomyces cerevisiae), and CsBCAT3 and CsBCAT7 with different substrate preferences acted in a reverse reaction. The transgenic approach demonstrated that the overexpression of the three CsBCATs resulted in early flowering phenotypes, which were associated with the upregulation of FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) in a manner in which they were dependent on GIGANTEA (GI)/CONSTANS (CO) and SHORT VEGETATIVE PHASE (SVP)/FLOWERING LOCUS C (FLC) modules. Our results, which are observed in conjunction, suggest that there is an interconnection between BCAT genes that function in BCAA metabolism and the flowering time in plants.

Understanding the microbial basis of body odor in pre-pubescent children and teenagers

BACKGROUND

Even though human sweat is odorless, bacterial growth and decomposition of specific odor precursors in it is believed to give rise to body odor in humans. While mechanisms of odor generation have been widely studied in adults, little is known for teenagers and pre-pubescent children who have distinct sweat composition from immature apocrine and sebaceous glands, but are arguably more susceptible to the social and psychological impact of malodor.

RESULTS

We integrated information from whole microbiome analysis of multiple skin sites (underarm, neck, and head) and multiple time points (1 h and 8 h after bath), analyzing 180 samples in total to perform the largest metagenome-wide association study to date on malodor. Significant positive correlations were observed between odor intensity and the relative abundance of Staphylococcus hominis, Staphylococcus epidermidis, and Cutibacterium avidum, as well as negative correlation with Acinetobacter schindleri and Cutibacterium species. Metabolic pathway analysis highlighted the association of isovaleric and acetic acid production (sour odor) from enriched S. epidermidis (teen underarm) and S. hominis (child neck) enzymes and sulfur production from Staphylococcus species (teen underarm) with odor intensity, in good agreement with observed odor characteristics in pre-pubescent children and teenagers. Experiments with cultures on human and artificial sweat confirmed the ability of S. hominis and S. epidermidis to independently produce malodor with distinct odor characteristics.

CONCLUSIONS

These results showcase the power of skin metagenomics to study host-microbial co-metabolic interactions, identifying distinct pathways for odor generation from sweat in pre-pubescent children and teenagers and highlighting key enzymatic targets for intervention.

Insight into anaerobic methanotrophy from 13C/12C- amino acids and 14C/12C-ANME cells in seafloor microbial ecology

Oceanic methane from global deep-sea sediment is largely consumed through microbially mediated sulfate-coupled oxidation, resulting in ¹³C-depleted cell biomass of anaerobic methanotrophic archaea (ANME). The general ecological importance of subseafloor ANME has been well recognized in the last two decades. However, the crucial biochemical pathways for the overall anaerobic oxidation of methane (AOM) still remain enigmatic. Here, methanotrophic pathways were analyzed to trace ¹³C-depleted amino acid biosynthesis in two clades of ANME (ANME-1 and ANME-2) from the Black Sea. Compound-specific analysis of ANME-dominated microbial mats showed a significant ¹³C-depletion trend in association with increasing carbon numbers in protein-derived amino acid families (e.g., the pyruvate family in the order of alanine, valine, isoleucine and leucine was down to −114‰). This result indicates a stepwise elongation of ¹³C-depleted carbon during amino acid biosynthesis. The overall results suggest that intracellular protein amino acids and the most ¹³C-depleted signature of leucine, which has a specific branched-chain structure, are potentially propagated as isoprenoid precursor molecules into archaeal biosynthesis, resulting in the extremely ¹³C- and ¹⁴C-depleted nature of ANME cells in the deep microbial oasis.

Species Pervasiveness Within the Group of Coagulase-Negative Staphylococci Associated With Meat Fermentation Is Modulated by pH

During spontaneous meat fermentations, Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus are generally the most prevailing species within the communities of coagulase-negative staphylococci (CNS). There is an interest to introduce CNS isolates from artisan-style spontaneous meat fermentations as starter cultures in more industrialized processes, as to confer additional quality benefits. However, staphylococcal competitiveness within the meat matrix is affected by the processing conditions, which vary considerably among product types. A major factor of variability relates to the intensity of acidification, driven by the concentration of added carbohydrates. The effect of pH on CNS prevalence was studied in both a mince-based meat fermentation model and in fermented sausages produced on pilot scale. Roughly, from all experiments combined, it appeared that a pH of 5.3 corresponded with a breakpoint for CNS selection. Above this value, a general prevalence by S. xylosus was found, even overruling the addition of starter cultures consisting of S. equorum and S. saprophyticus strains. At pH values below 5.3, S. xylosus was also accompanied by S. equorum (following a mild pH drop) and S. saprophyticus (following a stronger pH drop). Still, addition of starter cultures affected the volatile profile compared to the control batch, even if those starter cultures were not able to dominate during the ripening process. This study nonetheless provides a warning for an overly confident use of specific CNS species as starter cultures, especially when in a given processing context the prevailing conditions do not allow superior growth compared to the CNS from the background microbiota.

Nonconventional starter cultures of coagulase-negative staphylococci to produce animal-derived fermented foods, a SWOT analysis

Coagulase-negative staphylococci (CNS) are ubiquitous micro-organisms that are commonly present on animal skin and animal-derived foods. They are members of the beneficial microbial consortia of several fermented food products where they contribute to quality. Currently, only a few CNS species are included in commercial starter cultures, although many other ones with promising properties have been isolated from diverse food ecosystems. In the present study, a Strengths-Weaknesses-Opportunities-Threats (SWOT) analysis of the potential use of unconventional CNS starter cultures for the fermentation of animal-derived foods is carried out. An overview of both their desirable and worrisome metabolic traits is given. In general, the application of innovative CNS-based starter cultures offers opportunities to modulate flavour, improve the safety and health aspects and develop novel colour development strategies for clean label products. Yet, their implementation is often not straightforward as nontrivial obstacles or threats are encountered, which relate to technological, food safety and legal concerns. As most of the desirable and undesirable characteristics of CNS species are strain dependent, a case-by-case evaluation is needed when evaluating specific strains for their potential use as novel starter cultures.

Potential of Lentibacillus sp. NS12IITR for production of lipids with enriched branched-chain fatty acids for improving biodiesel properties along with hydrocarbon co-production

Hypersaline environment is inhabited by array of microbes which have the potential to produce industrially important products. This study explored biomass and lipid production potential of the halophilic bacterium, strain NS12IITR which was isolated from Sambhar Lake, Rajasthan. Sequencing and phylogenetic analysis revealed that the bacterium belonged to genus Lentibacillus. The salient feature of the isolate is its ability to accumulate total cellular lipid up to 18.9 ± 0.45% of dry cell weight. In addition, trans-esterification of extracted lipid yielded 77.6 ± 5.56% of total esters as methyl ester of branched-chain fatty acids (BCFAs). To assess the nature of extracted lipid, lipid sample was fractionated on the silicic acid column, which demonstrated that 49.03 ± 1.35% of the total lipids was neutral in nature. Trans-esterification of the neutral lipid fraction yielded 60.62 ± 4.88% of total esters as methyl ester of BCFAs. Methyl esters of BCFAs were present in trans-esterified products of neutral as well as polar lipid fractions. Furthermore, the isolate produced hydrocarbons both extracellularly (C₁₀-C₃₀) and intra-cellularly (C₁₅-C₂₈). The concentration of extracellular hydrocarbon (21.11 ± 0.78 mg/L) synthesized by strain NS12IITR is in close agreement with the yield reported from other hydrocarbon producing bacteria. This is hereby a first report on the co-production of lipids and hydrocarbon from a halophilic bacterium. The production of neutral lipid with high percentage of BCFAs and co-production of hydrocarbons makes the isolate NS12IITR a potential claimant for biofuel production.

1H HR-MAS NMR spectroscopy to study the metabolome of the protozoan parasite Giardia lamblia

Knowledge of the metabolic profile and exchange processes in the protozoan parasite Giardia lamblia is of importance for a better understanding of the biochemical processes and for the development of drugs to control diseases caused by G. lamblia. In the current paper, ¹H High Resolution Magic Angle Spinning (HR-MAS) NMR spectroscopy was directly applied to G. lamblia trophozoite suspensions to analyze the detectable small metabolites with a minimum of intervention. Thirty-one components were identified with main contributions from amino acids such as alanine and ornithine. The reproducibility, variability, and stability of the metabolites were investigated. Citrulline was found to be formed as an intermediate and citrulline levels depended on the stage of cell growth. Glucose-1-phosphate was found to be formed in relatively high amounts after cell harvesting if enzymes were not inactivated. In addition, the metabolic footprint of Giardia trophozoites, i.e. changes in the culture medium induced by G. lamblia, was investigated by liquid state NMR spectroscopy of culture media before and after inoculation. A quantitative comparison of the NMR spectra revealed component changes in the culture media during growth. The results suggested that not glucose but rather arginine serves as main energy supply. Biochemical functions of intracellular components and their metabolic exchange with the culture medium are discussed. The results provide an important basis for the design of HR-MAS NMR based metabolomic studies of G. lamblia in particular and any protozoan parasite samples in general.

Insight into the Genome of Staphylococcus xylosus, a Ubiquitous Species Well Adapted to Meat Products

Staphylococcus xylosus belongs to the vast group of coagulase-negative staphylococci. It is frequently isolated from meat products, either fermented or salted and dried, and is commonly used as starter cultures in sausage manufacturing. Analysis of the S. xylosus genome together with expression in situ in a meat model revealed that this bacterium is well adapted to meat substrates, being able to use diverse substrates as sources of carbon and energy and different sources of nitrogen. It is well-equipped with genes involved in osmotic, oxidative/nitrosative, and acidic stress responses. It is responsible for the development of the typical colour of cured meat products via its nitrate reductase activity. It contributes to sensorial properties, mainly by the the catabolism of pyruvate and amino acids resulting in odorous compounds and by the limiting of the oxidation of fatty acids, thereby avoiding rancidity.

Genomic, transcriptomic, and proteomic approaches towards understanding the molecular mechanisms of salt tolerance in Frankia strains isolated from Casuarina trees

Background

Soil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using fast growing, nitrogen fixing actinorhizal trees such as the Casuarina. The salt tolerance of Casuarina is enhanced by the nitrogen-fixing symbiosis that they form with the actinobacterium Frankia. Identification and molecular characterization of salt-tolerant Casuarina species and associated Frankia is imperative for the successful utilization of Casuarina trees in saline soil reclamation efforts. In this study, salt-tolerant and salt-sensitive Casuarina associated Frankia strains were identified and comparative genomics, transcriptome profiling, and proteomics were employed to elucidate the molecular mechanisms of salt and osmotic stress tolerance.

Results

Salt-tolerant Frankia strains (CcI6 and Allo2) that could withstand up to 1000 mM NaCl and a salt-sensitive Frankia strain (CcI3) which could withstand only up to 475 mM NaCl were identified. The remaining isolates had intermediate levels of salt tolerance with MIC values ranging from 650 mM to 750 mM. Comparative genomic analysis showed that all of the Frankia isolates from Casuarina belonged to the same species (Frankia casuarinae). Pangenome analysis revealed a high abundance of singletons among all Casuarina isolates. The two salt-tolerant strains contained 153 shared single copy genes (most of which code for hypothetical proteins) that were not found in the salt-sensitive(CcI3) and moderately salt-tolerant (CeD) strains. RNA-seq analysis of one of the two salt-tolerant strains (Frankia sp. strain CcI6) revealed hundreds of genes differentially expressed under salt and/or osmotic stress. Among the 153 genes, 7 and 7 were responsive to salt and osmotic stress, respectively. Proteomic profiling confirmed the transcriptome results and identified 19 and 8 salt and/or osmotic stress-responsive proteins in the salt-tolerant (CcI6) and the salt-sensitive (CcI3) strains, respectively.

Conclusion

Genetic differences between salt-tolerant and salt-sensitive Frankia strains isolated from Casuarina were identified. Transcriptome and proteome profiling of a salt-tolerant strain was used to determine molecular differences correlated with differential salt-tolerance and several candidate genes were identified. Mechanisms involving transcriptional and translational regulation, cell envelop remodeling, and previously uncharacterized proteins appear to be important for salt tolerance. Physiological and mutational analyses will further shed light on the molecular mechanism of salt tolerance in Casuarina associated Frankia isolates.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4056-0) contains supplementary material, which is available to authorized users.

Genetic dissection of metabolite variation in Arabidopsis seeds: evidence for mQTL hotspots and a master regulatory locus of seed metabolism

To gain insight into genetic factors controlling seed metabolic composition and its relationship to major seed properties, an Arabidopsis recombinant inbred line (RIL) population, derived from accessions Col-0 and C24, was studied using an MS-based metabolic profiling approach. Relative intensities of 311 polar primary metabolites were used to identify associated genomic loci and to elucidate their interactions by quantitative trait locus (QTL) mapping. A total of 786 metabolic QTLs (mQTLs) were unequally distributed across the genome, forming several hotspots. For the branched-chain amino acid leucine, mQTLs and candidate genes were elucidated in detail. Correlation studies displayed links between metabolite levels, seed protein content, and seed weight. Principal component analysis revealed a clustering of samples, with PC1 mapping to a region on the short arm of chromosome IV. The overlap of this region with mQTL hotspots indicates the presence of a potential master regulatory locus of seed metabolism. As a result of database queries, a series of candidate regulatory genes, including bZIP10, were identified within this region. Depending on the search conditions, metabolic pathway-derived candidate genes for 40-61% of tested mQTLs could be determined, providing an extensive basis for further identification and characterization of hitherto unknown genes causal for natural variation of Arabidopsis seed metabolism.

The Use of Starter Cultures in Traditional Meat Products

Starter cultures could play an essential role in the manufacture of traditional cured meat products. In order to achieve objectives related to meat products’ quality and safety improvement, the selection of particular strains constituting a starter culture should be carried out in the context of its application, since its functionality will depend on the type of sausage and process conditions. Also, strain selection should comply with particular requirements to warrant safety. The aim of the current review is to update the knowledge on the use of starter cultures in traditional meat products, with focus on dry-fermented products. In this manuscript, we will try to give answers to some relevant questions: Which starter cultures are used and why? Why are LAB used? What are their role and their specific mode of action? Which other groups of microorganisms (bacteria and fungi) are used as starter cultures and how do they act? A particular revision of omics approach regarding starter cultures is made since the use of these techniques allows rapid screening of promising wild strains with desirable functional characteristics, enabling the development of starter cultures better adapted to the meat matrix.

Adaptation of Staphylococcus xylosus to Nutrients and Osmotic Stress in a Salted Meat Model

Staphylococcus xylosus is commonly used as starter culture for meat fermentation. Its technological properties are mainly characterized in vitro, but the molecular mechanisms for its adaptation to meat remain unknown. A global transcriptomic approach was used to determine these mechanisms. S. xylosus modulated the expression of about 40-50% of the total genes during its growth and survival in the meat model. The expression of many genes involved in DNA machinery and cell division, but also in cell lysis, was up-regulated. Considering that the S. xylosus population remained almost stable between 24 and 72 h of incubation, our results suggest a balance between cell division and cell lysis in the meat model. The expression of many genes encoding enzymes involved in glucose and lactate catabolism was up-regulated and revealed that glucose and lactate were used simultaneously. S. xylosus seemed to adapt to anaerobic conditions as revealed by the overexpression of two regulatory systems and several genes encoding cofactors required for respiration. In parallel, genes encoding transport of peptides and peptidases that could furnish amino acids were up-regulated and thus concomitantly a lot of genes involved in amino acid synthesis were down-regulated. Several genes involved in glutamate homeostasis were up-regulated. Finally, S. xylosus responded to the osmotic stress generated by salt added to the meat model by overexpressing genes involved in transport and synthesis of osmoprotectants, and Na(+) and H(+) extrusion.

Amino Acid Metabolism of Thermoanaerobacter Strain AK90: The Role of Electron-Scavenging Systems in End Product Formation

The catabolism of the 20 amino acids by Thermoanaerobacter strain AK90 (KR007667) was investigated under three different conditions: as single amino acids without an electron-scavenging system, in the presence of thiosulfate, and in coculture with a hydrogenotrophic methanogen. The strain degraded only serine without an alternative electron acceptor but degraded 11 amino acids (alanine, cysteine, isoleucine, leucine, lysine, methionine, phenylalanine, serine, threonine, tyrosine, and valine) under both of the electron-scavenging systems investigated. Acetate was the dominant end product from alanine, cysteine, lysine, serine, and threonine under electron-scavenging conditions. The branched-chain amino acids, isoleucine, leucine, and valine, were degraded to their corresponding fatty acids under methanogenic conditions and to a mixture of their corresponding fatty acids and alcohols in the presence of thiosulfate. The partial pressure of hydrogen seems to be of importance for the branched-chain alcohol formation. This was suggested by low but detectable hydrogen concentrations at the end of cultivation on the branched-chain amino acid in the presence of thiosulfate but not when cocultured with the methanogen. A more detailed examination of the role of thiosulfate as an electron acceptor was performed with Thermoanaerobacter ethanolicus (DSM 2246) and Thermoanaerobacter brockii (DSM 1457).

Branched-chain alcohol formation by thermophilic bacteria within the genera of Thermoanaerobacter and Caldanaerobacter

Fifty-six thermophilic strains including members of Caldanaerobacter, Caldicellulosiruptor, Caloramator, Clostridium, Thermoanaerobacter, and Thermoanaerobacterium, were investigated for branched-chain amino acid degradation in the presence of thiosulfate in batch culture. All of the Thermoanaerobacter and Caldanaerobacter strains (24) degraded the branched-chain amino acids (leucine, isoleucine, and valine) to a mixture of their corresponding branched-chain fatty acids and branched-chain alcohols. Only one Caloramator strain degraded the branched-chain amino acids to the corresponding branched-chain fatty acids. The ratio of branched-chain fatty acid production over branched-chain alcohol production for Thermoanaerobacter was 7.15, 6.61, and 11.53 for leucine, isoleucine, and valine, respectively. These values for Caldanaerobacter were 3.49, 4.13, and 7.31, respectively. This indicates that members within Caldanaerobacter produce proportionally more of the alcohols as compared with Thermoanaerobacter. No species within other genera investigated produced branched-chain alcohols from branched-chain amino acids in the presence of thiosulfate.

Amino acid conversions by coagulase-negative staphylococci in a rich medium: Assessment of inter- and intraspecies heterogeneity

The ability of coagulase-negative staphylococci (CNS) to convert amino acids into volatile compounds and biogenic amines was investigated after 24h and 48 h of incubation in a rich medium (brain heart infusion). Volatile compounds were measured with static-headspace gas chromatography and mass spectrometry (SH-GC-MS); biogenic amine measurements were carried out with a newly developed method based on ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS). In total, 56 CNS strains from five different species were used, namely Staphylococcus carnosus, Staphylococcus epidermidis, Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus. With respect to the production of volatile compounds, the leucine-derived 3-methyl butanol was produced over time by most CNS strains, up to 52 μM for S. xylosus W1-1 after 48 h of incubation. The average production by strains of S. xylosus was significantly higher than for strains of S. carnosus, whereas strains of S. epidermidis turned out to be poor producers. Yet, differences between species were blurred to a large degree because of the high strain variability. A few strains also produced 3-methyl butanal on top of the amount that was already present in the medium background, although most CNS led to a decrease of this compound. Concerning biogenic amines, the average total concentrations per species remained below 100 μM after 48 h of incubation. The most abundant variant was 2-phenylethylamine (PEA), especially within S. carnosus (average of 65 μM after 48 h of incubation). Yet, some individual strains were able to produce higher concentrations, as found for the PEA production of 295 μM by S. epidermidis ATCC 12228 after 48 h of incubation. The insights obtained during this study indicate heterogeneity and are of importance in view of both starter culture development and the evaluation of a spontaneously established CNS microbiota in artisan-type meat fermentations.

Functional metagenomic profiling of intestinal microbiome in extreme ageing

Age-related alterations in human gut microbiota composition have been thoroughly described, but a detailed functional description of the intestinal bacterial coding capacity is still missing. In order to elucidate the contribution of the gut metagenome to the complex mosaic of human longevity, we applied shotgun sequencing to total fecal bacterial DNA in a selection of samples belonging to a well-characterized human ageing cohort. The age-related trajectory of the human gut microbiome was characterized by loss of genes for shortchain fatty acid production and an overall decrease in the saccharolytic potential, while proteolytic functions were more abundant than in the intestinal metagenome of younger adults. This altered functional profile was associated with a relevant enrichment in "pathobionts", i.e. opportunistic pro-inflammatory bacteria generally present in the adult gut ecosystem in low numbers. Finally, as a signature for long life we identified 116 microbial genes that significantly correlated with ageing. Collectively, our data emphasize the relationship between intestinal bacteria and human metabolism, by detailing the modifications in the gut microbiota as a consequence of and/or promoter of the physiological changes occurring in the human host upon ageing.

Genome-wide analysis of branched-chain amino acid levels in Arabidopsis seeds

Branched-chain amino acids (BCAAs) are three of the nine essential amino acids in human and animal diets and are important for numerous processes in development and growth. However, seed BCAA levels in major crops are insufficient to meet dietary requirements, making genetic improvement for increased and balanced seed BCAAs an important nutritional target. Addressing this issue requires a better understanding of the genetics underlying seed BCAA content and composition. Here, a genome-wide association study and haplotype analysis for seed BCAA traits in Arabidopsis thaliana revealed a strong association with a chromosomal interval containing two branched-chain amino acid transferases, BCAT1 and BCAT2. Linkage analysis, reverse genetic approaches, and molecular complementation analysis demonstrated that allelic variation at BCAT2 is responsible for the natural variation of seed BCAAs in this interval. Complementation analysis of a bcat2 null mutant with two significantly different alleles from accessions Bayreuth-0 and Shahdara is consistent with BCAT2 contributing to natural variation in BCAA levels, glutamate recycling, and free amino acid homeostasis in seeds in an allele-dependent manner. The seed-specific phenotype of bcat2 null alleles, its strong transcription induction during late seed development, and its subcellular localization to the mitochondria are consistent with a unique, catabolic role for BCAT2 in BCAA metabolism in seeds.

The essentiality of staphylococcal Gcp is independent of its repression of branched-chain amino acids biosynthesis

Our previous studies revealed that the staphylococcal protein Gcp is essential for bacterial growth; however, the essential function of Gcp remains undefined. In this study, we demonstrated that Gcp plays an important role in the modulation of the branched-chain amino acids biosynthesis pathway. Specifically, we identified that the depletion of Gcp dramatically elevated the production of key enzymes that are encoded in the ilv-leu operon and responsible for the biosynthesis of the branched-chain amino acids isoleucine, leucine, and valine (ILV) using proteomic approaches. Using qPCR and promoter-lux reporter fusions, we established that Gcp negatively modulates the transcription of the ilv-leu operon. Gel-shift assays revealed that Gcp lacks the capacity to bind the promoter region of ilv. Moreover, we found that the depletion of Gcp did not influence the transcription level of CodY, a known repressor of the ilv-leu operon, while induced the transcription of CcpA, a known positive regulator of the ilv-leu operon. In addition, the depletion of Gcp decreased the biosynthesis of N⁶-threonylcarbamoyladenosine (t6A). To elucidate whether the essentiality of Gcp is attributable to its negative modulation of ILV biosynthesis, we determined the impact of the ilv-leu operon on the requirement of Gcp for growth, and revealed that the deletion of the ilv-leu operon did not affect the essentiality of Gcp. Taken together, our results indicate that the essentiality of Gcp isn’t attributable to its negative regulation of ILV biosynthesis in S. aureus. These findings provide new insights into the biological function of the staphylococcal Gcp.

The genetic architecture of branched-chain amino acid accumulation in tomato fruits

Previous studies of the genetic architecture of fruit metabolic composition have allowed us to identify four strongly conserved co-ordinate quantitative trait loci (QTL) for the branched-chain amino acids (BCAAs). This study has been extended here to encompass the other 23 enzymes described to be involved in the pathways of BCAA synthesis and degradation. On coarse mapping the chromosomal location of these enzymes, it was possible to define the map position of 24 genes. Of these genes eight co-localized, or mapped close to BCAA QTL including those encoding ketol-acid reductoisomerase (KARI), dihydroxy-acid dehydratase (DHAD), and isopropylmalate dehydratase (IPMD). Quantitative evaluation of the expression levels of these genes revealed that the S. pennellii allele of IPMD demonstrated changes in the expression level of this gene, whereas those of KARI and DHAD were invariant across the genotypes. Whilst the antisense inhibition of IPMD resulted in increased BCAA, the antisense inhibition of neither KARI nor DHAD produced a clear effect in fruit BCAA contents. The results are discussed both with respect to the roles of these specific enzymes within plant amino acid metabolism and within the context of current understanding of the regulation of plant branched-chain amino acid metabolism.

Acid stress-mediated metabolic shift in Lactobacillus sanfranciscensis LSCE1

Lactobacillus sanfranciscensis LSCE1 was selected as a target organism originating from recurrently refreshed sourdough to study the metabolic rerouting associated with the acid stress exposure during sourdough fermentation. In particular, the acid stress induced a metabolic shift toward overproduction of 3-methylbutanoic and 2-methylbutanoic acids accompanied by reduced sugar consumption and primary carbohydrate metabolite production. The fate of labeled leucine, the role of different nutrients and precursors, and the expression of the genes involved in branched-chain amino acid (BCAA) catabolism were evaluated at pH 3.6 and 5.8. The novel application of the program XCMS to the solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) data allowed accurate separation and quantification of 2-methylbutanoic and 3-methylbutanoic acids, generally reported as a cumulative datum. The metabolites coming from BCAA catabolism increased up to seven times under acid stress. The gene expression analysis confirmed that some genes associated with BCAA catabolism were overexpressed under acid conditions. The experiment with labeled leucine showed that 2-methylbutanoic acid originated also from leucine. While the overproduction of 3-methylbutanoic acid under acid stress can be attributed to the need to maintain redox balance, the rationale for the production of 2-methylbutanoic acid from leucine can be found in a newly proposed biosynthesis pathway leading to 2-methylbutanoic acid and 3 mol of ATP per mol of leucine. Leucine catabolism to 3-methylbutanoic and 2-methylbutanoic acids suggests that the switch from sugar to amino acid catabolism supports growth in L. sanfranciscensis in restricted environments such as sourdough characterized by acid stress and recurrent carbon starvation.