Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase

Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei

Lacticaseibacillus paracasei is an economically important bacterial species, used in the food industry and as a probiotic. Here, we investigate the roles of N6-methyladenine (6mA) modification in L. paracasei using multi-omics and high-throughput chromosome conformation capture (Hi-C) analyses. The distribution of 6mA-modified sites varies across the genomes of 28 strains, and appears to be enriched near genes involved in carbohydrate metabolism. A pglX mutant, defective in 6mA modification, shows transcriptomic alterations but only modest changes in growth and genomic spatial organization.

The Potential of an Inexpensive Plant-Based Medium for Halal and Vegetarian Starter Culture Preparation

The restrictions for halal and vegetarian fermented products apply not only to the food ingredients, but also to the inoculum media. The utilization of a medium for lactic acid bacteria (LAB) leads to some issues from animal-derived proteins sources that may be doubtful for halal and/or vegetarian use. This study aimed to develop a plant-based medium for culturing and maintaining LAB. The result demonstrated that 10 g/L soybean powder in sweet potato extract was suitable for cultivating Lactiplantibacillus plantarum TISTR 2075 with no significant difference (p < 0.05) from MRS (de Man, Rogosa and Sharpe) in the cell number (9.12 log CFU/mL) and specific growth rate (0.04). The feasibility of a plant-based medium to grow and maintain the LAB strains from different origins was evaluated. Compared to MRS, Lpb. plantarum TISTR 2075, Lpb. plantarum MW3, and Lacticaseibacillus casei TISTR 1463 could grow almost as well in a plant-based medium. This medium was also suitable for maintaining the viability of LAB during storage, especially when subjected to slant agar stock culture. It is practical and costs at least 10 times less than MRS. Thus, this study created a low-cost plant-based medium that could be used in laboratories, especially for applications in halal and vegetarian food products.

Gut bacteria reflect the adaptation of Diestrammena japanica (Orthoptera: Rhaphidophoridae) to the cave

The gut microbiota is essential for the nutrition, growth, and adaptation of the host. Diestrammena japanica, a scavenger that provides energy to the cave ecosystem, is a keystone species in the karst cave in China. It inhabits every region of the cave, regardless of the amount of light. However, its morphology is dependent on the intensity of light. Whether the gut bacteria reflect its adaptation to the cave environment remains unknown. In this research, D. japanica was collected from the light region, weak light region, and dark region of three karst caves. The gut bacterial features of these individuals, including composition, diversity, potential metabolism function, and the co-occurrence network of their gut microbiota, were investigated based on 16S rRNA gene deep sequencing assay. The residues of amino acids in the ingluvies were also evaluated. In addition, we explored the contribution of gut bacteria to the cave adaptation of D. japanica from three various light zones. Findings showed that gut bacteria were made up of 245 operational taxonomic units (OTUs) from nine phyla, with Firmicutes being the most common phylum. Although the composition and diversity of the gut bacterial community of D. japanica were not significantly different among the three light regions, bacterial groups may serve different functions for D. japanica in differing light strengths. D. japanica has a lower rate of metabolism in cave habitats than in light regions. We infer that the majority of gut bacteria are likely engaged in nutrition and supplied D. japanica with essential amino acids. In addition, gut bacteria may play a role in adapting D. japanica's body size. Unveiling the features of the gut bacterial community of D. japanica would shed light on exploring the roles of gut bacteria in adapting hosts to karst cave environments.

Macroalgal biomass as a potential resource for lactic acid fermentation

Lactic acid is an essential platform chemical with various applications in the chemicals, food, pharmaceutical, and cosmetic industries. Currently, the demand for lactic acid is driven by the role of lactic acid as the starting material for the production of bioplastic polylactide. Microbial fermentation for lactic acid production is favored due to the production of enantiomerically pure lactic acid required for polylactide synthesis, as opposed to the racemic mixture obtained via chemical synthesis. The utilization of first-generation feedstock for commercial lactic acid production is challenged by feedstock costs and sustainability issues. Macroalgae are photosynthetic benthic aquatic plants that contribute tremendously towards carbon capture with subsequent carbon-rich biomass production. Macroalgae are commercially cultivated to extract hydrocolloids, and recent studies have focused on applying biomass as a fermentation feedstock. This review provides comprehensive information on the design and development of sustainable and cost-effective, algae-based lactic acid production. The central carbon regulation in lactic acid bacteria and the metabolism of seaweed-derived sugars are described. An exhaustive compilation of lactic acid fermentation of macroalgae hydrolysates revealed that lactic acid bacteria can effectively ferment the mixture of sugars present in the hydrolysate with comparable yields. The environmental impacts and economic prospects of macroalgal lactic acid are analyzed. Valorization of the vast amounts of spent macroalgal biomass residue post hydrocolloid extraction in a biorefinery is a viable strategy for cost-effective lactic acid production.

Culture media based on effluent derived from soy protein concentrate production for Lacticaseibacillus paracasei 90 biomass production: statistical optimisation, mineral characterization, and metabolic activities

The waste and by-products of the soybean industry could be an economic source of nutrients to satisfy the high nutritional demands for the cultivation of lactic acid bacteria. The aims of this work were to maximize the biomass production of Lacticaseibacillus paracasei 90 (L90) in three culture media formulated from an effluent derived from soy protein concentrate production and to assess the effects these media have on the enzymatic activity of L90, together with their influence on its fermentation profile in milk. The presence of essential minerals and fermentable carbohydrates (sucrose, raffinose, and stachyose) in the effluent was verified. L90 reached high levels of microbiological counts (∼ 9 log cfu mL^-1) and dry weight (> 1 g L^-1) on the three optimized media. Enzymatic activities (lactate dehydrogenase and β-galactosidase) of L90, and its metabolism of lactose and citric acid, as well as lactic acid and pyruvic acid production in milk, were modified depending on the growth media. The ability of the L90 to produce the key flavour compounds (diacetyl and acetoin) was maintained or improved by growing in the optimized media in comparison with MRS.

Transcriptional and Metabolic Response of Wine-Related Lactiplantibacillus plantarum to Different Conditions of Aeration and Nitrogen Availability

Lactic acid bacteria (LAB) perform the process of malolactic fermentation (MLF) in wine. Availability of oxygen and nitrogen nutrients could influence LAB growth, malolactic activity, and other metabolic pathways, impacting the subsequent wine quality. The impact of these two factors has received limited investigation within LAB, especially on a transcriptome level. The aim of this study was to evaluate metabolic changes in the strain Lactiplantibacillus plantarum IWBT B063, growing in synthetic grape juice medium (GJM) under different oxygen exposure conditions, and with low availability of nitrogen-based nutrients. Next-generation sequencing was used to analyze expression across the transcriptome (RNA-seq), in combination with conventional microbiological and chemical analysis. L. plantarum consumed the malic acid present in all the conditions evaluated, with a slight delay and impaired growth for nitrogen limitation and for anaerobiosis. Comparison of L. plantarum transcriptome during growth in GJM with and without O2 revealed differential expression of 148 functionally annotated genes, which were mostly involved in carbohydrate metabolism, genetic information processing, and signaling and cellular processes. In particular, genes with a protective role against oxidative stress and genes related to amino acid metabolism were differentially expressed. This study confirms the suitability of L. plantarum IWBT B063 to carry out MLF in different environmental conditions due to its potential adaption to the stress conditions tested and provides a better understanding of the genetic background of an industrially relevant strain.

Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria

BACKGROUND

Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq for Le. gelidum, Lc. piscium, and P. oligofermentans at 0 °C, 4 °C, 14 °C, 25 °C, and 28 °C.

RESULTS

We observed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene in all three species. Our results indicated that DEAD-box RNA helicase genes (cshA, cshB) also play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species, indicating that these genes could be part of the cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species. We identified transcription binding site motifs for heat-shock response genes in Le. gelidum and Lc. piscium. Finally, we showed that food spoilage-related genes were upregulated at cold temperatures.

CONCLUSIONS

The results of this study provide new insights on the cold- and heat-shock response of psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as targets for future studies.

Biological synthesis of iron nanoparticles using hydrolysates from a waste-based biorefinery

The purpose of this work was to produce iron nanoparticles (Fe-NP) by microbial pathway from anaerobic bacteria grown in anaerobic fluidized bed reactors (AnFBRs) that constitute a new stage of a waste-based biorefinery. Bioparticles from biological fluidized bed reactors from a biorefinery of organic fraction of municipal solid wastes (that produces hydrolysates rich in reducing sugars) were nanodecorated (embedded nanobioparticle or nanodecorated bioparticle, ENBP) by biological reduction of iron salts. Factors "origin of bioparticles" (either from hydrogenogenic or methanogenic fluidized bed reactor) and "type of iron precursor salt" (iron chloride or iron citrate) were explored. SEM and high-resolution transmission electron microscopy (HRTEM) showed amorphous distribution of nanoparticles (NP) on the bioparticles surface, although small structures that are nanoparticle-like could be seen in the SEM micrographs. Some agglomeration of NPs was confirmed by DLS. Average NP size was lower in general for NP in ENBP-M than ENBP-H according to HRTEM. The factors did not have a significant influence on the specific surface area of NPs, which was high and in the range 490 to 650 m² g^-1. Analysis by EDS displayed consistent iron concentration 60-65% iron in nanoparticles present in ENBP-M (bioparticles previously grown in methanogenic bioreactor), whereas the iron concentration in NPs present in ENBP-H (bioparticles previously grown in hydrogenogenic bioreactor) was more variable in a range from 8.5 to 62%, depending on the iron salt. X-ray diffraction patterns showed the typical peaks for magnetite at 35° (3 1 1), 43° (4 0 0), and 62° (4 0 0); moreover, siderite diffraction pattern was found at 26° (0 1 2), 38° (1 1 0), and 42° (1 1 3). Results of infrared analysis of ENBP in our work were congruent with presence of magnetite and occasionally siderite determined by XRD analysis as well as presence of both Fe⁺² and F⁺³ (and selected satellite signal peaks) observed by XPS. Our results on the ENBPs hold promise for water treatment, since iron NPs are commonly used in wastewater technologies that treat a wide variety of pollutants. Finally, the biological production of ENBP coupled to a biorefinery could become an environmentally friendly platform for nanomaterial biosynthesis as well as an additional source of revenues for a waste-based biorefinery.

Microbiomes in the Context of Refrigerated Raw Meat Spoilage

Meat spoilage is a complicated biological phenomenon taking place over the course of time. Several factors influence it, mainly external factors related to packaging and storage temperature but also internal ones related to contamination diversity and product ingredients. We conducted genomic studies of specific spoilage organisms (SSO) and investigated the spoilage microbiomes providing information about the factors that make a specific organism a competitive SSO, as well as the interactions between certain SSO and the most active species and pathways in packaged raw meat. Our studies showed that spoilage microbiomes are diverse, but certain aspects, such as oxygen content or added marinades, shape this diversity strongly. We have also characterized a new spoilage-associated pathway, i.e., heme-dependent respiration capability, in Leuconostoc gelidum subsp. gasicomitatum. The microbiome studies we conducted explain why this species has become a competitive SSO. It is a fast grower and gains advantage for its growth if oxygen is present in the packages. Since the contamination of psychrotrophic lactic acid bacteria is difficult to avoid in meat manufacture, leuconostocs cause spoilage problems from time to time especially in marinated products or those packaged under high-oxygen–containing atmospheres.

Effects of Dietary Inclusion of Bilberry and Walnut Leaves Powder on the Digestive Performances and Health of Tetra SL Laying Hens

Simple Summary

In poultry, diet composition influences growth performance, egg production, as well as digestion. In this study, the effects of dietary additives obtained from bilberry and walnut leaves powder on the digestive performances of Tetra SL hens were evaluated by histologic and morphometric analyses of the intestinal mucosa as well as by the enzymatic activity measurements of alpha-amylase, invertase, maltase, and trypsin correlated with cecum microbiota.

Abstract

The purpose of this study was to examine the effects of dietary inclusion of two additives at the final concentration of 0.5% bilberry (E1) and 1% walnut (E2) leaves powder in the basal diet on digestive health of hens. A total number of 90 Tetra SL hens were divided into two experimental groups (E1 and E2) and one control group (C) consisting of 30 hens each. After four weeks, 10 hens of each group were sacrificed and tissue samples and intestinal content were taken from the duodenum, jejunum, and cecum in order to perform histological, enzymatic, and microbiota analyses. In groups E1 and E2, the histological analysis showed a significant increase of villus height, resulting probably in increased absorption of nutrients in duodenum and jejunum. A decrease in the specific activity of alpha-amylase and trypsin in E1 and E2 for both duodenum and jejunum compared to the control one was also recorded. In addition, the maltase and invertase specific activity in duodenum increased, a tendency that was kept for maltase but not for invertase in jejunum. The cecal microbiota of E1 and E2 individuals was characterized by an increase of Firmicutes and Lactobacilli and a decrease of Enterobacteriaceae. In conclusion, our results indicate that bilberry and walnut leaves additives in feed may improve the health status of the poultry gastrointestinal tract.

Arginine and Citrulline Catabolic Pathways Encoded by the arc Gene Cluster of Lactobacillus brevis ATCC 367

High concentrations of l-arginine or l-citrulline in the growth medium provided the wine bacterium Lactobacillus brevis with a significant growth advantage. The arginine deiminase pathway (ADI) arc gene cluster of Lactobacillus brevis contains three genes-arcD, arcE1, and arcE2-encoding putative l-arginine/l-ornithine exchangers. Uptake experiments with Lactococcus lactis cells expressing the genes showed that all three transported l-ornithine with affinities in the micromolar range. Similarly, ArcD and ArcE2 transported l-arginine, while ArcE1 transported l-citrulline, an intermediate of the ADI pathway. Chase experiments showed very efficient exchange of l-arginine and l-ornithine by ArcD and ArcE2 and of l-citrulline and l-ornithine by ArcE1. Low affinities (millimolar range) combined with low translocation rates were found for ArcD and ArcE2 with l-citrulline and for ArcE1 with l-arginine. Resting cells of Lactobacillus brevis grown in the presence of l-arginine and l-citrulline rapidly consumed l-arginine and l-citrulline, respectively, while producing ammonia and l-ornithine. About 10% of l-arginine degraded was excreted by the cells as l-citrulline. Degradation of l-arginine and l-citrulline was not subject to carbon catabolite repression by glucose in the medium. At a high medium pH, l-citrulline in the medium was required for induction of the l-citrulline degradation pathway. Pathways are proposed for the catabolic breakdown of l-arginine and l-citrulline that merge at the level of ornithine transcarbamylase in the ADI pathway. l-Arginine uptake is catalyzed by ArcD and/or ArcE2, l-citrulline by ArcE1. l-Citrulline excretion during l-arginine breakdown is proposed to be catalyzed by ArcD and/or ArcE2 through l-arginine/l-citrulline exchange.IMPORTANCELactobacillus brevis, a bacterium isolated from wine, as well as other food environments, expresses a catabolic pathway for the breakdown of l-citrulline in the medium that consists of the l-citrulline/l-ornithine exchanger ArcE1 and part of the catabolic arginine deiminase (ADI) pathway enzymes. The proposed pathways for l-arginine and l-citrulline breakdown provide a mechanism for l-citrulline accumulation in fermented food products that is the precursor of the carcinogen ethyl carbamate.

Food Spoilage-Associated Leuconostoc, Lactococcus, and Lactobacillus Species Display Different Survival Strategies in Response to Competition

Psychrotrophic lactic acid bacteria (LAB) are the prevailing spoilage organisms in packaged cold-stored meat products. Species composition and metabolic activities of such LAB spoilage communities are determined by the nature of the meat product, storage conditions, and interspecies interactions. Our knowledge of system level responses of LAB during such interactions is very limited. To expand it, we studied interactions between three common psychrotrophic spoilage LAB (Leuconostoc gelidum, Lactococcus piscium, and Lactobacillus oligofermentans) by comparing their time course transcriptome profiles obtained during their growth in individual, pairwise, and triple cultures. The study revealed how these LAB employed different strategies to cope with the consequences of interspecies competition. The fastest-growing bacterium, Le. gelidum, attempted to enhance its nutrient-scavenging and growth capabilities in the presence of other LAB through upregulation of carbohydrate catabolic pathways, pyruvate fermentation enzymes, and ribosomal proteins, whereas the slower-growing Lc. piscium and Lb. oligofermentans downregulated these functions. These findings may explain the competitive success and predominance of Le. gelidum in a variety of spoiled foods. Peculiarly, interspecies interactions induced overexpression of prophage genes and restriction modification systems (mechanisms of DNA exchange and protection against it) in Lc. piscium and Lb. oligofermentans but not in Le. gelidum Cocultivation induced also overexpression of the numerous putative adhesins in Lb. oligofermentans These adhesins might contribute to the survival of this slowly growing bacterium in actively growing meat spoilage communities.IMPORTANCE Despite the apparent relevance of LAB for biotechnology and human health, interactions between members of LAB communities are not well known. Knowledge of such interactions is crucial for understanding how these communities function and, consequently, whether there is any possibility to develop new strategies to interfere with their growth and to postpone spoilage of packaged and refrigerated foods. With the help of controlled experiments, detailed regulation events can be observed. This study gives an insight into the system level interactions and the different competition-induced survival strategies related to enhanced uptake and catabolism of carbon sources, overexpression of adhesins and putative bacteriocins, and the induction of exchange of genetic material. Even though this experiment dealt with only three LAB strains in vitro, these findings agreed well with the relative abundance patterns typically reported for these species in natural food microbial communities.

Transcriptome Analysis of the Global Response of Pseudomonas fragi NMC25 to Modified Atmosphere Packaging Stress

Pseudomonas fragi is usually isolated from chilled meats in relation to their spoilage, while many studies have shown that the application of modified atmosphere packaging (MAP) inhibits the spoilage potential of P. fragi. The effects of MAP on P. fragi NMC25 metabolism were determined in the present study by exposing this organism to different air conditions and comparing the resulting transcriptome profiles. We found 559 differentially expressed genes by RNA-seq, and the results revealed that MAP decreases the expression of genes involved in the electron transport chain (nuoAB), resulting in an inhibition of aerobic respiration. Meanwhile, MAP also induced the downregulation of genes responsible for ATP-binding cassette transporters, flagellar and type I fimbrial proteins, and DNA replication and repair, which may further influence nutrient uptake, motility, and growth. In addition, NMC25 cells modified their pathways for energy production, amino acid synthesis, membrane lipid composition, and other metabolic patterns to adapt to MAP. These data show that P. fragi NMC25 survives under MAP but reduces part of its metabolism related to its spoilage ability.