Fatty acid production from amino acids and alpha-keto acids by Brevibacterium linens BL2

Recent Advances in Food Waste Transformations into Essential Bioplastic Materials

Lignocellulose is a major biopolymer in plant biomass with a complex structure and composition. It consists of a significant amount of high molecular aromatic compounds, particularly vanillin, syringeal, ferulic acid, and muconic acid, that could be converted into intracellular metabolites such as polyhydroxyalkanoates (PHA) and hydroxybutyrate (PHB), a key component of bioplastic production. Several pre-treatment methods were utilized to release monosaccharides, which are the precursors of the relevant pathway. The consolidated bioprocessing of lignocellulose-capable microbes for biomass depolymerization was discussed in this study. Carbon can be stored in a variety of forms, including PHAs, PHBs, wax esters, and triacylglycerides. From a biotechnology standpoint, these compounds are quite adaptable due to their precursors' utilization of hydrogen energy. This study lays the groundwork for the idea of lignocellulose valorization into value-added products through several significant dominant pathways.

Trends and challenges in the valorization of kitchen waste to polyhydroxyalkanoates

Kitchen waste (KW) is frequently available for free or with a negative cost due to its huge production. It contains a large proportion of organic substances, especially fermentable sugars, which can be used for bioplastic (polyhydroxyalkanoates or PHA) synthesis. Nevertheless, due to the difficulties in processing, various pre-treatments of KW are being investigated to enhance the concentration of simple sugars released during its hydrolysis. The effective use of KW will help in minimizing the issues of its inappropriate disposal. However, the review on KW to bioplastic synthesis is rarely reported in the literature. Hence, this particular review provides a comprehensive summary of the updated research developments in KW valorization and its potency as a feedstock for PHAs synthesis. Additionally, the impacts of KW, its availability, the necessary pre-treatments for the biopolymerization process, as well as the prospects and challenges for industrially generating sustainable PHAs, are critically discussed.

Oral administration of Brevibacterium linens from washed cheese increases the proportions of short-chain fatty acid-producing bacteria and lactobacilli in the gut microbiota of mice

Brevibacterium linens (B. linens) is a dairy microorganism used in the production of washed cheese. However, there has been little research on B. linens, especially regarding its effects in vivo. Herein, we report the morphological characteristics of B. linens, such as its two-phase growth and V- and Y-shaped bodies. We also report that oral administration of B. linens increased the diversity of the gut microbiota and promoted the growth of lactobacilli and short-chain fatty acid-producing bacteria, such as Lachnospiraceae and Muribaculaceae. These findings suggest that the ingestion of B. linens may have beneficial effects in humans and animals.

Monitoring the microbiome for food safety and quality using deep shotgun sequencing

In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix filtering step that improved microbe detection specificity to >99.96% during in silico validation. The pipeline identified 119 microbial genera per HPP sample on average with 65 genera present in all samples. The most abundant of these were Bacteroides, Clostridium, Lactococcus, Aeromonas, and Citrobacter. We also observed shifts in the microbial community corresponding to ingredient composition differences. When comparing culture-based results for Salmonella with total RNA sequencing, we found that Salmonella growth did not correlate with multiple sequence analyses. We conclude that microbiome sequencing is useful to characterize complex food microbial communities, while additional work is required for predicting specific species' viability from total RNA sequencing.

Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat

Background

Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds and red-orange pigments. The objective of the present study was to perform comparative genomic analyses in order to better understand the mechanisms involved in their ability to grow on the cheese surface and the differences between the strains.

Results

The genomes of 23 Brevibacterium strains, including twelve strains isolated from cheeses, were compared for their gene repertoire involved in salt tolerance, iron acquisition, bacteriocin production and the ability to use the energy compounds present in cheeses. All or almost all the genomes encode the enzymes involved in ethanol, acetate, lactate, 4-aminobutyrate and glycerol catabolism, and in the synthesis of the osmoprotectants ectoine, glycine-betaine and trehalose. Most of the genomes contain two contiguous genes encoding extracellular proteases, one of which was previously characterized for its activity on caseins. Genes encoding a secreted triacylglycerol lipase or involved in the catabolism of galactose and D-galactonate or in the synthesis of a hydroxamate-type siderophore are present in part of the genomes. Numerous Fe³⁺/siderophore ABC transport components are present, part of them resulting from horizontal gene transfers. Two cheese-associated strains have also acquired catecholate-type siderophore biosynthesis gene clusters by horizontal gene transfer. Predicted bacteriocin biosynthesis genes are present in most of the strains, and one of the corresponding gene clusters is located in a probable conjugative transposon that was only found in cheese-associated strains.

Conclusions

Brevibacterium strains show differences in their gene repertoire potentially involved in the ability to grow on the cheese surface. Part of these differences can be explained by different phylogenetic positions or by horizontal gene transfer events. Some of the distinguishing features concern biotic interactions with other strains such as the secretion of proteases and triacylglycerol lipases, and competition for iron or bacteriocin production. In the future, it would be interesting to take the properties deduced from genomic analyses into account in order to improve the screening and selection of Brevibacterium strains, and their association with other ripening culture components.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4322-1) contains supplementary material, which is available to authorized users.

Cross-talk between E. coli strains and a human colorectal adenocarcinoma-derived cell line

Although there is great interest in the specific mechanisms of how gut microbiota modulate the biological processes of the human host, the extent of host-microbe interactions and the bacteria-specific metabolic activities for survival in the co-evolved gastrointestinal environment remain unclear. Here, we demonstrate a comprehensive comparison of the host epithelial response induced by either a pathogenic or commensal strain of Escherichia coli using a multi-omics approach. We show that Caco-2 cells incubated with E. coli display an activation of defense response genes associated with oxidative stress. Indeed, in the bacteria co-culture system, the host cells experience an altered environment compared with the germ-free system that includes reduced pH, depletion of major energy substrates, and accumulation of fermentation by-products. Measurement of intracellular Caco-2 cell metabolites revealed a significantly increased lactate concentration, as well as changes in TCA cycle intermediates. Our results will lead to a deeper understanding of acute microbial-host interactions.

S-methyl thioesters are produced from fatty acids and branched-chain amino acids by brevibacteria: focus on L-leucine catabolic pathway and identification of acyl-CoA intermediates

Despite their importance as potent odors that contribute to the aroma of numerous cheeses, S-methyl thioesters formation pathways have not been fully established yet. In a first part of our work, we demonstrated that Brevibacterium antiquum and Brevibacterium aurantiacum could produce S-methyl thioesters using short-chain fatty acids or branched-chain amino acids as precursors. Then, we focused our work on L-leucine catabolism using liquid chromatography tandem mass spectrometry and gas chromatography-mass spectrometry analyses coupled with tracing experiments. For the first time, several acyl-CoAs intermediates of the L-leucine to thioesters conversion pathway were identified. S-methyl thioisovalerate was produced from L-leucine, indicating that this amino acid was initially transaminated. Quite interestingly, data also showed that other S-methyl thioesters, e.g., S-methyl thioacetate or S-methyl thioisobutyrate, were produced from L-leucine. Enzymatic and tracing experiments allowed for postulating catabolic pathways leading to S-methyl thioesters biosynthesis.

Production of branched-chain aroma compounds by Propionibacterium freudenreichii: links with the biosynthesis of membrane fatty acids

AIMS

Short branched-chain fatty acids (BCFAs) are cheese flavour compounds, which result from the conversion of branched-chain amino acids (BCAAs). In Swiss cheese, the production of short BCFAs is mainly performed by Propionibacterium freudenreichii and is strain dependent. Our aim was to investigate the possible links between the biosynthesis of short BCFAs and membrane BCFAs in P. freudenreichii.

METHODS AND RESULTS

Short and membrane BCFAs were analysed by gas chromatography-mass spectrometry. Two strains differing in their capacities to release short BCFAs were selected. Tri-deuterated-labelled leucine was used in both strains as a precursor of short extracellular iso-BCFAs and of membrane iso-BCFAs. The proportions of anteiso : iso BCFAs synthesized varied as function of the BCAAs provided in the growth medium, from 72 : 28 to 100 : 0, with leucine and valine, and with isoleucine as sole BC precursors, respectively. The branching pattern of short BCFAs exactly matched that of membrane BCFAs, whatever the exogenous BCAAs provided.

CONCLUSIONS

The biosynthesis of short BCFAs is closely related to that of membrane BCFAs in P. freudenreichii.

SIGNIFICANCE AND IMPACT OF THE STUDY

The biosynthesis of short BCFAs in P. freudenreichii depends more on the strain than on the presence of exogenous BC precursors.

Carbohydrate starvation causes a metabolically active but nonculturable state in Lactococcus lactis

This study characterized the ability of lactococci to become nonculturable under carbohydrate starvation while maintaining metabolic activity. We determined the changes in physiological parameters and extracellular substrate levels of multiple lactococcal strains under a number of environmental conditions along with whole-genome expression profiles. Three distinct phases were observed, logarithmic growth, sugar exhaustion, and nonculturability. Shortly after carbohydrate starvation, each lactococcal strain lost the ability to form colonies on solid media but maintained an intact cell membrane and metabolic activity for over 3.5 years. ML3, a strain that metabolized lactose rapidly, reached nonculturability within 1 week. Strains that metabolized lactose slowly (SK11) or not at all (IL1403) required 1 to 3 months to become nonculturable. In all cases, the cells contained at least 100 pM of intracellular ATP after 6 months of starvation and remained at that level for the remainder of the study. Aminopeptidase and lipase/esterase activities decreased below detection limits during the nonculturable phase. During sugar exhaustion and entry into nonculturability, serine and methionine were produced, while glutamine and arginine were depleted from the medium. The cells retained the ability to transport amino acids via proton motive force and peptides via ATP-driven translocation. The addition of branched-chain amino acids to the culture medium resulted in increased intracellular ATP levels and new metabolic products, indicating that branched-chain amino acid catabolism resulted in energy and metabolic products to support survival during starvation. Gene expression analysis showed that the genes responsible for sugar metabolism were repressed as the cells entered nonculturability. The genes responsible for cell division were repressed, while autolysis and cell wall metabolism genes were induced neither at starvation nor during nonculturability. Taken together, these observations verify that carbohydrate-starved lactococci attain a nonculturable state wherein sugar metabolism, cell division, and autolysis are repressed, allowing the cells to maintain transcription, metabolic activity, and energy production during a state that produces new metabolites not associated with logarithmic growth.

Identification of the leucine-to-2-methylbutyric acid catabolic pathway of Lactococcus lactis

Nutrient starvation and nonculturability in bacteria lead to changes in metabolism not found during the logarithmic phase. Substrates alternate to those used during growth are metabolized in these physiological states, yielding secondary metabolites. In firmicutes and actinobacteria, amino acid catabolic pathways are induced during starvation and nonculturability. Examination of lactococci showed that the population entered a nonculturable state after carbohydrate depletion and was incapable of growth on solid media; however, the cells gained the ability to produce branched-chain fatty acids from amino acids. Gene expression profiling and in silico pathway analysis coupled with nuclear magnetic resonance spectroscopy were used to delineate the leucine catabolic pathway. Lactococci produced acetic and propionic acid during logarithmic growth and starvation. At the onset of nonculturability, 2-methylbutyric acid was produced via hydroxymethyl-glutaryl-coenzyme A (CoA) and acetyl-CoA, along with ATP and oxidation/reduction precursors. Gene expression profiling and genome sequence analysis showed that lactococci contained redundant genes for branched-chain fatty acid production that were regulated by an unknown mechanism linked to carbon metabolism. This work demonstrated the ability of a firmicute to induce new metabolic capabilities in the nonculturable state for producing energy and intermediates needed for transcription and translation. Phylogenetic analyses showed that homologues of these enzymes and their functional motifs were widespread across the domains of life.