Evolution of lactic acid bacteria in the order Lactobacillales as depicted by analysis of glycolysis and pentose phosphate pathways

Integrated Metabolomics and Metagenomics Unveiled Biomarkers of Antioxidant Potential in Fermented Brewer's Grains

About one-third of the global food supply is wasted. Brewers' spent grain (BSG), being produced in enormous amounts by the brewery industry, possesses an eminence nutritional profile, yet its recycling is often neglected for multiple reasons. We employed integrated metagenomics and metabolomics techniques to assess the effects of enzyme treatments and Lactobacillus fermentation on the antioxidant capacity of BSG. The biotreated BSG revealed improved antioxidant capability, as evidenced by significantly increased (p < 0.05) radical scavenging activity and flavonoid and polyphenol content. Untargeted metabolomics revealed that Lactobacillus fermentation led to the prominent synthesis (p < 0.05) of 15 novel antioxidant peptides, as well as significantly higher (p < 0.05) enrichment of isoflavonoid and phenylpropanoid biosynthesis pathways. The correlation analysis demonstrated that Lactiplantibacillus plantarum exhibited strong correlation (p < 0.05) with aucubin and carbohydrate-active enzymes, namely, glycoside hydrolases 25, glycosyl transferases 5, and carbohydrate esterases 9. The fermented BSG has potential applications in the food industry as a culture medium, a functional food component for human consumption, and a bioactive feed ingredient for animals.

Screening the Protective Agents Able to Improve the Survival of Lactic Acid Bacteria Strains Subjected to Spray Drying Using Several Key Enzymes Responsible for Carbohydrate Utilization

The aim of this study was to identify the most effective protectants for enhancing the viability of specific lactic acid bacteria (LAB) strains (Lactobacillus delbrueckii subsp. bulgaricus CICC 6097, Lactiplantibacillus plantarum CICC 21839, Lactobacillus acidophilus NCFM) by assessing their enzymatic activity when exposed to spray drying (inlet/outlet temperature: 135 °C/90 °C). Firstly, it was found that the live cell counts of the selected LAB cells from the 10% (w/v) recovered skim milk (RSM) group remained above 107 CFU/g after spray drying. Among all the three groups (1% w/v RSM group, 10% w/v RSM group, and control group), the two enzymes pyruvate kinase (PK) and lactate dehydrogenase (LDH) were more sensitive to spray drying than hexokinase (HK) and β-galactosidase (β-GAL). Next, transcriptome data of Lb. acidophilus NCFM showed that 10% (w/v) RSM improved the down-regulated expressions of genes encoding PK (pyk) and LDH (ldh) after spray drying compared to 1% (w/v) RSM. Finally, four composite protectants were created, each consisting of 10% (w/v) RSM plus a different additive-sodium glutamate (CP-A group), sucrose (CP-B group), trehalose (CP-C group), or a combination of sodium glutamate, sucrose, and trehalose (CP-D group)-to encapsulate Lb. acidophilus NCFM. It was observed that the viable counts of strain NCFM (8.56 log CFU/g) and enzymatic activity of PK and LDH in the CP-D group were best preserved compared to the other three groups. Therefore, our study suggested that measuring the LDH and PK activity could be used as a promising tool to screen the effective spray-dried protective agent for LAB cells.

Metabolomics analysis of okara probiotic beverages fermented with Lactobacillus gasseri and Limosilactobacillus fermentum by LC-QTOF-MS/MS

In this study, okara was fermented with probiotic strains Lactobacillus gasseri LAC 343 and Limosilactobacillus fermentum PCC, respectively. Significant increases in cell count (by 2.22 log CFU/mL for LAC and 0.82 log CFU/mL for PCC) and significant decreases in pH (by 1.31 for LAC and 1.03 for PCC) were found in fermented okara slurry. In addition, strain LAC tended to produce amino acids, while strain PCC depleted most amino acids. An untargeted metabolomic-based approach using liquid chromatography coupled with quadrupole time-of-flight mass spectrometry was used to further understand the compositional changes and potential health benefits by identifying bioactive metabolites in fermented okara slurry. We successfully identified various beneficial bioactive compounds including γ-aminobutyric acid, indolelactic acid, d-phenyllactic acid, and p-hydroxyphenyllactic acid which had differences in fold-changes in okara slurry fermented with different strains. Our study indicated the feasibility of using probiotics to ferment okara for novel functional food development.

Citrate metabolism in lactic acid bacteria: is there a beneficial effect for Oenococcus oeni in wine?

Lactic acid bacteria (LAB) are Gram positive bacteria frequently used in the food industry for fermentation, mainly transformation of carbohydrates into lactic acid. In addition, these bacteria also have the capacity to metabolize citrate, an organic acid commonly found in food products. Its fermentation leads to the production of 4-carbon compounds such as diacetyl, resulting in a buttery flavor desired in dairy products. Citrate metabolism is known to have several beneficial effects on LAB physiology. Nevertheless, a controversial effect of citrate has been described on the acid tolerance of the wine bacterium Oenococcus oeni. This observation raises questions about the effect of citrate on the capacity of O. oeni to conduct malolactic fermentation in highly acidic wines. This review aims to summarize the current understanding of citrate metabolism in LAB, with a focus on the wine bacterium O. oeni. Metabolism with the related enzymes is detailed, as are the involved genes organized in cit loci. The known systems of cit locus expression regulation are also described. Finally, the beneficial effects of citrate catabolism on LAB physiology are reported and the negative impact observed in O. oeni is discussed.

Metagenomic Studies Reveal the Evidence of Akkermansia muciniphila and Other Probiotic Bacteria in the Gut of Healthy and Enterocytozoon hepatopenaei (EHP)-Infected Farmed Penaeus vannamei

Penaeus vannamei (whiteleg shrimp) is the most widely cultured shrimp globally. Enterocytozoon hepatopenaei (EHP), a microsporidian parasite, infects P. vannamei and causes severe growth retardation, subsequent production, and economic losses in the shrimp culture. The influence of EHP infection in the shrimp gut microbiota is poorly studied, and this would be an interesting area to investigate since the gut microbiome of shrimp influences a number of key host processes such as digestion and immunity. In this study, a metagenomic approach was followed to compare the overall species richness of the gut microbiota of EHP-infected and healthy P. vannamei. Bacterial genomic DNA from the healthy and EHP-infected gut sample were profiled for the bacterial 16S rRNA gene, targeting the V3-V4 conserved region. Operational taxonomic units (OTUs), an approximation of definitive taxonomic identity, were identified based on the sequence similarity within the sample reads and clustered together using a cut-off of 97% identity using UCLUST. The OTUs were then used for the computation of alpha diversity and beta diversity for each sample. EHP-infected gut sample showed lower bacterial abundance throughout the family, class, order, genus, and species levels when compared to healthy gut sample. This study shows that the shrimp gut microbiota is sensitive and exhibits a high level of plasticity during a microsporidian infection like EHP. Furthermore, Akkermansia muciniphila, a novel probiotic bacterium, has been reported in the shrimp gut for the first time.

Decentralised system for demand-oriented collection of food waste - Assessment of biomethane potential, pathogen development and microbial community structure

Enormous amounts of food waste (FW) are produced worldwide, requiring efficient disposal strategies, both economically and ecologically. Anaerobic digestion to produce biomethane is among the most promising strategies, but requires proper solutions for storage and delivery of the waste material. Here, a decentralized system for demand-oriented FW storage and its practical usability was assessed. FW was stored under batch and fed-batch strategies at 5 °C, 20 °C and 30 °C for 28 days. The results showed that FW can be stored without cooling since bacterially produced lactic acid rapidly stabilized the material and inactivated pathogens. While FW storage worked well under all storage conditions and strategies, 16S analysis revealed a distinct microbiota, which was highly characteristic for each storage temperature. Moreover, FW storage had no negative impact on methane yield and stored FW contained readily degradable substances for demand-oriented biogas production.

Recent advances in modified poly (lactic acid) as tissue engineering materials

As an emerging science, tissue engineering and regenerative medicine focus on developing materials to replace, restore or improve organs or tissues and enhancing the cellular capacity to proliferate, migrate and differentiate into different cell types and specific tissues. Renewable resources have been used to develop new materials, resulting in attempts to produce various environmentally friendly biomaterials. Poly (lactic acid) (PLA) is a biopolymer known to be biodegradable and it is produced from the fermentation of carbohydrates. PLA can be combined with other polymers to produce new biomaterials with suitable physicochemical properties for tissue engineering applications. Here, the advances in modified PLA as tissue engineering materials are discussed in light of its drawbacks, such as biological inertness, low cell adhesion, and low degradation rate, and the efforts conducted to address these challenges toward the design of new enhanced alternative biomaterials.

Complexity of acclimatization substrate affects anaerobic digester microbial community response to organic load shocks

This study elucidated the changes in the short-term response to organic load shocks of the anaerobic digestion (AD) microbiome acclimatized to a simple substrate and a complex substrate. Batch vial reactors were inoculated with AD sludge acclimatized to either a simple (starch and hipolypeptone) or a complex (dog food and starch) substrate, both with carbon-to-nitrogen ratio of 25. Organic loads in the form of an easily degradable substrate mix (starch and hipolypeptone) with concentrations varying from 0 to 5 g VS/L were applied to the reactors. Runs utilizing the inoculum acclimatized to a complex substrate sustained its methane productivity despite the high organic load shocks which the inoculum acclimatized to a simple substrate was unable to handle efficiently. The alpha-diversity of the microbiome decreased with increase in organic load for inoculum acclimatized with a simple substrate but was unaffected for the case of the inoculum acclimatized with a complex substrate. LactobacillalesandCloacimonadales were inferred to be major players in starch degradation pathways for the inoculum acclimatized using a simple substrate as predicted by the bioinformatics package PICRUSt2. However, acclimatizing using a complex substrate did not support their growth and were replaced by Coriobacteriales which provided higher flexibility in terms of the predicted regulated metabolic functions. The predicted functional regulation of Synergistales and Syntrophales increased with acclimatization using a complex substrate which also showed increase in the flexibility of the microbiome towards handling organic load shocks. Acetoclastic pathway was upregulated with increase in organic load regardless of the acclimatization substrate while the hydrogenotrophic pathway was downregulated. Overall, acclimatization using a complex substrate increased the robustness and flexibility of the microbiome towards organic load shocks.

Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism

Energy conservation in microorganisms is classically categorized into respiration and fermentation; however, recent work shows some species can use mixed or alternative bioenergetic strategies. We explored the use of extracellular electron transfer for energy conservation in diverse lactic acid bacteria (LAB), microorganisms that mainly rely on fermentative metabolism and are important in food fermentations. The LAB Lactiplantibacillus plantarum uses extracellular electron transfer to increase its NAD⁺/NADH ratio, generate more ATP through substrate-level phosphorylation, and accumulate biomass more rapidly. This novel, hybrid metabolism is dependent on a type-II NADH dehydrogenase (Ndh2) and conditionally requires a flavin-binding extracellular lipoprotein (PplA) under laboratory conditions. It confers increased fermentation product yield, metabolic flux, and environmental acidification in laboratory media and during kale juice fermentation. The discovery of a single pathway that simultaneously blends features of fermentation and respiration in a primarily fermentative microorganism expands our knowledge of energy conservation and provides immediate biotechnology applications.

Bacteria produce the energy they need to live through two processes, respiration and fermentation. While respiration is often more energetically efficient, many bacteria rely on fermentation as their sole means of energy production. Respiration normally depends on the presence of small soluble molecules, such as oxygen, that can diffuse inside the cell, but some bacteria can use metals or other insoluble compounds found outside the cell to perform ‘extracellular electron transfer’.

Lactic acid bacteria are a large group of bacteria that have several industrial uses and live in many natural environments. These bacteria survive using fermentation, but they also carry a group of genes needed for extracellular electron transfer. It is unclear whether they use these genes for respiration or if they have a different purpose.

Tejedor-Sanz, Stevens et al. used a lactic acid bacterium called Lactiplantibacillus plantarum to study whether and how this group of bacteria use extracellular electron transfer. Analysis of L. plantarum and its effect on its surroundings showed that these bacteria use a hybrid process to produce energy: the cells use aspects of extracellular respiration to increase the yield and efficiency of fermentation. Combining these two approaches may allow L. plantarum to adapt to different environments and grow faster, allowing it to compete against other species.

Tejedor-Sanz, Stevens et al. provide new information on a widespread group of bacteria that are often used in food production and industry. The next step will be to understand how the hybrid system is controlled and how it varies among species. Understanding this process could result in new biotechnologies and foods that are healthier, produce less waste, or have different tastes and textures.

Dimethyl phthalate damages Staphylococcus aureus by changing the cell structure, inducing oxidative stress and inhibiting energy metabolism

Dimethyl phthalate (DMP), used as a plasticizer in industrial products, exists widely in air, water and soil. Staphylococcus aureus is a typical model organism representing Gram-positive bacteria. The molecular mechanisms of DMP toxicology in S. aureus were researched by proteomic and transcriptomic analyses. The results showed that the cell wall, membrane and cell surface characteristics were damaged and the growth was inhibited in S. aureus by DMP. Oxidative stress was induced by DMP in S. aureus. The activities of succinic dehydrogenase (SDH) and ATPase were changed by DMP, which could impact energy metabolism. Based on proteomic and transcriptomic analyses, the oxidative phosphorylation pathway was enhanced and the glycolysis/gluconeogenesis and pentose phosphate pathways were inhibited in S. aureus exposed to DMP. The results of real-time reverse transcription quantitative PCR (RT-qPCR) further confirmed the results of the proteomic and transcriptomic analyses. Lactic acid, pyruvic acid and glucose were reduced by DMP in S. aureus, which suggested that DMP could inhibit energy metabolism. The results indicated that DMP damaged the cell wall and membrane, induced oxidative stress, and inhibited energy metabolism and activation in S. aureus.

Global transcriptomic analysis of functional oligosaccharide metabolism in Pediococcus pentosaceus

Lactic acid bacteria (LAB) are important in food fermentation and may enhance overall host health. Previous studies to explore LAB metabolism mainly focused on the genera Lacticaseibacillus and Lactococcus. Pediococcus pentosaceus, historically recognized as an important food fermentation bacterial strain, can produce bacteriocins and occasionally demonstrated probiotic functionalities. This study thoroughly surveyed the growth kinetic of three P. pentosaceus isolates in various culture formulations, especially in fructooligosaccharide (FOS), xylooligosaccharide (XOS), or konjac mannooligosaccharide (KMOS) conditions. Results showed that P. pentosaceus effectively metabolized KMOS, the culture of which led to 23.6-fold population increase. However, FOS and XOS were less metabolized by P. pentosaceus. On functional oligosaccharide cultures, P. pentosaceus could result in higher population proliferation, more acidified fermentation environment, and higher glycoside hydrolysis activities in the culture. RNA-Seq analysis classified 1572 out of 1708 putative genes as mRNA-coding genes. The dataset also revealed that the three functional oligosaccharides led to extensive global functional gene regulations. Phosphate conservation and utilization efficiency enhancement may serve as a leading transcriptional regulation direction in functional oligosaccharide metabolisms. In summary, these discovered metabolic characteristics could be employed to support future studies. KEY POINTS: • Konjac mannooligosaccharides effectively promoted P. pentosaceus proliferation. • Functional genes were highly regulated in functional oligosaccharide utilization. • Phosphate conservation was an important transcriptional regulation direction.

Symbiotic microbiota may reflect host adaptation by resident to invasive ant species

Exotic invasive species can influence the behavior and ecology of native and resident species, but these changes are often overlooked. Here we hypothesize that the ghost ant, Tapinoma melanocephalum, living in areas that have been invaded by the red imported fire ant, Solenopsis invicta, displays behavioral differences to interspecific competition that are reflected in both its trophic position and symbiotic microbiota. We demonstrate that T. melanocephalum workers from S. invicta invaded areas are less aggressive towards workers of S. invicta than those inhabiting non-invaded areas. Nitrogen isotope analyses reveal that colonies of T. melanocephalum have protein-rich diets in S. invicta invaded areas compared with the carbohydrate-rich diets of colonies living in non-invaded areas. Analysis of microbiota isolated from gut tissue shows that T. melanocephalum workers from S. invicta invaded areas also have different bacterial communities, including a higher abundance of Wolbachia that may play a role in vitamin B provisioning. In contrast, the microbiota of workers of T. melanocephalum from S. invicta-free areas are dominated by bacteria from the orders Bacillales, Lactobacillales and Enterobacteriales that may be involved in sugar metabolism. We further demonstrate experimentally that the composition and structure of the bacterial symbiont communities as well as the prevalence of vitamin B in T. melanocephalum workers from S. invicta invaded and non-invaded areas can be altered if T. melanocephalum workers are supplied with either protein-rich or carbohydrate-rich food. Our results support the hypothesis that bacterial symbiont communities can help hosts by buffering behavioral changes caused by interspecies competition as a consequence of biological invasions.

Insects display a wide range of dependence on symbiotic bacteria for basic functions. Responses by resident species to selective pressures imposed by invasive species, as well as specific underlying mechanisms that give rise to these responses are still poorly understood. Here we investigate the role of the symbiotic bacteria of the ghost ant, Tapinoma melanocephalum, to changes in host behavior associated with interspecies competition in areas invaded by fire ants, Solenopsis invicta. We show that Wolbachia is significantly enriched in workers of T. melanocephalum from S. invicta infested areas, and that these bacteria also increase in abundance in colonies that have been supplied with protein-rich food. Our results suggest that bacterial symbiont communities can play an important role in enabling ants to tolerate changes in behavior and diet as a result of biological invasions.

Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes

Owing to their unique potential to ferment carbohydrates, both homo- and heterofermentative lactic acid bacteria (LAB) are widely used in the food industry. Deciphering the genetic basis that determine the LAB fermentation type, and hence carbohydrate utilization, is paramount to optimize LAB industrial processes. Deep sequencing of 24 LAB species and comparison with 32 publicly available genome sequences provided a comparative data set including five major LAB genera for further analysis. Phylogenomic reconstruction confirmed Leuconostoc and Pediococcus species as independently emerging from the Lactobacillus genus, within one of the three phylogenetic clades identified. These clades partially grouped LABs according to their fermentation types, suggesting that some metabolic capabilities were independently acquired during LAB evolution. In order to apply a genome-wide association study (GWAS) at the multigene family level, utilization of 49 carbohydrates was also profiled for these 56 LAB species. GWAS results indicated that obligately heterofermentative species lack 1-phosphofructokinase, required for d-mannose degradation in the homofermentative pathway. Heterofermentative species were found to often contain the araBAD operon, involved in l-arabinose degradation, which is important for heterofermentation. Taken together, our results provide helpful insights into the genetic determinants of LAB carbohydrate metabolism, and opens for further experimental research, aiming at validating the role of these candidate genes for industrial applications.

Response of Pseudomonas fluorescens to dimethyl phthalate

Dimethyl phthalate (DMP) is a ubiquitous pollutant that is very harmful to organisms due to its mutagenicity, teratogenicity and carcinogenicity. Pseudomonas fluorescens (P. fluorescens) is one of the most important bacteria in the environment. In this study, the response of P. fluorescens to DMP was investigated. It was found that DMP greatly inhibited the growth and glucose utilization of P. fluorescens when the concentration of DMP was ranged from 20 to 40 mg/l. The surface hydrophobicity and membrane permeability of P. fluorescens were also increased by DMP. DMP could lead to the deformations of cell membrane and the mis-opening of membrane channels. RNA-Seq and RT-qPCR results showed that the expression of some genes in P. fluorescens were altered, including the genes involved in energy metabolism, ATP-binding cassette (ABC) transporting and two-component systems. Additionally, the productions of lactic acid and pyruvic acid were reduced and the activity of hexokinase was inhibited in P. fluorescens by DMP. Clearly, the results suggested that DMP contamination could alter the biological function of P. fluorescens in the environment.

Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification

The genus Lactobacillus includes over 200 species that are widely used in fermented food preservation and biotechnology or that are explored for beneficial effects on health. Naming, classifying, and comparing lactobacilli have been challenging due to the high level of phenotypic and genotypic diversity that they display and because of the uncertain degree of relatedness between them and associated genera. The aim of this study was to investigate the feasibility of dividing the genus Lactobacillus into more homogeneous genera/clusters, exploiting genome-based data. The relatedness of 269 species belonging primarily to the families Lactobacillaceae and Leuconostocaceae was investigated through phylogenetic analysis (by the use of ribosomal proteins and housekeeping genes) and the assessment of the average amino acid identity (AAI) and the percentage of conserved proteins (POCP). For each subgeneric group that emerged, conserved signature genes were identified. Both distance-based and sequence-based metrics showed that the Lactobacillus genus was paraphyletic and revealed the presence of 10 methodologically consistent subclades, which were also characterized by a distinct distribution of conserved signature orthologues. We present two ways to reclassify lactobacilli: a conservative division into two subgeneric groups based on the presence/absence of a key carbohydrate utilization gene or a more radical subdivision into 10 groups that satisfy more stringent criteria for genomic relatedness.IMPORTANCE Lactobacilli have significant scientific and economic value, but their extraordinary diversity means that they are not robustly classified. The 10 homogeneous genera/subgeneric entities that we identify here are characterized by uniform patterns of the presence/absence of specific sets of genes which offer potential as discovery tools for understanding differential biological features. Reclassification/subdivision of the genus Lactobacillus into more uniform taxonomic nuclei will also provide accurate molecular markers that will be enabling for regulatory approval applications. Reclassification will facilitate scientific communication related to lactobacilli and prevent misidentification issues, which are still the major cause of mislabeling of probiotic and food products reported worldwide.

Evaluation of the infB and rpsB gene fragments as genetic markers intended for identification and phylogenetic analysis of particular representatives of the order Lactobacillales

Detailed differentiation, classification, and phylogenetic analysis of the order Lactobacillales are performed using molecular techniques that involve the comparison of whole genomes, multilocus sequence analysis, DNA-DNA hybridisation, and 16S rRNA sequencing. Despite the wide application of the latter two techniques, issues associated with them are extensively discussed. Although complete genomic analyses are the most appropriate for phylogenetic studies, they are time-consuming and require high levels of expertise. Many phylogenetic/identification markers have been proposed for enterococci, lactobacilli, streptococci, and lactobacilli. However, none have been established for vagococci and some genera within the order Lactobacillales. The objective of the study was to find novel alternative housekeeping genes for classification, typing, and phylogenetic analysis of selected genera within the order Lactobacillales. We designed primers flanking variable regions of the infB (504 nt) and rpsB (333 nt) genes and amplified and sequenced them in 56 strains of different genera within the order Lactobacillales. Statistical analysis and characteristics of the gene regions suggested that they could be used for taxonomic purposes. Phylogenetic analyses, including assessment of (in)congruence between individual phylogenetic trees indicated the possibility of using the concatenation of the two genes as an alternative tool for the evaluation of phylogeny compared with the 16S rRNA gene representing the standard phylogenetic marker of prokaryotes. Moreover, infB, rpsB regions and their concatenate were phylogenetically consistent with two widely applied alternative genetic markers in taxonomy of particular Lactobacillales genera encoding the 60 kDa chaperonin protein (GroEL-hsp60) and phenylalanyl-tRNA synthetase, alpha subunit (pheS).

Using glycolysis enzyme sequences to inform Lactobacillus phylogeny

The genus Lactobacillus encompasses a diversity of species that occur widely in nature and encode a plethora of metabolic pathways reflecting their adaptation to various ecological niches, including humans, animals, plants and food products. Accordingly, their functional attributes have been exploited industrially and several strains are commonly formulated as probiotics or starter cultures in the food industry. Although divergent evolutionary processes have yielded the acquisition and evolution of specialized functionalities, all Lactobacillus species share a small set of core metabolic properties, including the glycolysis pathway. Thus, the sequences of glycolytic enzymes afford a means to establish phylogenetic groups with the potential to discern species that are too closely related from a 16S rRNA standpoint. Here, we identified and extracted glycolysis enzyme sequences from 52 species, and carried out individual and concatenated phylogenetic analyses. We show that a glycolysis-based phylogenetic tree can robustly segregate lactobacilli into distinct clusters and discern very closely related species. We also compare and contrast evolutionary patterns with genome-wide features and transcriptomic patterns, reflecting genomic drift trends. Overall, results suggest that glycolytic enzymes provide valuable phylogenetic insights and may constitute practical targets for evolutionary studies.

Dietary changes during weaning shape the gut microbiota of red pandas (Ailurus fulgens)

Mammalian herbivores have developed numerous adaptations to utilize their plant-based diets including a modified gastrointestinal tract (GIT) and symbiosis with a GIT microbiota that plays a major role in digestion and the maintenance of host health. The red panda (Ailurus fulgens) is a herbivorous carnivore that lacks the specialized GIT common to other herbivores but still relies on microorganisms for survival on its almost entirely bamboo diet. The GIT microbiota is of further importance in young red pandas, as high cub mortality is problematic and has been attributed to failure to meet nutritional requirements. To gain insight into the establishment of the GIT microbiota of red pandas, we examined microbial communities in two individuals following dietary changes associated with weaning using next-generation 16S rRNA Illumina MiSeq paired-end sequencing of faecal samples. Across all four stages (pre-weaning, during weaning, post-weaning and adult), the GIT microbial community displayed low diversity and was dominated by bacteria in the phylum Firmicutes with lesser contributions from the Proteobacteria. A core community was found consistently across all weaning stages and included species within the taxa Escherichia-Shigella, Streptococcus, Clostridium and an unclassified Clostridiaceae. Analysis of the overall community composition and structure showed that although the GIT microbiota is established early in red pandas, dietary changes during weaning further shape the community and are correlated with the presence of new bacterial species. This work is the first analysis of the GIT microbiota for red panda cubs during weaning and provides a framework for understanding how diet and host microbiota impact the development of these threatened animals.

Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria

Obligate heterofermentative lactic acid bacteria (LAB) are well-known for their beneficial health effects in humans. To delineate the incompletely characterized metabolism that currently limits their exploitation, at systems-level, we developed a genome-scale metabolic model of the representative obligate heterofermenting LAB, Leuconostoc mesenteroides (iLME620). Constraint-based flux analysis was then used to simulate several qualitative and quantitative phenotypes of L. mesenteroides, thereby evaluating the model validity. With established predictive capabilities, we subsequently employed iLME620 to elucidate unique metabolic characteristics of L. mesenteroides, such as the limited ability to utilize amino acids as energy source, and to substantiate the role of malolactic fermentation (MLF) in the reduction of pH-homeostatic burden on F0F1-ATPase. We also reported new hypothesis on the MLF mechanism that could be explained via a substrate channelling-like phenomenon mainly influenced by intracellular redox state rather than the intermediary reactions. Model simulations further revealed possible proton-symporter dependent activity of the energy efficient glucose-phosphotransferase system in obligate heterofermentative LAB. Moreover, integrated transcriptomic analysis allowed us to hypothesize transcriptional regulatory bias affecting the intracellular redox state. The insights gained here about the low ATP-yielding metabolism of L. mesenteroides, dominantly controlled by the cellular redox state, could potentially aid strain design for probiotic and cell factory applications.

Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR

Lactobacilli represent a wide range of bacterial species with several implications for the human host. They play a crucial role in maintaining the ecological equilibrium of different biological niches and are essential for fermented food production and probiotic formulation. Despite the consensus about the ‘health-promoting’ significance of Lactobacillus genus, its genotypic and phenotypic characterization still poses several difficulties. The aim of this study was to assess the integration of different approaches, genotypic (16S rRNA gene sequencing), proteomic (MALDI-TOF MS) and metabolomic (¹H-NMR), for the taxonomic and metabolic characterization of Lactobacillus species. For this purpose we analyzed 40 strains of various origin (intestinal, vaginal, food, probiotics), belonging to different species. The high discriminatory power of MALDI-TOF for species identification was underlined by the excellent agreement with the genotypic analysis. Indeed, MALDI-TOF allowed to correctly identify 39 out of 40 Lactobacillus strains at the species level, with an overall concordance of 97.5%. In the perspective to simplify the MALDI TOF sample preparation, especially for routine practice, we demonstrated the perfect agreement of the colony-picking from agar plates with the protein extraction protocol. ¹H-NMR analysis, applied to both culture supernatants and bacterial lysates, identified a panel of metabolites whose variations in concentration were associated with the taxonomy, but also revealed a high intra-species variability that did not allow a species-level identification. Therefore, despite not suitable for mere taxonomic purposes, metabolomics can be useful to correlate particular biological activities with taxonomy and to understand the mechanisms related to the antimicrobial effect shown by some Lactobacillus species.

Effects of octahedral molecular sieve on treatment performance, microbial metabolism, and microbial community in expanded granular sludge bed reactor

This study evaluated the effects of synthesized octahedral molecular sieve (OMS-2) nanoparticles on the anaerobic microbial community in a model digester, expanded granular sludge bed (EGSB) reactor. The addition of OMS-2 (0.025 g/L) in the EGSB reactors resulted in an enhanced operational performance, i.e., COD removal and biogas production increased by 4% and 11% respectively, and effluent volatile fatty acid (VFA) decreased by 11% relative to the control group. The Biolog EcoPlate™ test was employed to investigate microbial metabolism in the EGSB reactors. Results showed that OMS-2 not only increased the microbial metabolic level but also significantly changed the community level physiological profiling of the microorganisms. The Illumina MiSeq high-throughput sequencing of 16S rRNA gene indicated OMS-2 enhanced the microbial diversity and altered the community structure. The largest bacterial genus Lactococcus, a lactic acid bacterium, reduced from 29.3% to 20.4% by abundance in the presence of 0.25 g/L OMS-2, which may be conducive to decreasing the VFA production and increasing the microbial diversity. OMS-2 also increased the quantities of acetogenic bacteria and Archaea, and promoted the acetogenesis and methanogenesis. The X-ray photoelectron spectroscopy illustrated that Mn(IV)/Mn(III) with high redox potential in OMS-2 were reduced to Mn(II) in the EGSB reactors; this in turn affected the microbial community.

End-product inhibition and acidification limit biowaste fermentation efficiency

Converting waste to resource may mitigate environmental pollution and global resource limitation. The platform chemical lactic acid can be produced from biowaste and its liquid fraction after solid-liquid separation. A fermentation step for lactic acid production prior to the conversion of biowaste to methane and organic fertilizer would increase the biowaste's value. Despite the huge potential and promising results of the treatment procedure, the reasons for efficiency loss observed previously need to be addressed in order to pave the way for an up-scaling of the fermentation process. Therefore, biowaste was fermented applying pH control, acid extraction and glucose addition in order to counteract reasons such as acidification, end-product inhibition and carbon limitation, respectively. The fermentation was competitive compared to other renewable lactic acid production substrates and reached a maximum productivity of >5 g Clactic acidg(-1)Ch(-1) and a concentration exceeding 30 g L(-1). A combination of acidification and end-product inhibition was identified as major obstacle. Lactobacillus crispatus and its closest relatives were identified as key lactic acid producers within the process using Miseq Illumina sequencing.

Characterizing Diversity of Lactobacilli Associated with Severe Early Childhood Caries: A Study Protocol

Lactobacilli have been consistently associated with dental caries for decades; however, knowledge of this group of bacteria in the etiology of the disease is limited to quantitative elucidation. Nowadays, explicit identification of oral Lactobacillus species is possible, despite their taxonomic complexity. Here we describe a combined approach involving both cultivation and genetic methods to ascertain and characterize the diversity and abundance of the Lactobacillus population in the oral cavities of children with severe early childhood caries (S-ECC). Eighty 3- to 6-year-old children (40 S-ECC and 40 caries free) who were seeking dental care at the Pediatric Dental Clinic of Bellevue Hospital in New York City were invited to participate in this study. Clinical data on socio-demographic information and oral health behavior were obtained from the primary caregiver. The data included a detailed dental examination, children's medical history, and a questionnaire survey. Combined non-stimulated saliva and supra-gingival plaque samples were collected from each child and cultivated on selective media for quantitative measures of lactobacilli levels. The procedure for Lactobacillus species screening will include the random selection of 50 colonies per plate, extraction of DNA from each colony, and genotyping by arbitrarily primed polymerase chain reaction (AP-PCR). Each unique Lactobacillus AP-PCR genotype will be selected for taxonomic assessment by 16S rRNA gene sequencing analysis. Lactobacillus species will be identified by comparing the 16S rRNA sequences with the Ribosomal Database and the Human Oral Microbiome Database. Meanwhile, the same set of clinical samples will be independently subjected to genomic DNA isolation, 16S rRNA amplification with Lactobacillus genus-specific primers, sequencing, and taxonomic identification, both at genus and species levels with a customized pipeline. The distribution and phylogenetic differences of these Lactobacillus species will be compared between children with or without S-ECC. One of the main objectives of this study is to establish a study protocol for the identification and characterization of lactobacilli in the oral cavity. Future caries risk assessments can include lactobacilli counts (quantitative) and the presence/absence of specific cariogenic genetic signatures of a Lactobacillus species (qualitative) associated with S-ECC.

The domestication of the probiotic bacterium Lactobacillus acidophilus

Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population.

Timely approaches to identify probiotic species of the genus Lactobacillus

Over the past decades the use of probiotics in food has increased largely due to the manufacturer’s interest in placing “healthy” food on the market based on the consumer’s ambitions to live healthy. Due to this trend, health benefits of products containing probiotic strains such as lactobacilli are promoted and probiotic strains have been established in many different products with their numbers increasing steadily. Probiotics are used as starter cultures in dairy products such as cheese or yoghurts and in addition they are also utilized in non-dairy products such as fermented vegetables, fermented meat and pharmaceuticals, thereby, covering a large variety of products.

To assure quality management, several pheno-, physico- and genotyping methods have been established to unambiguously identify probiotic lactobacilli. These methods are often specific enough to identify the probiotic strains at genus and species levels. However, the probiotic ability is often strain dependent and it is impossible to distinguish strains by basic microbiological methods.

Therefore, this review aims to critically summarize and evaluate conventional identification methods for the genus Lactobacillus, complemented by techniques that are currently being developed.