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G3 (Bethesda, Md.) Dec 2022Lactobacillaceae are an important family of lactic acid bacteria that play key roles in the gut microbiome of many animal species. In the honey bee (Apis mellifera) gut...
Lactobacillaceae are an important family of lactic acid bacteria that play key roles in the gut microbiome of many animal species. In the honey bee (Apis mellifera) gut microbiome, many species of Lactobacillaceae are found, and there is functionally important strain-level variation in the bacteria. In this study, we completed whole-genome sequencing of 3 unique Lactobacillaceae isolates collected from hives in Virginia, USA. Using 107 genomes of known bee-associated Lactobacillaceae and Limosilactobacillus reuteri as an outgroup, the phylogenetics of the 3 isolates was assessed, and these isolates were identified as novel strains of Apilactobacillus kunkeei, Lactobacillus kullabergensis, and Bombilactobacillus mellis. Genome rearrangements, conserved orthologous genes (COG) categories and potential prophage regions were identified across the 3 novel strains. The new A. kunkeei strain was enriched in genes related to replication, recombination and repair, the L. kullabergensis strain was enriched for carbohydrate transport, and the B. mellis strain was enriched in transcription or transcriptional regulation and in some genes with unknown functions. Prophage regions were identified in the A. kunkeei and L. kullabergensis isolates. These new bee-associated strains add to our growing knowledge of the honey bee gut microbiome, and to Lactobacillaceae genomics more broadly.
Topics: Bees; Animals; United States; Lactobacillaceae; Gastrointestinal Microbiome; Bacteria; Phylogeny; Genomics
PubMed: 36331337
DOI: 10.1093/g3journal/jkac286 -
Microbial Genomics Jul 2022The genus (formerly ) contains multiple species considered to be adapted to vertebrates, yet their genomic diversity has not been explored. In this study, we performed...
The genus (formerly ) contains multiple species considered to be adapted to vertebrates, yet their genomic diversity has not been explored. In this study, we performed comparative genomic analysis of (22 species; 332 genomes) isolated from different niches, further focusing on human strains (11 species; 74 genomes) and their adaptation features to specific body sites. Phylogenomic analysis of showed misidentification of some strains deposited in public databases and existence of putative novel species. The pangenome analysis revealed a remarkable genomic diversity (only 1.3 % of gene clusters are shared), and we did not observe a strong association of the accessory genome with different niches. The pangenome of and was open, suggesting that acquisition of genes is still occurring. Although most were predicted as antibiotic susceptible (83%), acquired antibiotic-resistance genes were common in from food-producing animals. Genes related to lactic acid isoform production (>95 %) and putative bacteriocins (70.2%) were identified in most strains, while prophages (55.4%) and CRISPR-Cas systems (32.0%) were less prevalent. Among strains from human sources, several metabolic pathways were predicted as conserved and completed. Their accessory genome was highly variable and did not cluster according to different human body sites, with some exceptions (urogenital , , and or gastrointestinal ). Moreover, we identified 12 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues that were significantly enriched in strains from particular body sites. We concluded that evolution of the highly diverse is complex and not always related to niche or human body site origin.
Topics: Genome; Genomics; Lactobacillaceae
PubMed: 35838756
DOI: 10.1099/mgen.0.000847 -
Microbial Biotechnology Jan 2024Lactobacilli are ubiquitous in nature and symbiotically provide health benefits for countless organisms including humans, animals and plants. They are vital for the... (Review)
Review
Lactobacilli are ubiquitous in nature and symbiotically provide health benefits for countless organisms including humans, animals and plants. They are vital for the fermented food industry and are being extensively explored for healthcare applications. For all these reasons, there is considerable interest in enhancing and controlling their capabilities through the engineering of genetic modules and circuits. One of the most robust and reliable microbial chassis for these synthetic biology applications is the widely used Lactiplantibacillus plantarum species. However, the genetic toolkit needed to advance its applicability remains poorly equipped. This mini-review highlights the genetic parts that have been discovered to achieve food-grade recombinant protein production and speculates on lessons learned from these studies for L. plantarum engineering. Furthermore, strategies to identify, create and optimize genetic parts for real-time regulation of gene expression and enhancement of biosafety are also suggested.
Topics: Animals; Humans; Food; Gene Regulatory Networks; Synthetic Biology; Lactobacillaceae
PubMed: 37638848
DOI: 10.1111/1751-7915.14335 -
PloS One 2012The analysis of collections of lactic acid bacteria (LAB) from traditional fermented plant foods in tropical countries may enable the detection of LAB with interesting...
The analysis of collections of lactic acid bacteria (LAB) from traditional fermented plant foods in tropical countries may enable the detection of LAB with interesting properties. Binding capacity is often the main criterion used to investigate the probiotic characteristics of bacteria. In this study, we focused on a collection of 163 Lactobacillaceace comprising 156 bacteria isolated from traditional amylaceous fermented foods and seven strains taken from a collection and used as controls. The collection had a series of analyses to assess binding potential for the selection of new probiotic candidates. The presence/absence of 14 genes involved in binding to the gastrointestinal tract was assessed. This enabled the detection of all the housekeeping genes (ef-Tu, eno, gap, groEl and srtA) in the entire collection, of some of the other genes (apf, cnb, fpbA, mapA, mub) in 86% to 100% of LAB, and of the other genes (cbsA, gtf, msa, slpA) in 0% to 8% of LAB. Most of the bacteria isolated from traditional fermented foods exhibited a genetic profile favorable for their binding to the gastrointestinal tract. We selected 30 strains with different genetic profiles to test their binding ability to non-mucus (HT29) and mucus secreting (HT29-MTX) cell lines as well as their ability to degrade mucus. Assays on both lines revealed high variability in binding properties among the LAB, depending on the cell model used. Finally, we investigated if their binding ability was linked to tighter cross-talk between bacteria and eukaryotic cells by measuring the expression of bacterial genes and of the eukaryotic MUC2 gene. Results showed that wild LAB from tropical amylaceous fermented food had a much higher binding capacity than the two LAB currently known to be probiotics. However their adhesion was not linked to any particular genetic equipment.
Topics: Bacterial Adhesion; Gene Expression Regulation, Bacterial; Genome, Bacterial; HT29 Cells; Humans; Intestinal Mucosa; Lactobacillaceae; Mucin-2; Mucins
PubMed: 22675431
DOI: 10.1371/journal.pone.0038034 -
Journal of Dairy Science Dec 2023β-galactosidase (enzymatic class 3.2.1.23) is one of the dairy industry's most important and widely used enzymes. The enzyme is part of a large family known to catalyze... (Review)
Review
β-galactosidase (enzymatic class 3.2.1.23) is one of the dairy industry's most important and widely used enzymes. The enzyme is part of a large family known to catalyze hydrolysis and transglycosylation reactions. Its hydrolytic activity is commonly used to decrease lactose content in dairy products, while its transglycosylase activity has recently been used to synthesize galacto-oligosaccharides (GOS). During the past couple of years, researchers have focused on studying β-galactosidase isolated and purified from lactic acid bacteria. This review will focus on β-galactosidase purified and characterized from what used to be the Lactobacillus genera. Furthermore, particular emphasis is given to its kinetics, biochemical characteristics, GOS production, market, and utilization by Lactobacilllaceae species.
Topics: Animals; Lactobacillaceae; Oligosaccharides; Lactose; Catalysis; beta-Galactosidase; Galactose
PubMed: 37678769
DOI: 10.3168/jds.2023-23392 -
Microbial Biotechnology Jun 2023The S-layer or surface layer protein (SLP) is the most ancient biological envelope, highly conserved in several Bacteria and Archaea. In lactic acid bacteria (LAB), SLP...
The S-layer or surface layer protein (SLP) is the most ancient biological envelope, highly conserved in several Bacteria and Archaea. In lactic acid bacteria (LAB), SLP is only found in species belonging to the Lactobacillaceae family, many of them considered probiotic microorganisms. New reclassification of members within the Lactobacillaceae family (International Journal of Systematic and Evolutionary Microbiology, 2020, 70, 2782) and newly sequenced genomes demands an updated revision on SLP genes and domain organization. There is growing information concerning SLP occurrence, molecular biology, biophysical properties, and applications. Here, we focus on the prediction of slp genes within the Lactobacillaceae family, and specifically, on the neat interconnection between the two different modular SLP domain organizations and the new reclassified genera. We summarize the results in a concise tabulated manner to review the present knowledge on SLPs and discuss the most relevant and updated concepts regarding SLP sequence clustering. Our assessment is based on sequence alignments considering the new genera classification and protein domain definition with post-translational modifications. We analyse the difficulties encountered to resolve the SLPs 3D structure, describing the need for structure prediction approaches and the relation between protein structure and its anchorage mechanism to the cell wall. Finally, we enumerate new SLP applications regarding heterologous display, pathogen exclusion, immunostimulation, and metal binding.
Topics: Bacterial Proteins; Membrane Glycoproteins; Membrane Proteins; Lactobacillaceae
PubMed: 36752119
DOI: 10.1111/1751-7915.14230 -
Gut Microbes Jul 2017The existence of an implicit living microscopic world, composed primarily of bacteria, has been known for centuries. The exact mechanisms that govern the contribution of... (Review)
Review
The existence of an implicit living microscopic world, composed primarily of bacteria, has been known for centuries. The exact mechanisms that govern the contribution of bacteria to human health and disease have only recently become the subject of intense research efforts. Within this very evident shift in paradigms, the rational design of probiotic formulations has led to the creation of an industry that seeks to progress the engineering of probiotic bacteria that produce metabolites that may enhance human host health and prevent disease. The promotion of probiotics is often made in the absence of quality scientific and clinically plausible data. The latest incursions into the probiotic market of claims have posited the amelioration of oxidative stress via potent antioxidant attributes or limiting the administration of probiotics to those species that do not produce D-Lactic acid (i.e., claims that D-Lactic acid acidosis is linked to chronic health conditions) or are strain-specific (shaping an industry point of difference) for appraising a therapeutic effect. Evidence-based research should guide clinical practice, as there is no place in science and medicine that supports unsubstantiated claims. Extravagant industry based notions continue to fuel the imprimatur of distrust and skepticism that is leveled by scientists and clinicians at an industry that is already rife with scientific and medical distrust and questionable views on probiotics. Ignoring scientifically discordant data, when sorting through research innovations and false leads relevant to the actions of probiotics, drives researcher discomfit and keeps the bar low, impeding the progress of knowledge. Biologically plausible posits are obligatory in any research effort; companies formulating probiotics often exhibit a lack of analytical understanding that then fuels questionable investigations failing to build on research capacity.
Topics: Acidosis, Lactic; Animals; Humans; Lactobacillaceae; Oxidative Stress; Probiotics; Species Specificity
PubMed: 28080206
DOI: 10.1080/19490976.2017.1279379 -
BioMed Research International 2018One of the most promising areas of development in the human nutritional field over the last two decades has been the use of probiotics and recognition of their role in... (Review)
Review
One of the most promising areas of development in the human nutritional field over the last two decades has been the use of probiotics and recognition of their role in human health and disease. Lactic acid-producing bacteria are the most commonly used probiotics in foods. It is well known that probiotics have a number of beneficial health effects in humans and animals. They play an important role in the protection of the host against harmful microorganisms and also strengthen the immune system. Some probiotics have also been found to improve feed digestibility and reduce metabolic disorders. They must be safe, acid and bile tolerant, and able to adhere and colonize the intestinal tract. The means by which probiotic bacteria elicit their health effects are not understood fully, but may include competitive exclusion of enteric pathogens, neutralization of dietary carcinogens, production of antimicrobial metabolites, and modulation of mucosal and systemic immune function. So far, lactic acid bacteria isolated only from the human gastrointestinal tract are recommended by the Food and Agriculture Organization (FAO) and World Health Organization (WHO) for use as probiotics by humans. However, more and more studies suggest that strains considered to be probiotics could be isolated from fermented products of animal origin, as well as from non-dairy fermented products. Traditional fermented products are a rich source of microorganisms, some of which may exhibit probiotic properties. They conform to the FAO/WHO recommendation, with one exception; they have not been isolated from human gastrointestinal tract. In light of extensive new scientific evidence, should the possibility of changing the current FAO/WHO requirements for the definition of probiotic bacteria be considered?
Topics: Animals; Gastrointestinal Tract; Humans; Immunity, Mucosal; Lactobacillaceae; Probiotics
PubMed: 30402482
DOI: 10.1155/2018/5063185 -
The Journal of Nutrition Jul 2019A link between high-fat diet consumption and obesity-related diseases is the disruption of the gut bacterial population, which promotes local and systemic inflammation....
BACKGROUND
A link between high-fat diet consumption and obesity-related diseases is the disruption of the gut bacterial population, which promotes local and systemic inflammation. Wheat germ (WG) is rich in bioactive components with antioxidant and anti-inflammatory properties.
OBJECTIVE
The aim of this study was to investigate the effects of WG supplementation in modulating the gut bacterial population and local and systemic inflammatory markers of mice fed a high-fat, high-sucrose (HFS) diet.
METHODS
Six-week-old male C57BL/6 mice were randomly assigned to 4 groups (n = 12/group) and fed a control (C; 10% kcal fat, 10% kcal sucrose) or HFS (60% kcal fat, 20% kcal sucrose) diet with or without 10% WG (wt:wt) for 12 wk. Cecal bacteria was assessed via 16S rDNA sequencing, fecal short-chain fatty acids by GC, small intestinal CD4+ lymphocytes using flow cytometry, and gut antimicrobial peptide genes and inflammatory markers by quantitative polymerase chain reaction. Statistical analyses included Kruskal-Wallis/Dunn's test and 2-factor ANOVA using HFS and WG as factors.
RESULTS
There was a 4-fold increase (P = 0.007) in the beneficial bacterial family, Lactobacillaceae, in the HFS + WG compared with the HFS group. Fecal propionic and n-butyric acids were elevated at least 2-fold in C + WG compared with the other groups (P < 0.0001). WG tended to increase (≥7%; P-trend = 0.12) small intestinal regulatory T cell:Th17 ratio, indicating a potential to induce an anti-inflammatory gut environment. WG elevated (≥35%) ileal gene expression of the anti-inflammatory cytokine Il10 compared to the unsupplemented groups (P = 0.038). Ileal gene expression of the antimicrobial peptides Reg3b and Reg3g was upregulated (≥95%) in the HFS + WG compared with other groups (P ≤ 0.040). WG reduced serum concentrations of the pro-inflammatory cytokines, interleukin (IL)-1B, IL-6, interferon-γ, and tumor necrosis factor-α (≥17%; P ≤ 0.012).
CONCLUSIONS
WG selectively increased gut Lactobacillaceae, upregulated ileal antimicrobial peptides, and attenuated circulating pro-inflammatory cytokines of C57BL/6 mice fed a HFS diet. These changes may be vital in preventing HFS diet-induced comorbidities.
Topics: Animals; Anti-Inflammatory Agents; Antioxidants; Diet, High-Fat; Dietary Sucrose; Dietary Supplements; Fatty Acids, Volatile; Gastrointestinal Microbiome; Inflammation Mediators; Interleukin-10; Lactobacillaceae; Male; Mice; Mice, Inbred C57BL; Triticum
PubMed: 31162575
DOI: 10.1093/jn/nxz061 -
Gut Microbes 2022The are an intensively studied family of bacteria widely used in fermented food and probiotics, and many are native to the gut and vaginal microbiota of humans and...
The are an intensively studied family of bacteria widely used in fermented food and probiotics, and many are native to the gut and vaginal microbiota of humans and other animals. Various studies have shown that specific species produce metabolites that can inhibit the colonization of fungal and bacterial pathogens, but less is known about how affect individual bacterial species in the endogenous animal microbiota. Here, we show that numerous species inhibit the growth of the family and the S24-7 group, two dominant clades of bacteria within the gut. We demonstrate that inhibitory activity is a property common to homofermentative species, but not to species that use heterofermentative metabolism. We observe that homofermentative species robustly acidify their environment, and that acidification alone is sufficient to inhibit growth of and S24-7 growth, but not related species from the or orders. This study represents one of the first in-depth explorations of the dynamic between species and commensal intestinal bacteria, and contributes valuable insight toward deconvoluting their interactions within the gut microbial ecosystem.
Topics: Animals; Bacteria; Clostridiales; Female; Gastrointestinal Microbiome; Lactobacillaceae; Lactobacillus; Microbiota
PubMed: 35266847
DOI: 10.1080/19490976.2022.2046452