Bacteria

The common bean (Phaseolus vulgaris L.) is a significant vegetable crop, grown because it is a rich source of protein, carbohydrates, and vitamin B complex. Fusarium solani and Rhizoctonia solani are the most widely known pathogens contributing to large yield losses for this crop. The use of cultural and chemical control practices has been ineffective. Therefore, a sustainable, affordable, and effective control method is urgently required. In this study, we aimed to isolate and characterize Bacillus velezensis from Lake Bogoria as a potential biocontrol agent for Fusarium solani. Bacteria were isolated from soil and sediments using the serial dilution technique. Molecular characterization was performed using the 16S rRNA gene. A total of 13 bacteria were isolated from soil and sediments. Based on the partial sequences, BLAST analysis showed two isolates, B20 (Bacillus velezensis strain QH03-23) and B30 (Bacillus velezensis strain JS39D), belonging to Bacillus velezensis. Other isolates were identified as Bacillus tequilensis, Brevibacillus brevis, Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus licheniformis. The effectiveness of their antifungal properties was determined via co-culturing, and we found mycelial inhibition rates of 28.17% (for B20) and 33.33% (for B30) for the Fusarium solani isolates. The characterization of the Bacillus velezensis strain revealed that they were Gram-positive and grew well at pH 7.0 and 8.5, although growth was recorded at pH 5.0 and 10.0. In terms of temperature, the optimal temperature conditions were 30−35 °C, with an optimum salinity of 0–0.5 M NaCl. When these isolates were tested for their ability to produce secondary metabolites, they were found to produce phosphate, pectinase, chitinase, protease, indole -3- acetic acid (IAA), and hydrogen cyanide (HCD), making them potential biocontrol agents. Full article

Pseudomonas aeruginosa (PA) is an opportunistic Gram-negative bacteria that affects patients in intensive care units and chronic respiratory disease patients. Compared to other bacteria, it has a wide genome (around 6.3-Mb) that supports its metabolic versatility and antimicrobial resistance. Fosfomycin (FF) is primarily used as an oral treatment for urinary tract infections (UTIs). FF diffuses inside the cell via glycerol-3-phosphate transporter (GlpT) PA, as well as in other bacteria. In other bacteria, such as E. coli, glucose-6-phosphate transporter (UhpT) functions as FF transporter. Since mutant GlpT leads to FF resistant PA, it is assumed that GlpT is the only FF transporter. However, it is also assumed that PA uses glucose-6-phosphate and, thus, homologous proteins of UhpT may be present in its genome. Here, we present an attempt to find a distant related homologue of UhpT in PA. A Hidden Markov Model (HMM) was created to seek for Major facilitator family (MFS) domain in 21 PA genomes of 14 CF patients annotated with prokka and the statistical analysis was performed (MCC: 0.84, ACC: 0.99). Then, the HMM was applied to PA genomes. Besides the actual GlpT, annotated as glpt_1, one more GlpT protein was found in 21 out of 21 genomes, annotated as glpt_2. Since glpt_2 clusters closer to UhpT than GlpT, glpt_2 was selected to build a model. Computing a structural superimposition, the model and the template of UhpT have 0.6 Å of RMSD. The model of glpt_2 has some characteristics that are fundamental to UhpT functions. The binding site, consisting of 2 arginines (Arg46 and Arg275) and Lys45, is totally conserved, as well as the topology of the structure. Asp90 is also conserved in glpt_2 model. No studies aimed at searching for distant related homologous of UhpT. Since the high genetic exchange and high mutational rate in bacteria, it is likely that PA has a UhpT-like protein in the PA genome. The binding site is superimposable to UhpT protein as well as the overall topology. In fact, the 12 TMs are completely comparable, suggesting a well-defined folding of the protein across the bilayer lipid membrane. To enforce our hypothesis, in all 21 PA genomes, we also found a protein annotated as membrane sensor protein UhpC, important for expression and function of UhpT in E. coli. Since PA strains are wild-type, we can assume that most of the PA have proteins like this. The presence of a homologue of UhpT suggests that this protein is conserved in PA genome. Full article

The human gastrointestinal (GI) tract contains a diverse mixture of commensal and pathogenic microbes, forming the gut microbiome. These gut microbes and their potential to improve human health are a topic of great interest to the scientific community. Many intestinal and age-related complications are linked to dysbiosis of the gut microbiome, often associated with a weakened immune system. A decrease in beneficial microbes, generally, along with decreased microbial diversity in the gut, can, in many cases, result in disease, particularly in older individuals. Probiotics, which are ingestible beneficial microorganisms, have the potential to positively modulate the indigenous gut microbiota. There are two predominant and conventional classes of lactic acid bacterial probiotics, lactobacilli and bifidobacteria, which have been confirmed for their health benefits and role in preventing certain gut-related disorders. The proper use of probiotics and/or supplements, along with a consistently healthy lifestyle, is a promising holistic approach to maintaining or improving gut health and minimizing other age-linked disorders. There are many properties that bacterial probiotics possess, which may allow for these beneficial effects in the gut. For instance, probiotics have adhesion capacities (capability to stay in GI tract) that are effective in excluding pathogens, while other probiotics have the potential to stimulate or modulate the intestinal immune system by regulating genes that reside within and outside of the gut environment. This review discussed the possible underlying mechanics of probiotics, evidence of probiotic-based mitigation of age-related disease, and the role of probiotics in modulating gut health and, in turn, maintaining brain health. Full article

Tularemia is a severe infectious disease caused by the Gram-negative bacteria Francisella tularensis. F. tularensis is currently divided into three subspecies, holarctica, tularensis, and mediasiatica, which differ in their virulence and geographic distribution. Subspecies mediasiatica is the least studied because of its very low documented virulence for humans and limited geographic distribution. It was discovered in sparsely populated regions of Central Asia. Since 2011, a new subsp. mediasiatica lineage was identified in Altai (Russia). In 2021, we isolated one subsp. mediasiatica strain in Krasnoyarsk Territory. In spite of its geographic origin, 500 km east from Altai, this strain belongs to the Altai lineage and contributes surprisingly little genetic diversity to previous knowledge. Full article

Xanthomonas bacteria are known phytopathogens difficult to control in the field, which cause great losses in many economically important crops. Genomic islands are fragments acquired by horizontal transference that are important for evolution and adaptation to diverse ecological niches. Virulence and pathogenicity islands (PAIs) enhance molecular mechanisms related to host adaptation. In this work, we have analyzed 81 genomes belonging to X. campestris, and a complex group of X. citri, X. axonopodis, and X. fuscans belonging to nine different pathovars and three subspecies, to analyze and compare their genomic contents. Xanthomonas pan-genome is open and has a massive accessory genome. Each genome showed between three and 15 exclusive PAIs, well conserved through strains of the same pathovar or subspecies. X. axonopodis pv. anacardii had higher general similarity to X. citri subsp. citri and X. fuscans subsp. aurantifolii, with which a few PAIs were shared. Genomic synteny was even for almost all strains, with few rearrangements found in X. axonopodis pv. anacardii. The prophage regions identified in the genomes were mostly questionable or incomplete, and PAI13 in X. campestris pv. campestris ATCC33913 matched a prophage region of 19 transposable elements. Finally, PAIs in Xanthomonas are pathovar-specific, requiring individual strategies of combat. Full article

Angular leaf spot of cashew tree in Brazil has been attributed to pigmented and nonpigmented strains of Xanthomonas citri pv. anacardii. Due to the possibility of dissemination of the disease by propagating material, it is necessary to understand the survival mechanisms of the causal agent. Thus, the present study aimed to characterize the behavior of viable but non-cultivable cells (VBNC) in two pigmented strains (CCRMTAQ13 and CCRMTAQ18) and one nonpigmented strain (IBSBF2579) of X. citri pv. anacardii, integrating in silico, in vitro, and in vivo studies. Thirteen genes associated with the VBNC phase were identified in the genomes of these strains. The log phase was observed at 24, 48, and 120 h for CCRMTAQ13, CCRMTAQ18, and IBSBF2579 strains, respectively. The death phase was observed at 96 h for both pigmented strains and 168 h for the nonpigmented strain. Using qPCR analyses, it was possible to characterize the occurrence of VBNC for the three strains. When inoculated, the strains showed 100% incidence during the VBNC phase, with the IBSBF2579 strain having the longest incubation period (IP). The strains did not differ concerning final severity (FS) in the VBNC phase. To our knowledge, this is the first report of the occurrence of the VBNC mechanism in X. citri pv. anacardii strains. Furthermore, it has been demonstrated that X. citri pv. anacardii in the VBNC state is potentially infective when they meet their host’s apoplast, which points to the need to use integrated practices to detect this bacterium in cashew seedlings. Full article

BF2P4-5 was isolated from the rhizosphere soil of tomato plants, and its potential to promote plant growth was investigated in tomato plants. An in vitro test revealed that the strain could fix nitrogen, solubilize phosphate and potassium, and synthesize indole acetic acid. The bacterial strain was identified and characterized as a kind of Pseudarthrobacter chlorophenolicus based on the analysis of culture characteristics, physiological and biochemical characteristics, and 16S rRNA gene sequence (GenBank accession number OP135548.1). pH 7.0, 15% NaCl, and 35 °C temperature were ideal for optimal strain growth under culture conditions. Tomato plants grown on a cocopeat substrate were inoculated with BF2P4-5 suspension (OD₆₀₀ 2.0). Positive control plants were inoculated with Nitrogen Phosphorus Potassium (NPK) fertilizer. This BF2P4-5 strain and NPK treatments were complemented with a negative control, in which only tap water was applied to tomato roots, thus, establishing three distinct treatment modalities with five replications each. Two months of greenhouse trials of inoculated tomato plants improved growth parameters. Interestingly, in most of the growth metrics evaluated, tomato plants treated with strain BF2P4-5 showed little to no variation with NPK fertilizer treatment, including plant height, stem length, girth, leaf number per plant, and chlorophyll content, when compared to uninoculated plants. Furthermore, the conditions for the cocopeat plants, including pH, EC, and moisture, were within acceptable limits. Furthermore, inoculation with BF2P4-5 increased the nitrogen, phosphorus, and potassium content available in the cocopeat medium. The results showed that the strain exhibited traits for the promotion of plant growth and could be deployed as an eco-friendly microbial biofertilizer for tomatoes and probably other essential crops. Full article

In this study, we used the sequence of the aac(6′)-Ii gene, which is responsible for the intrinsic low-level aminoglycoside resistance of Enterococcus faecium, to design novel species-specific primers. Two oligonucleotide pairs named EF_200 and EF_120 were designed, generating amplification products with sizes of 200 bp and 120 bp, respectively. They were successfully applied for the identification of various isolates of clinical or environmental origins in both pure cultures and complex food samples. The obtained results indicated that both primer pairs permitted the highly specific, simple, fast and inexpensive detection of E. faecium isolates. Full article

Bifidobacterium breve is among the first microorganisms colonizing the intestinal tract in humans and is a predominant species in the gut microbiota of newborns and children. This bacterium is widely used in the probiotic industry due to its capacity to improve host health. The search for new targets with probiotic properties is an increasing trend with the help of next-generation sequencing as they facilitate the characterization of the bacterial features. B. breve 110^1A was isolated from the faeces of healthy children in Brazil and therefore could play a protective role in the gut. To investigate the beneficial properties of this strain, the present study performed a comprehensive characterization of the genetic features involved in the bacterium resistance and adaptation to gastrointestinal conditions, production of nutrients, and immunomodulatory compounds. Furthermore, this study carried out the prediction of genomic elements (plasmids, prophages, CRISPR-Cas systems, insertion sequences, genomic islands, antibiotic resistance genes) to evaluate the safety of B. breve 110^1A. A comparative genomics approach using 45 B. breve complete genomes based on pangenome and phylogenomic analysis was also performed to identify specific genes in B. breve 110^1A. The prediction of genetic elements, possibly safety-related, did not detect plasmids, but only one incomplete prophage, two non-functional CRISPR systems, and seven genomic islands. Additionally, three antibiotic resistance genes were identified: ileS (resistance to mupirocin), rpoB, and erm(X). In the comparative genomic analysis, the pangenome was revealed to be open, and B. breve 110^1A presented 63 unique genes associated with several processes, such as transmembrane transport, membrane components, DNA processes, and carbohydrate metabolism. In conclusion, B. breve 110^1A is potentially safe and well-adapted for intestinal disorder therapeutics, although the role of its unique genetic repertoire needs further investigation. Full article

Lactiplantibacillus plantarum strains are used in the food industry for their probiotic properties. Some of these bacteria have immunomodulatory effects on the host and are able to improve resistance against different pathogens, including viruses. However, to date, the bacterial genes involved in the immunomodulatory effect are not known. In this work, the complete genomes of L. plantarum MPL16, CRL1506, CRL681 and TL2766 were used to perform comparative genomics with the aim of identifying the genes involved in their differential immunomodulatory effects. L. plantarum WCFS1, a strain with proven probiotic activity, was also used for comparisons. The analysis of the genes involved in the metabolic pathways of the five strains did not reveal differences in the metabolism of amino acids, lipids, nucleotides, cofactors and vitamins, nor in the genes associated with energy metabolism or the biosynthesis of lipoproteins and teichoic acids. However, differences were found between the five strains when considering carbohydrate metabolism pathways, particularly in the presence/absence of glycosylhydrolases and glycosyltransferases. In addition, a great variability was detected in the predicted surface proteins of each L. plantarum strain. These results suggest that the surface molecules expressed in the different strains of L. plantarum could be involved in their differential ability to modulate the innate antiviral immune response. Full article

Gram-positive bacteria are some of the earliest known life forms, diverging from gram-negative bacteria 2 billion years ago. These organisms utilize sortase enzymes to attach proteins to their peptidoglycan cell wall, a structural feature that distinguishes the two types of bacteria. The transpeptidase activity of sortases make them an important tool in protein engineering applications, e.g., in sortase-mediated ligations or sortagging. However, due to relatively low catalytic efficiency, there are ongoing efforts to create better sortase variants for these uses. Here, we use bioinformatics tools, principal component analysis and ancestral sequence reconstruction, in combination with protein biochemistry, to analyze natural sequence variation in these enzymes. Principal component analysis on the sortase superfamily distinguishes previously described classes and identifies regions of relatively high sequence variation in structurally-conserved loops within each sortase family, including those near the active site. Using ancestral sequence reconstruction, we determined sequences of ancestral Staphylococcus and Streptococcus Class A sortase proteins. Enzyme assays revealed that the ancestral Streptococcus enzyme is relatively active and shares similar sequence variation with other Class A Streptococcus sortases. Taken together, we highlight how natural sequence variation can be utilized to investigate this important protein family, arguing that these and similar techniques may be used to discover or design sortases with increased catalytic efficiency and/or selectivity for sortase-mediated ligation experiments. Full article

Infections by antibiotic-resistant bacteria are a significant and complex global health issue. In this context, Acinetobacter baumannii is particularly important because of its ability to withstand treatments by β-lactams, such as carbapenem. The objective of this work was to investigate, through systematic analysis and meta-analysis, the chance of resistance to carbapenem in A. baumannii strains. For this, a search was conducted for the PubMed and Cochrane databases based on the keywords: “Acinetobacter baumannii” AND “beta-lactam” OR “penicillin” OR “cephalosporin” OR “cephamycin” OR “carbapenem” OR “monobactam”. The initial search resulted in a total of 90,475 articles. It was filtered based on eligibility criteria, and eight articles were selected for analysis. An odds ratio value equivalent to 3.55 was obtained, indicating a high chance of resistance to the carbapenem of strains of the species. Therefore, it is supposed that A. baumannii infection cases have a high probability of not responding adequately to treatments based on carbapenem. Full article

Neisseria gonorrhoeae has become a significant global public health problem due to growing infection rates and antibiotic resistance development. In 2012, N. gonorrhoeae positive samples isolated from Southeast Asia were reported to be the first strains showing resistance to all first-line antibiotics. To date, N. gonorrhoeae’s antimicrobial resistance has since been identified against a wide range of antimicrobial drugs globally. Hence, the World Health Organization (WHO) listed N. gonorrhoeae’s drug resistance as high-priority, necessitating novel therapy development. The persistence of N. gonorrhoeae infections globally underlines the need to better understand the molecular basis of N. gonorrhoeae infection, growing antibiotic resistance, and treatment difficulties in underdeveloped countries. Historically, Africa has had minimal or rudimentary N. gonorrhoeae monitoring systems, and while antimicrobial-resistant N. gonorrhoeae is known to exist, the degree of resistance is unknown. This review looks at the gender-related symptomatic gonorrhoeae disease and provides an overview of the essential bacterial factors for the different stages of pathogenesis, including transmission, immune evasion, and antibiotic resistance. Finally, we deliberate on how molecular epidemiological studies have informed our current understanding of sexual networks in the Sub-Saharan region. Full article

Bees’ and beehives’ health are strongly influenced by the honeybees’ gut microbiota which in turn is strongly dependent on many different factors, including environmental factors as well as anthropogenic pressure. In this study, in four locations in Bulgaria differing strongly in environmental conditions and anthropogenic pressure, an assessment was made using several obligatory core symbiont species and genera for reference, such as Lactobacillus sp., Bifidobacterium sp., Snodgrassiella alvi, Gilliamella apicola, Frishella perrara, and Commensalibacter sp., as well as an observation of the overall number of species. A snapshot of the relative abundances of the total number of species and the core species was made using a next-generation sequencing (NGS)-based metagenomic approach using the Illumina 2 × 250 bp paired-end platform. It was found that the two forms of anthropogenic pressure, the agricultural and the urban/industrial, have distinct effects, affecting different core genera and species. It was also demonstrated that both types of anthropogenic pressure cause a reduction in the overall number of bacterial species. Full article

Using Enterococcus faecium strains as probiotics raises several controversies related to their antibiotic resistance (AR). In the current study, we examined isolates of E. faecium obtained from human breast milk. Catalase-negative and γ-haemolytic isolates were identified by analyzing the sequences of 16S rRNA gene and their phenotypic resistance to antibiotics was investigated. We examined the expression of genes that were found on plasmids. The majority of isolates tested were resistant to erythromycin (96%), followed by trimethoprim (67%), tetracycline (57%), and gentamicin (55%). Ninety-seven percent of E. faecium isolates were resistant to at least two antibiotics. We detected the presence of the following genes on plasmids: ErmB (erythromycin), dfrA17 (trimethoprim), tetO, tetK (tetracycline), Aph(3′)-IIIa (neomycin), and marA (rifampicin). TetO was not expressed in all cases, dfrA14 was not expressed in CDCP1449, while tetK was only expressed in CDCP1128 and CDCP1331 isolates. In the majority of isolates, AR genes were located on chromosomes since they were not detected on plasmids. Our study shows that due to the spread of AR, human milk could be one of the first sources of the bacteria resistant to antimicrobials to infants. Full article

A recent publication described the construction and utility of a comprehensive “Chromatic Bacteria” toolbox containing a set of genetic tools that allows for fluorescently tagging a variety of Proteobacteria. In an effort to expand the range of bacteria taggable with the Chromatic Bacteria toolbox, a series of Himar1 transposon vectors was constructed to mediate insertion of fluorescent protein and antibiotic resistant genes. The Himar1 transposon was chosen as it is known to function in a wide range of bacterial species. To test the suitability of the new Himar1 Chromatic Bacteria plasmid derivatives, conjugations were attempted on recently isolated non-model organisms. Although we were unsuccessful in delivering the plasmids into Gram-positive bacterial isolates, we successfully modified previously recalcitrant isolates to the first set of the Chromatic Bacteria toolbox, such as Sphingomonas sp. Leaf357 and Acidovorax sp. Leaf84. This manuscript reports on the currently available plasmids and transposition success in different bacteria. Full article

There is little evidence on the role of prior infection in patients with external ventricular drains (EVDs) and lumbar drains (LDs). In this study, our aim is to investigate whether previous bacteremia is a risk factor for cerebrospinal fluid drain infection (CSFDI) in patients with EVDs and LDs and to describe the microorganisms implicated. We designed a retrospective, single-center cohort study. We recorded patients’ demographic and clinical characteristics, as well as microbiology laboratory data. We used non-parametric statistical methods to identify possible risk factors for CSFDI. We found 799 neurosurgical admissions during the study period, 70 of which fulfilled the inclusion criteria. Acinetobacter baumannii was the most frequent single pathogen isolated in the cerebrospinal fluid (CSF). Acinetobacter baumannii bacteremia was more common in patients with Acinetobacter baumannii CSFDI (p = 0.01). The distribution of the pathogens in the CSF differed from that of the pathogens isolated in blood (p = 0.001). In the univariate analysis, prior bacteremia was more common in patients with CSFDI (p = 0.027), but, in the multivariate model, prior bacteremia was not identified as an independent risk factor (OR = 0.456, CI: 0.138–1.512, p = 0.2). In an ICU population, the most frequently isolated pathogens were Gram-negative Enterobacteriaceae and Acinetobacter baumannii. Previous bacteremia was significantly more probable among patients with EVDs or LDs who developed a CSFDI, and its role warrants further investigation. Full article

Asinibacterium spp. (Family Chitinophagaceae, Phylum Bacteroidota) are abundant in environments contaminated with heavy metals. We characterized the physiology and genome of two Asinibacterium species to elucidate their ability to survive and grow at ambient conditions in the uranium-contaminated environments. Both strains were able to grow at pH 4.5 or 50 mM nitrate under aerobic conditions and did not grow with alternative electron acceptors under anaerobic conditions. Asinibacterium sp. OR53 grew in medium with uranium concentrations up to 300 µM uranium while Asinibacterium sp. OR43 could not grow at uranium concentrations > 200 µM. Elemental mapping using energy dispersive X-ray spectroscopy indicate that uranium co-localized with phosphorus-containing compounds on the cell surface. Genes potentially encoding resistance mechanisms to a variety of heavy metals were detected in the genomes of both strains. The localization of uranium and missing acidic and alkaline phosphatase genes in the genome suggest that biosorption of uranium to the lipopolysaccharide layer might be the mechanism of uranium resistance. In summary, Asinibacterium spp. OR43 and OR53 are physiologically similar to closely related strains within the Chitinophagaceae family but are uniquely acclimated to the presence of uranium and other heavy metals prevalent in the subsurface at Oak Ridge, Tennessee. Full article

We used machine-learning algorithms to evaluate demographic and clinical data in an administrative data set to identify relevant predictors of mortality due to Listeria monocytogenes infection. We used the Spanish Minimum Basic Data Set at Hospitalization (MBDS-H) to estimate the impacts of several predictors on mortality. The MBDS-H is a mandatory registry of clinical discharge reports. Data were coded with International Classification of Diseases, either Ninth or Tenth Revisions, codes. Diagnoses and clinical conditions were defined using recorded data from these codes or a combination of them. We used two different statistical approaches to produce two predictive models. The first was logistic regression, a classic statistical approach that uses data science to preprocess data and measure performance. The second was a random forest algorithm, a strategy based on machine learning and feature selection. We compared the performance of the two models using predictive accuracy and the area under the curve. Between 2001 and 2016, a total of 5603 hospitalized patients were identified as having any clinical form of listeriosis. Most patients were adults (94.9%). Among all hospitalized individuals, there were 2318 women (41.4%). We recorded 301 pregnant women and 287 newborns with listeriosis. The mortality rate was 0.13 patients per 100,000 population. The performance of the model produced by logistic regression after intense preprocessing was similar to that of the model produced by the random forest algorithm. Predictive accuracy was 0.83, and the area under the receiver operating characteristic curve was 0.74 in both models. Sepsis, age, and malignancy were the most relevant features related to mortality. Our combined use of data science, preprocessing, conventional statistics, and machine learning provides insights into mortality due to Listeria-related infection. These methods are not mutually exclusive. The combined use of several methods would allow researchers to better explain results and understand data related to Listeria monocytogenes infection. Full article