Molecular characterization of hsp20, encoding a small heat shock protein of bifidobacterium breve UCC2003

Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules

Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3358 orthologous clusters, including 1775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.

Adaptive response of the holdase chaperone network of Acidithiobacillus ferrooxidans ATCC 23270 to stresses and energy sources

Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophilic bacterium belonging to microbial communities involved in sulfide ore bioleaching. This microorganism possesses redundancy of genes encoding ATP-independent chaperone holdases like Hsp20 (hps20.1, hsp20.2, and hsp20.3), Hsp31, Hsp33, RidA (ridA.1 and ridA.2), and Lon (lon.1, lon.2, and lon.3), and single copy genes encoding SlyD and CnoX. We evaluated the response of these holdases to short and long-term stresses induced by changes in temperature (30° to 37 °C), pH (1.6 to 1.2 or 2.0), and oxidative status (1 mM H2O2) as well as to different energy sources (iron, sulfur, pyrite, sphalerite or chalcopyrite). Cells adapted under thermal and oxidative stress conditions showed a generalized upregulation of holdase genes, while short-term stress led to more discrete increases in transcript levels, with only hsp20.2 and hsp31 showing higher mRNA levels. hsp31 was also upregulated under acidic stresses, sulfur and sulfides. hsp20 variants showed different mRNA levels under different conditions, and cnoX was induced under oxidative conditions. Cells cultured on chalcopyrite had similar responses to those grown with peroxide. With some exceptions, stresses led to significant increases in intracellular ROS content, and decreases in ATP. These results pave the way to understanding proteostasis systems in extreme acidophilic bacteria.

Whole-Genome Sequencing of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Isolated from Human Bloodstream Infections

Klebsiella pneumoniae is a Gram-negative bacterium commonly associated with bloodstream infections (BSIs), which can lead to severe clinical outcomes, especially in immunocompromised individuals or patients with underlying health conditions. The increasing prevalence of K. pneumoniae that produces extended-spectrum β-lactamases (ESBL) poses a significant challenge for treatment and infection control, necessitating a swift diagnostic approach and tailored antimicrobial therapy to improve patient outcomes. A total of 32 K. pneumoniae isolates were recovered from BSIs from December 2021 to August 2022. Whole-genome sequencing (WGS) was performed on the 14 ESBL-producing isolates. All ESBL isolates carried the blaCTX-M-15 gene, together with other β-lactamase-encoding genes (blaTEM-1, blaSHV-28, blaSHV-26, or blaOXA-1). Three of the isolates also carried the blaKPC-3 gene. Resistance genes to quinolones, sulfonamides, tetracycline, aminoglycosides, and chloramphenicol were also detected. We can conclude that the presence of ESBL-producing isolates among K. pneumoniae of BSIs raises concerns, since these enzymes limit the available treatment options, and future research must include studies on alternative therapies for dealing with resistant bacterial infections and developing new approaches to disease treatment.

The identification of small molecule inhibitors with anthelmintic activities that target conserved proteins among ruminant gastrointestinal nematodes

Gastrointestinal nematode (GIN) infections are a major concern for the ruminant industry worldwide and result in significant production losses. Naturally occurring polyparasitism and increasing drug resistance that potentiate disease outcomes are observed among the most prevalent GINs of veterinary importance. Within the five major taxonomic clades, clade Va represents a group of GINs that predominantly affect the abomasum or small intestine of ruminants. However, the development of effective broad-spectrum anthelmintics against ruminant clade Va GINs has been challenged by a lack of comprehensive druggable genome resources. Here, we first assembled draft genomes for three clade Va species (Cooperia oncophora, Trichostrongylus colubriformis, and Ostertagia ostertagi) and compared them with closely related ruminant GINs. Genome-wide phylogenetic reconstruction showed a relationship among ruminant GINs structured by taxonomic classification. Orthogroup (OG) inference and functional enrichment analyses identified 220 clade Va-specific and Va-conserved OGs, enriched for functions related to cell cycle and cellular senescence. Further transcriptomic analysis identified 61 taxonomically and functionally conserved clade Va OGs that may function as drug targets for new broad-spectrum anthelmintics. Chemogenomic screening identified 11 compounds targeting homologs of these OGs, thus having potential anthelmintic activity. In in vitro phenotypic assays, three kinase inhibitors (digitoxigenin, K-252a, and staurosporine) exhibited broad-spectrum anthelmintic activities against clade Va GINs by obstructing the motility of exsheathed L3 (xL3) or molting of xL3 to L4. These results demonstrate valuable applications of the new ruminant GIN genomes in gaining better insights into their life cycles and offer a contemporary approach to discovering the next generation of anthelmintics.IMPORTANCEGastrointestinal nematode (GIN) infections in ruminants are caused by parasites that inhibit normal function in the digestive tract of cattle, sheep, and goats, thereby causing morbidity and mortality. Coinfection and increasing drug resistance to current therapeutic agents will continue to worsen disease outcomes and impose significant production losses on domestic livestock producers worldwide. In combination with ongoing therapeutic efforts, advancing the discovery of new drugs with novel modes of action is critical for better controlling GIN infections. The significance of this study is in assembling and characterizing new GIN genomes of Cooperia oncophora, Ostertagia ostertagi, and Trichostrongylus colubriformis for facilitating a multi-omics approach to identify novel, biologically conserved drug targets for five major GINs of veterinary importance. With this information, we were then able to demonstrate the potential of commercially available compounds as new anthelmintics.

CO2 uptake in ethanol-driven chain elongation system: Microbial metabolic mechanisms

CO2 as a byproduct of organic waste/wastewater fermentation has an important impact on the carboxylate chain elongation. In this study, a semi-continuous flow reactor was used to investigate the effects of CO2 loading rates (Low = 0.5 LCO2·L-1·d-1, Medium = 1.0 LCO2·L-1·d-1, High = 2.0 LCO2·L-1·d-1) on chain elongation system Ethanol and acetate were utilized as the electron donor and electron acceptor, respectively. The results demonstrate that low loading rate of CO2 has a positive effect on chain elongation. The maximum production of caproate and CH4 were observed at a low CO2 loading rate. Caproate production reached 1.88 g COD·L-1·d-1 with a selectivity of 62.55 %, while CH4 production reached 129.7 ml/d, representing 47.4 % of the total. Metagenomic analysis showed that low loading rate of CO2 favored the enrichment of Clostridium kluyveri, with its abundance being 3.8 times higher than at of high CO2 loading rate. Metatranscriptomic analysis revealed that high CO2 loading rate induced oxidative stress in microorganisms, as evidenced by increased expression of heat shock proteins and superoxide dismutase genes. Further investigation suggested that genes associated with the reverse β-oxidation pathway, CO2 uptake pathway and hydrogenotrophic methanogenesis pathway were reduced at high CO2 loading rate. These findings provide insight into the underlying mechanisms of how CO2 affects chain elongation, and it could be a crucial reason for the poor performance of chain elongation systems with high endogenous CO2 production.

bglG Regulates the Heterogeneity Driven by the Acid Tolerance Response in Lacticaseibacillus paracasei L9

The acid tolerance of lactic acid bacteria is crucial for their fermentation and probiotic functions. Acid adaption significantly enhances the acid tolerance of strains, and the phenotypic heterogeneity driven by the acid tolerance response (ATR) contributes to this process by providing a selective advantage in harsh environments. The mechanism of heterogeneity under the ATR is not yet clear, but individual gene expression differences are recognized as the cause. In this study, we observed four heterogeneous subpopulations (viable, injured, dead, and unstained) of Lacticaseibacillus paracasei L9 (L9) induced by acid adaption (pH 5.0, 40 min) using flow cytometry. The viable subpopulation represented a significantly superior acid tolerance to the injured subpopulation or total population. Different subpopulations were sorted and transcriptomic analysis was performed. Five genes were found to be upregulated in the viable subpopulation and downregulated in the injured subpopulation, and bglG (LPL9_RS14735) was identified as having a key role in this process. Using salicin (glucoside)-inducing gene expression and gene insertion mutagenesis, we verified that bglG regulated the heterogeneity of the acid stress response and that the relevant mechanisms might be related to activating hsp20. This study provides new evidence for the mechanism of the ATR and may contribute to the theoretical basis of improving the acid tolerance of Lacticaseibacillus paracasei L9.

A Review on the Involvement of Heat Shock Proteins (Extrinsic Chaperones) in Response to Stress Conditions in Aquatic Organisms

Heat shock proteins (HSPs) encompass both extrinsic chaperones and stress proteins. These proteins, with molecular weights ranging from 14 to 120 kDa, are conserved across all living organisms and are expressed in response to stress. The upregulation of specific genes triggers the synthesis of HSPs, facilitated by the interaction between heat shock factors and gene promoter regions. Notably, HSPs function as chaperones or helper molecules in various cellular processes involving lipids and proteins, and their upregulation is not limited to heat-induced stress but also occurs in response to anoxia, acidosis, hypoxia, toxins, ischemia, protein breakdown, and microbial infection. HSPs play a vital role in regulating protein synthesis in cells. They assist in the folding and assembly of other cellular proteins, primarily through HSP families such as HSP70 and HSP90. Additionally, the process of the folding, translocation, and aggregation of proteins is governed by the dynamic partitioning facilitated by HSPs throughout the cell. Beyond their involvement in protein metabolism, HSPs also exert a significant influence on apoptosis, the immune system, and various characteristics of inflammation. The immunity of aquatic organisms, including shrimp, fish, and shellfish, relies heavily on the development of inflammation, as well as non-specific and specific immune responses to viral and bacterial infections. Recent advancements in aquatic research have demonstrated that the HSP levels in populations of fish, shrimp, and shellfish can be increased through non-traumatic means such as water or oral administration of HSP stimulants, exogenous HSPs, and heat induction. These methods have proven useful in reducing physical stress and trauma, while also facilitating sustainable husbandry practices such as vaccination and transportation, thereby offering health benefits. Hence, the present review discusses the importance of HSPs in different tissues in aquatic organisms (fish, shrimp), and their expression levels during pathogen invasion; this gives new insights into the significance of HSPs in invertebrates.

Stress Response in Bifidobacteria

Bifidobacteria naturally inhabit diverse environments, including the gastrointestinal tracts of humans and animals. Members of the genus are of considerable scientific interest due to their beneficial effects on health and, hence, their potential to be used as probiotics. By definition, probiotic cells need to be viable despite being exposed to several stressors in the course of their production, storage, and administration. Examples of common stressors encountered by probiotic bifidobacteria include oxygen, acid, and bile salts. As bifidobacteria are highly heterogenous in terms of their tolerance to these stressors, poor stability and/or robustness can hamper the industrial-scale production and commercialization of many strains. Therefore, interest in the stress physiology of bifidobacteria has intensified in recent decades, and many studies have been established to obtain insights into the molecular mechanisms underlying their stability and robustness. By complementing traditional methodologies, omics technologies have opened new avenues for enhancing the understanding of the defense mechanisms of bifidobacteria against stress. In this review, we summarize and evaluate the current knowledge on the multilayered responses of bifidobacteria to stressors, including the most recent insights and hypotheses. We address the prevailing stressors that may affect the cell viability during production and use as probiotics. Besides phenotypic effects, molecular mechanisms that have been found to underlie the stress response are described. We further discuss strategies that can be applied to improve the stability of probiotic bifidobacteria and highlight knowledge gaps that should be addressed in future studies.

In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and adaptational functions to extreme environments

Members of the Bacillus genus are industrial cell factories due to their capacity to secrete significant quantities of biomolecules with industrial applications. The Bacillus paralicheniformis strain Bac84 was isolated from the Red Sea and it shares a close evolutionary relationship with Bacillus licheniformis. However, a significant number of proteins in its genome are annotated as functionally uncharacterized hypothetical proteins. Investigating these proteins' functions may help us better understand how bacteria survive extreme environmental conditions and to find novel targets for biotechnological applications. Therefore, the purpose of our research was to functionally annotate the hypothetical proteins from the genome of B. paralicheniformis strain Bac84. We employed a structured in-silico approach incorporating numerous bioinformatics tools and databases for functional annotation, physicochemical characterization, subcellular localization, protein-protein interactions, and three-dimensional structure determination. Sequences of 414 hypothetical proteins were evaluated and we were able to successfully attribute a function to 37 hypothetical proteins. Moreover, we performed receiver operating characteristic analysis to assess the performance of various tools used in this present study. We identified 12 proteins having significant adaptational roles to unfavorable environments such as sporulation, formation of biofilm, motility, regulation of transcription, etc. Additionally, 8 proteins were predicted with biotechnological potentials such as coenzyme A biosynthesis, phenylalanine biosynthesis, rare-sugars biosynthesis, antibiotic biosynthesis, bioremediation, and others. Evaluation of the performance of the tools showed an accuracy of 98% which represented the rationality of the tools used. This work shows that this annotation strategy will make the functional characterization of unknown proteins easier and can find the target for further investigation. The knowledge of these hypothetical proteins' potential functions aids B. paralicheniformis strain Bac84 in effectively creating a new biotechnological target. In addition, the results may also facilitate a better understanding of the survival mechanisms in harsh environmental conditions.

Genome-Wide Assessment of Stress-Associated Genes in Bifidobacteria

Over the last decade, the genomes of several Bifidobacterium strains have been sequenced, delivering valuable insights into their genetic makeup. However, bifidobacterial genomes have not yet been systematically mined for genes associated with stress response functions and their regulation. In this work, a list of 76 genes related to stress response in bifidobacteria was compiled from previous studies. The prevalence of the genes was evaluated among the genome sequences of 171 Bifidobacterium strains. Although genes of the protein quality control and DNA repair systems appeared to be highly conserved, genome-wide in silico screening for consensus sequences of putative regulators suggested that the regulation of these systems differs among phylogenetic groups. Homologs of multiple oxidative stress-associated genes are shared across species, albeit at low sequence similarity. Bee isolates were confirmed to harbor unique genetic features linked to oxygen tolerance. Moreover, most studied Bifidobacterium adolescentis and all Bifidobacterium angulatum strains lacked a set of reactive oxygen species-detoxifying enzymes, which might explain their high sensitivity to oxygen. Furthermore, the presence of some putative transcriptional regulators of stress responses was found to vary across species and strains, indicating that different regulation strategies of stress-associated gene transcription contribute to the diverse stress tolerance. The presented stress response gene profiles of Bifidobacterium strains provide a valuable knowledge base for guiding future studies by enabling hypothesis generation and the identification of key genes for further analyses.

IMPORTANCE Bifidobacteria are Gram-positive bacteria that naturally inhabit diverse ecological niches, including the gastrointestinal tract of humans and animals. Strains of the genus Bifidobacterium are widely used as probiotics, since they have been associated with health benefits. In the course of their production and administration, probiotic bifidobacteria are exposed to several stressors that can challenge their survival. The stress tolerance of probiotic bifidobacteria is, therefore, an important selection criterion for their commercial application, since strains must maintain their viability to exert their beneficial health effects. As the ability to cope with stressors varies among Bifidobacterium strains, comprehensive understanding of the underlying stress physiology is required for enabling knowledge-driven strain selection and optimization of industrial-scale production processes.

Role of hsp20 in the Production of Spores and Insecticidal Crystal Proteins in Bacillus thuringiensis

The small heat shock protein plays an important role in response to stresses. We wanted to investigate how Hsp20 affects sporulation and production of insecticidal crystal proteins (ICPs) in Bacillus thuringiensis (Bt) at the stationary growth phase when cells are starved. The hsp20 gene was knocked out in Bt4.0718 (wide type), which is a B. thuringiensis strain screened in our laboratory, using endonuclease I-SceI mediated unmarked gene replacement method. Deletion of Hsp20 resulted in a decrease in both sporulation and ICPs production. Bt4-Δhsp20 cells and its ICP did not have a significant difference in shape and size but entered the decline phase 2 h earlier than the Bt4.0718. In order to find the mechanism that underlies these phenotypes, we completed a proteomic study of differentially expressed proteins (DEPs). In Bt4-Δhsp20 cells, 11 DEPs were upregulated and 184 DEPs downregulated. These affected DEPs are involved in multiple metabolic pathways: (1) six DEPs (two upregulated and four downregulated) are directly related to the sporulation and ICPs synthesis; (2) supply of amino acids including amino acid synthesis and protein recycling; (3) the energy supplementation (the tricarboxylic acid cycle and glycolysis); (4) purine metabolism and mRNA stability. These results suggest that hsp20 may be critical in maintaining the homeostasis of B. thuringiensis during the production of spores and ICPs, and could provide new sight into the sporulation and ICPs formation in B. thuringiensis.

Functional signature analysis of extreme Prakriti endophenotypes in gut microbiome of western Indian rural population

Ayurveda is practiced in India from ancient times and stratifies the individuals based on their Prakriti constitution. Advancements in modern science have led to the association of Prakriti with molecular, biochemical, genomic and other entities. We have recently explored the gut microbiome composition and microbial signatures in healthy extreme Prakriti endo-phenotypes. However, their functional potentials are still lacking. The present study includes 63 females (29 Vata, 11 Pitta, and 23 Kapha) and 50 males (13 Vata, 18 Pitta, and 19 Kapha) samples. The predictive functional profiling and organism level functional traits of the human gut microbiome have been carried out in Prakriti groups using imputed metagenomic approach. A higher functional level redundancy is found than the taxonomy across the Prakriti groups, however the dominant taxa contributing to the functional profiles are found to be different. A high number of functional signatures specific to the Prakriti groups were identified in female datasets. Some of the functional signatures were found to be gender specific. For example, a higher abundance of microbes contributing potential pathogenic and stress tolerance related functions was found in Kapha in female and Pitta in male. The functional signatures correlated well with phenotypes and disease predisposition of Prakriti groups.

Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan

Bifidobacterium longum subsp. longum represents one of the most prevalent bifidobacterial species in the infant, adult and elderly (human) gut. In the current study, we performed a comparative genome analysis involving 145 B. longum representatives, including 113 B. longum subsp. longum strains obtained from healthy Japanese subjects aged between 0 and 98 years. Although MCL clustering did not reveal any correlation between isolated strains and subject age, certain characteristics appear to be more prevalent among strains corresponding to specific host ages, such as genes involved in carbohydrate metabolism and environmental response. Remarkably, a substantial number of strains appeared to have been transmitted across family members, a phenomenon that was shown not to be confined to mother-infant pairs. This suggests that the ubiquitous distribution of B. longum subsp. longum across the human lifespan is at least partly due to extensive transmission between relatives. Our findings form a foundation for future research aimed at unraveling the mechanisms that allow B. longum strains to successfully transfer between human hosts, where they then colonize and persist in the gut environment throughout the host's lifespan.

Anaerobic Probiotics: The Key Microbes for Human Health

Human gastrointestinal microbiota (HGIM) incorporate a large number of microbes from different species. Anaerobic bacteria are the dominant organisms in this microbial consortium and play a crucial role in human health. In addition to their functional role as the main source of many essential metabolites for human health, they are considered as biotherapeutic agents in the regulation of different human metabolites. They are also important in the prevention and in the treatment of different physical and mental diseases. Bifidobacteria are the dominant anaerobic bacteria in HGIM and are widely used in the development of probiotic products for infants, children and adults. To develop bifidobacteria-based bioproducts, therefore, it is necessary to develop a large-scale biomass production platform based on a good understanding of the ideal medium and bioprocessing parameters for their growth and viability. In addition, high cell viability should be maintained during downstream processing and storage of probiotic cell powder or the final formulated product. In this work we review the latest information about the biology, therapeutic activities, cultivation and industrial production of bifidobacteria.

Molecular Characterization of Six Small Heat Shock Proteins and Their Responses Under Cadmium Stress in Oxya chinensis (Orthoptera: Acridoidea)

Small heat shock proteins (sHSPs) have been implicated in many physiological processes and play important roles in the response to various stresses. In this study, the full-length sequences of six sHSPs: OcHSP19.1, 19.8, 20.4, 20.7, 21.1, and 23.8 were obtained from the rice grasshopper Oxya chinensis transcriptome database. The deduced amino acid sequences of the six OcsHSPs contain a typical α-crystallin domain, which consists of approximately 100 amino acid residues and five β-strands. The phylogenetic analysis suggested that OcHSP23.8 was orthologous to the sHSPs of other species and that OcHSP19.1, 20.4, 20.7, and 21.1 were species specific, whereas OcHSP19.8 did not cluster closely to Orthoptera but was placed on the basal end of the cluster. Developmental stage-dependent and tissue-specific expression patterns were evaluated using quantitative real-time polymerase chain reaction. The six genes were expressed in all developmental stages and showed clear tissue specificity. The cadmium acute experiment indicates that Cd(2+) can induce the six genes. However, various response patterns were observed among these genes under Cd(2+) stress conditions. OcHSP19.1, 19.8, 20.4, and 20.7 were highly induced by 2.61 mM Cd(2+) at 24 h. OcHSP23.8 was significantly upregulated by 2.61 mM Cd(2+) at 6 h. For OcHSP21.1, the highest expression levels were found after treatment with 0.87 mM Cd(2+) for 24 h, 1.74 mM Cd(2+) for 36 h, and 2.61 mM Cd(2+) for 12 h. These differential characteristics will facilitate future investigations into the physiological functions of sHSPs.

Proteomic Analyses of Chlorhexidine Tolerance Mechanisms in Delftia acidovorans Biofilms

Protein expression and fatty acid profiles of biofilm cells of chlorhexidine-tolerant Delftia acidovorans (MIC = 15 µg/ml) and its chlorhexidine-susceptible mutant (MIC = 1 µg/ml) were investigated. The chlorhexidine-susceptible mutant (MT51) was derived from the parental strain (WT15) using Tn5 transposon mutagenesis. The disrupted gene was identified as tolQ, a component of the tolQRAB gene cluster known to be involved in outer membrane stability. Proteomic responses of biofilm cells were compared by differential in-gel electrophoresis following exposure to chlorhexidine at sub-MIC (10 µg/ml) and above-MIC (30 µg/ml) concentrations. Numerous changes in protein abundance were observed in biofilm cells following chlorhexidine exposure, suggesting that molecular changes occurred during adaptation to chlorhexidine. Forty proteins showing significant differences (≥1.5-fold; P < 0.05) were identified by mass spectrometry and were associated with various functions, including amino acid and lipid biosynthesis, protein translation, energy metabolism, and stress-related functions (e.g., GroEL, aspartyl/glutamyl-tRNA amidotransferase, elongation factor Tu, Clp protease, and hydroxymyristoyl-ACP dehydratase). Several proteins involved in fatty acid synthesis were affected by chlorhexidine, in agreement with fatty acid analysis, wherein chlorhexidine-induced shifts in the fatty acid profile were observed in the chlorhexidine-tolerant cells, primarily the cyclic fatty acids. Transmission electron microscopy revealed more prominent changes in the cell envelope of chlorhexidine-susceptible MT51 cells. This study suggests that multiple mechanisms involving both the cell envelope (and likely TolQ) and panmetabolic regulation play roles in chlorhexidine tolerance in D. acidovorans. IMPORTANCE Delftia acidovorans has been associated with a number of serious infections, including bacteremia, empyema, bacterial endocarditis, and ocular and urinary tract infections. It has also been linked with a variety of surface-associated nosocomial infections. Biofilm-forming antimicrobial-resistant D. acidovorans strains have also been isolated, including ones displaying resistance to the common broad-spectrum agent chlorhexidine. The mechanisms of chlorhexidine resistance in D. acidovorans are not known; hence, a chlorhexidine-susceptible mutant of the tolerant wild-type strain was obtained using transposon mutagenesis, and the proteome and ultrastructural changes of both strains were compared under chlorhexidine challenge.

Identification and expression analysis of a heat-shock protein 70 gene in Polycelis sp

Heat-shock protein 70 (HSP70) is ubiquitously found in a variety of organisms and plays an important role in cytoprotection, environmental monitoring, and disease resistance. In this study, the full-length complementary DNA (cDNA) of hsp70 from planarian Polycelis sp. was first cloned using rapid amplification of cDNA ends (RACE). The expression levels of Pyhsp70 were analyzed in the presence of various stressors by real-time PCR, and its temporal-spatial expression patterns were also examined in both intact and regenerative animals by whole-mount in situ hybridization. The results show that (1) the deduced amino acid sequence of Pyhsp70 includes three typical HSP70 family signature motifs and is highly conserved during evolution; (2) Pyhsp70 expression is induced by prolonged starvation, tissue damage, and ionic liquid but inhibited by high or low temperatures; and (3) Pyhsp70 mRNA is mainly expressed in the head peripheral region and in the regenerating blastema during regeneration. These results suggest that the highly expressed Pyhsp70 gene may contribute to enhance cytoprotection and tolerance against stress-induced molecular damage, and the migration of neoblasts to the wound, which might also be involved in the proliferation and differentiation of neoblasts. Our work provides basic data for the study of stress responses and regenerative mechanism in freshwater planarians.

Integrated transcriptomic and proteomic analysis of the bile stress response in a centenarian-originated probiotic Bifidobacterium longum BBMN68

Bifidobacteria are natural inhabitants of the human gastrointestinal tract and well known for their health-promoting effects. Tolerance to bile stress is crucial for bifidobacteria to survive in the colon and to exert their beneficial actions. In this work, RNA-Seq transcriptomic analysis complemented with proteomic analysis was used to investigate the cellular response to bile in Bifidobacterium longum BBMN68. The transcript levels of 236 genes were significantly changed (≥ threefold, p < 0.001) and 44 proteins were differentially abundant (≥1.6-fold, p < 0.01) in B. longum BBMN68 when exposed to 0.75 g l(-1) ox-bile. The hemolysin-like protein and bile efflux systems were significantly over produced, which might prevent bile adsorption and exclude bile, respectively. The cell membrane composition was modified probably by an increase of cyclopropane fatty acid and a decrease of transmembrane proteins, resulting in a cell membrane more impermeable to bile salts. Our hypothesis was later confirmed by surface hydrophobicity assay. The transcription of genes related to xylose utilization and bifid shunt were up-regulated, which increased the production of ATP and reducing equivalents to cope with bile-induced damages in a xylan-rich colon environment. Bile salts signal the B. longum BBMN68 to gut entrance and enhance the expression of esterase and sortase associated with adhesion and colonization in intestinal tract, which was supported by a fivefold increased adhesion ability to HT-29 cells by BBMN68 upon bile exposure. Notably, bacterial one-hybrid and EMSA assay revealed that the two-component system senX3-regX3 controlled the expression of pstS in bifidobacteria and the role of this target gene in bile resistance was further verified by heterologous expression in Lactococcus lactis. Taken altogether, this study established a model for global response mechanisms in B. longum to bile.

Comparative genome analysis of wheat blue dwarf phytoplasma, an obligate pathogen that causes wheat blue dwarf disease in China

Wheat blue dwarf (WBD) disease is an important disease that has caused heavy losses in wheat production in northwestern China. This disease is caused by WBD phytoplasma, which is transmitted by Psammotettix striatus. Until now, no genome information about WBD phytoplasma has been published, seriously restricting research on this obligate pathogen. In this paper, we report a new sequencing and assembling strategy for phytoplasma genome projects. This strategy involves differential centrifugation, pulsed-field gel electrophoresis, whole genome amplification, shotgun sequencing, de novo assembly, screening of contigs from phytoplasma and the connection of phytoplasma contigs. Using this scheme, the WBD phytoplasma draft genome was obtained. It was comprised of six contigs with a total size of 611,462 bp, covering ∼94% of the chromosome. Five-hundred-twenty-five protein-coding genes, two operons for rRNA genes and 32 tRNA genes were identified. Comparative genome analyses between WBD phytoplasma and other phytoplasmas were subsequently carried out. The results showed that extensive arrangements and inversions existed among the WBD, OY-M and AY-WB phytoplasma genomes. Most protein-coding genes in WBD phytoplasma were found to be homologous to genes from other phytoplasmas; only 22 WBD-specific genes were identified. KEGG pathway analysis indicated that WBD phytoplasma had strongly reduced metabolic capabilities. However, 46 transporters were identified, which were involved with dipeptides/oligopeptides, spermidine/putrescine, cobalt and Mn/Zn transport, and so on. A total of 37 secreted proteins were encoded in the WBD phytoplasma chromosome and plasmids. Of these, three secreted proteins were similar to the reported phytoplasma virulence factors TENGU, SAP11 and SAP54. In addition, WBD phytoplasma possessed several proteins that were predicted to play a role in its adaptation to diverse environments. These results will provide clues for research on the pathogenic mechanisms of WBD phytoplasma and will also provide a perspective about the genome sequencing of other phytoplasmas and obligate organisms.

Changes in the expression of four heat shock proteins during the aging process in Brachionus calyciflorus (rotifera)

Heat shock proteins (HSPs) are molecular chaperones and have an important role in the refolding and degradation of misfolded proteins, and these functions are related to aging. Rotifer is a useful model organism in aging research, owing to small body size (0.1-1 mm), short lifespan (6-14 days), and senescence phenotypes that can be measured relatively easily. Therefore, we used rotifer as a model to determine the role of four typical hsp genes on the aging process in order to provide a better understanding of rotifer aging. We cloned cDNA encoding hsp genes (hsp40, hsp60, hsp70, and hsp90) from the rotifer Brachionus calyciflorus Pallas, analyzed their molecular characteristics, determined its modulatory response under different temperatures and H2O2 concentrations and investigated the changes in expression of these genes during the aging process. We found that Bchsp70 mRNA expression significantly decreased with aging. In addition, we also studied the effects of dietary restriction (DR) and vitamin E on rotifer lifespan and reproduction and analyzed the changes in expression of these four Bchsp genes in rotifers treated with DR and vitamin E. The results showed that DR extended the lifespan of rotifers and reduced their fecundity, whereas vitamin E had no significant effect on rotifer lifespan or reproduction. Real-time PCR indicated that DR increased the expression of these four Bchsps. However, vitamin E only improved the expression of Bchsp60, and reduced the expression of Bchsp40, Bchsp70, and Bchsp90. DR pretreatment also increased rotifer survival rate under paraquat-induced oxidative stress. These results indicated that hsp genes had an important role in the anti-aging process.

Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability

The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N. dassonvillei subsp. dassonvillei DSM 43111^T. The core genome of 1,993 orthologous and paralogous gene clusters was identified, and the pan-genomic reservoir was found not only to accommodate more than 22,000 genes, but also to be open. The top ten paralogous genes in terms of copy number could be referred to three functional categories: transcription regulators, transporters, and synthases related to bioactive metabolites. Based on phylogenomic reconstruction, we inferred past evolutionary events, such as gene gains and losses, and identified a list of clade-specific genes implicated in environmental adaptation. These results provided insights into the genetic causes of environmental adaptability in this cosmopolitan actinobacterial group and the contributions made by its inherent features, including genome dynamics and the constituents of core and accessory proteins.

Molecular and functional characterization of HdHSP20: a biomarker of environmental stresses in disk abalone Haliotis discus discus

Heat shock proteins (HSPs) production in cell is inducible by many physical and chemical stressors, providing adaptive significance for organisms when faced with environmental changes. In this study, we characterized a novel small HSP gene from disk abalone, designated as HdHSP20, and investigated its temporal expression by different environmental stimuli. The full-length genome sequence of HdHSP20 is composed of three exons and two introns. The 5' flanking region contains multiple putative transcription factor binding sites related to stress response. The open reading frame of the HdHSP20 cDNA is 480 bp and encodes 160 amino acid residues with 18.76 kDa molecular mass. The deduced amino acid sequence shares highest similarity with HSP20 genes from other invertebrates. HdHSP20 also shows several structural signatures of small HSP, including the conserved α-crystallin domain, the absence of cysteine residues, a high number of Glx/Asx residues and the compact β-sandwich structure in the C-terminal region. Overexpression of recombinant HdHSP20 protein conveyed enhanced thermotolerance to Escherichia coli cells, suggesting its functional activity in the cellular chaperone network. qRT-PCR measurements of HdHSP20 mRNA level have shown rapid and drastic induction by extreme temperatures, extreme salinities, heavy metals and the microbial infections. Collectively, our results suggest that HdHSP20 gene is likely involved in the stress resistant mechanisms in disk abalone. Its expression may serve as a potential biomarker capable to indicate a stress state in abalone due to extreme environmental change and pathogen infection.

Biotechnical applications of small heat shock proteins from bacteria

The stress responses of most bacteria are thought to involve the upregulation of small heat shock proteins. We describe here some of the most pertinent aspects of small heat shock proteins, to highlight their potential for use in various applications. Bacterial species have between one and 13 genes encoding small heat shock proteins, the precise number depending on the species considered. Major efforts have recently been made to characterize the protein protection and membrane stabilization mechanisms involving small heat shock proteins in bacteria. These proteins seem to be involved in the acquisition of cellular heat tolerance. They could therefore potentially be used to maintain cell viability under unfavorable conditions, such as heat shock or chemical treatments. This review highlights the potential roles of applications of small heat shock proteins in stabilizing overproduced heterologous proteins in Escherichia coli, purified bacterial small heat shock proteins in protein biochip technology, proteomic analysis and food technology and the potential impact of these proteins on some diseases. This article is part of a Directed Issue entitled: Small HSPs in physiology and pathology.

Determination of the ribosome-binding sequence and spacer length between binding site and initiation codon for efficient protein expression in Bifidobacterium longum 105-A

The frequency of the ribosome-binding site (RBS) and spacer length between binding site and initiation codon were analyzed using informatics, and compared the activities of various synthetic RBSs and spacers in Bifidobacterium longum 105-A. As the result, AAGGAG and a 5 nt spacer length produced the most efficient protein expression.

Global genome transcription profiling of Bifidobacterium bifidum PRL2010 under in vitro conditions and identification of reference genes for quantitative real-time PCR

Bifidobacteria have attracted significant scientific attention due to their perceived role as health-promoting microorganisms, although the genetics of the bacterial group is still underexplored. In this study, we investigated the transcriptome of Bifidobacterium bifidum PRL2010 during in vitro growth by microarray technology. When B. bifidum PRL2010 was grown in liquid broth, 425 of the 1,644 PRL2010 genes represented on the array were expressed in at least one of the three investigated growth phases, i.e., the lag, exponential, and stationary phases. These transcriptional analyses identified a core in vitro transcriptome encompassing 150 genes that are expressed in all phases. A proportion of these genes were further investigated as potential reference genes by quantitative real-time reverse transcription-PCR (qRT-PCR) assays. Their expression stability was evaluated under different growth conditions, which included cultivation on different carbon sources, exposure to environmental stresses (thermal, acidic, and osmotic), and growth phases. Our analyses validated six reference genes suitable for normalizing mRNA expression levels in qRT-PCR experiments applied to bifidobacteria.

Enhancing the stress responses of probiotics for a lifestyle from gut to product and back again

Before a probiotic bacterium can even begin to fulfill its biological role, it must survive a battery of environmental stresses imposed during food processing and passage through the gastrointestinal tract (GIT). Food processing stresses include extremes in temperature, as well as osmotic, oxidative and food matrix stresses. Passage through the GIT is a hazardous journey for any bacteria with deleterious lows in pH encountered in the stomach to the detergent-like properties of bile in the duodenum. However, bacteria are equipped with an array of defense mechanisms to counteract intracellular damage or to enhance the robustness of the cell to withstand lethal external environments. Understanding these mechanisms in probiotic bacteria and indeed other bacterial groups has resulted in the development of a molecular toolbox to augment the technological and gastrointestinal performance of probiotics. This has been greatly aided by studies which examine the global cellular responses to stress highlighting distinct regulatory networks and which also identify novel mechanisms used by cells to cope with hazardous environments. This review highlights the latest studies which have exploited the bacterial stress response with a view to producing next-generation probiotic cultures and highlights the significance of studies which view the global bacterial stress response from an integrative systems biology perspective.

The hsp 16 gene of the probiotic Lactobacillus acidophilus is differently regulated by salt, high temperature and acidic stresses, as revealed by reverse transcription quantitative PCR (qRT-PCR) analysis

Small heat shock proteins (sHsps) are ubiquitous conserved chaperone-like proteins involved in cellular proteins protection under stressful conditions. In this study, a reverse transcription quantitative PCR (RT-qPCR) procedure was developed and used to quantify the transcript level of a small heat shock gene (shs) in the probiotic bacterium Lactobacillus acidophilus NCFM, under stress conditions such as heat (45 °C and 53 °C), bile (0.3% w/v), hyperosmosis (1 M and 2.5 M NaCl), and low pH value (pH 4). The shs gene of L. acidophilus NCFM was induced by salt, high temperature and acidic stress, while repression was observed upon bile stress. Analysis of the 5′ noncoding region of the hsp16 gene reveals the presence of an inverted repeat (IR) sequence (TTAGCACTC-N9-GAGTGCTAA) homologue to the controlling IR of chaperone expression (CIRCE) elements found in the upstream regulatory region of Gram-positive heat shock operons, suggesting that the hsp16 gene of L. acidophilus might be transcriptionally controlled by HrcA. In addition, the alignment of several small heat shock proteins identified so far in lactic acid bacteria, reveals that the Hsp16 of L. acidophilus exhibits a strong evolutionary relationship with members of the Lactobacillus acidophilus group.

How do bifidobacteria counteract environmental challenges? Mechanisms involved and physiological consequences

An effective response to stress is of paramount importance for probiotic bifidobacteria administered in foods, since it determines their performance as beneficial microorganisms. Firstly, bifidobacteria have to be resistant to the stress sources typical in manufacturing, including heating, exposure to low water activities, osmotic shock and presence of oxygen. Secondly, and once they are orally ingested, bifidobacteria have to overcome physiological barriers in order to arrive in the large intestine biologically active. These barriers are mainly the acid pH in the stomach and the presence of high bile salt concentrations in the small intestine. In addition, the large intestine is, in terms of microbial amounts, a densely populated environment in which there is an extreme variability in carbon source availability. For this reason, bifidobacteria harbours a wide molecular machinery allowing the degradation of a wide variety of otherwise non-digestible sugars. In this review, the molecular mechanisms allowing this bacterial group to favourably react to the presence of different stress sources are presented and discussed.

Molecular and biochemical modulation of heat shock protein 20 (Hsp20) gene by temperature stress and hydrogen peroxide (H₂O₂) in the monogonont rotifer, Brachionus sp

The monogonont rotifer, Brachionus sp. has been regarded as a potential model for reproductive physiology, evolution, and environmental genomics. To uncover the role of the heat shock protein upon temperature stress and hydrogen peroxide (H₂O₂) exposure, we cloned heat shock protein 20 (Hsp20) and determined its modulatory response under different temperatures and H₂O₂ concentrations. Under different temperature stresses (10 °C and 37 °C), the rotifer Brachionus sp. Hsp20 (Br-Hsp20) gene was highly expressed over time, and reached the maximum level 90 min after exposure, indicating that Br-Hsp20 gene would be involved in the chaperoning process to protect proteins at both low and high temperatures. To test the ability of thermotolerance of the recombinant Br-Hsp20-containing transformed Escherichia coli, we expressed the recombinant Br-Hsp20 protein with 1mM IPTG for 18 h at 30 °C, exposed them at 54 °C with time course (10 to 60 min), and measured cell survival. In this elevated temperature shock (54 °C), the cell survival was significantly higher at the Br-Hsp20 transformed E. coli, compared to the control (vector only). To analyze the modulatory effect of Br-Hsp20 gene on oxidative stress, we initially exposed 0.1 mM H₂O₂ over time and measured antioxidant enzyme activities along with the expression level of Br-Hsp20 mRNA. Upon H₂O₂ exposure, Br-Hsp20 gene was time-dependently upregulated and glutathione peroxidase (GPx), glutathione S-transferase (GST), and glutathione reductase (GR) activities were also elevated at the 12h-exposed group in a dose-dependent manner, indicating that the Br-Hsp20 gene would be an important gene in response to oxidative and temperature stress. Here, we demonstrated the role of the Hsp20 gene in the rotifer, Brachionus sp. providing a better understanding of the ecophysiology at environmental stress in this species.

Progress in genomics, metabolism and biotechnology of bifidobacteria

Members of the genus Bifidobacterium were first described over a century ago and were quickly associated with a healthy intestinal tract due to their numerical dominance in breast-fed babies as compared to bottle-fed infants. Health benefits elicited by bifidobacteria to its host, as supported by clinical trials, have led to their wide application as probiotic components of health-promoting foods, especially in fermented dairy products. However, the relative paucity of genetic tools available for bifidobacteria has impeded development of a comprehensive molecular understanding of this genus. In this review we present a summary of current knowledge on bifidobacterial metabolism, classification, physiology and genetics and outline the currently available methods for genetically accessing and manipulating the genus.

Differentiation of Bifidobacterium species using partial RNA polymerase {beta}-subunit (rpoB) gene sequences

Partial RNA polymerase β-subunit gene (rpoB) sequences (315 bp) were determined and used to differentiate the type strains of 23 species of the genus Bifidobacterium. The sequences were compared with those of the partial hsp60 (604 bp) and 16S rRNA genes (1475 or 1495 bp). The rpoB gene sequences showed nucleotide sequence similarities ranging from 84.1 % to 99.0 %, while the similarities of the hsp60 sequences ranged from 78.5 % to 99.7 % and the 16S rRNA gene sequence similarities ranged from 89.4 % to 99.2 %. The phylogenetic trees constructed from the sequences of these three genes showed similar clustering patterns, with the exception of several species. The Bifidobacterium catenulatum-Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum subsp. pseudolongum-Bifidobacterium pseudolongum subsp. globosum and Bifidobacterium gallinarum-Bifidobacterium pullorum-Bifidobacterium saeculare groups were more clearly differentiated in the partial rpoB and hsp60 gene sequence trees than they were in the 16S rRNA gene tree. Based on sequence similarities and tree topologies, the newly determined rpoB gene sequences are suitable molecular markers for the differentiation of species of the genus Bifidobacterium and support various other molecular tools used to determine the relationships among species of this genus.

Genomic insights into bifidobacteria

Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.

HspR mutations are naturally selected in Bifidobacterium longum when successive heat shock treatments are applied

The development of molecular tools allowed light to be shed on several widespread genetic mechanisms aiming at limiting the effect of molecular damage on bacterial survival. For some bacterial taxa, there are limited tools in the genetic toolbox, which restricts the possibilities to investigate the molecular basis of their stress response. In that case, an alternative strategy is to study genetic variants of a strain under stress conditions. The comparative study of the genetic determinants responsible for their phenotypes, e.g., an improved tolerance to stress, offers precious clues on the molecular mechanisms effective in this bacterial taxon. We applied this approach and isolated two heat shock-tolerant strains derived from Bifidobacterium longum NCC2705. A global analysis of their transcriptomes revealed that the dnaK operon and the clpB gene were overexpressed in both heat shock-tolerant strains. We sequenced the hspR gene coding for the negative regulator of dnaK and clpB and found point mutations affecting protein domains likely responsible for the binding of the regulators to the promoter DNA. Complementation of the mutant strains by the wild-type regulator hspR restored its heat sensitivity and thus demonstrated that these mutations were responsible for the observed heat tolerance phenotype.

An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003

Members of the genus Bifidobacterium are gram-positive bacteria that commonly are found in the gastrointestinal tract (GIT) of mammals, including humans. Because of their perceived probiotic properties, they frequently are incorporated as functional ingredients in food products. From probiotic production to storage and GIT delivery, bifidobacteria encounter a plethora of stresses. To cope with these environmental challenges, they need to protect themselves through stress-induced adaptive responses. We have determined the response of B. breve UCC2003 to various stresses (heat, osmotic, and solvent) using transcriptome analysis, DNA-protein interactions, and GusA reporter fusions, and we combined these with results from an in silico analysis. The integration of these results allowed the formulation of a model for an interacting regulatory network for stress response in B. breve UCC2003 where HspR controls the SOS response and the ClgR regulon, which in turn regulates and is regulated by HrcA. This model of an interacting regulatory network is believed to represent the paradigm for stress adaptation in bifidobacteria.