Lysinibacillus louembei sp. nov., a spore-forming bacterium isolated from Ntoba Mbodi, alkaline fermented leaves of cassava from the Republic of the Congo

Ureibacillus aquaedulcis sp. nov., isolated from freshwater well and reclassification of Lysinibacillus yapensis and Lysinibacillus antri as Ureibacillus yapensis comb. nov. and Ureibacillus antri comb. Nov

A Gram-stain-positive aerobic, rod-shaped, spore-producing bacterium forming colonies with convex elevation and a smooth, intact margin was isolated from a freshwater sample collected from a well situated in an agricultural field. The 16S rRNA gene sequence of the isolated strain BA0131T showed the highest sequence similarity to Lysinibacillus yapensis ylb-03T (99.25%) followed by Ureibacillus chungkukjangi 2RL3-2T (98.91%) and U. sinduriensis BLB-1T (98.65%). The strain BA0131T was oxidase and catalase positive and urease negative. It also tested positive for esculin hydrolysis and reduction of potassium nitrate, unlike its phylogenetically closest relatives. The predominant fatty acids in strain BA0131T included were anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C14:0 and the major polar lipids comprised were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The respiratory quinones identified in strain BA0131T were MK8 (H2) (major) and MK8 (minor). The strain BA0131T shared the lowest dDDH values with L. yapensis ylb-03T (21%) followed by U. chungkukjangi 2RL3-2T (24.2%) and U. sinduriensis BLB-1T (26.4%) suggesting a closer genetic relationship U. sinduriensis BLB-1T. The ANI percentage supported the close relatedness with U. sinduriensis BLB-1T (83.61%) followed by U. chungkukjangi 2RL3-2T (82.03%) and U. yapensis ylb-03T (79.57%). The core genome-based phylogeny constructed using over 13,704 amino acid positions and 92 core genes revealed the distinct phylogenetic position of strain BA0131T among the genus Ureibacillus. The distinct physiological, biochemical characteristics and genotypic relatedness data indicate the strain BA0131T represents a novel species of the genus Ureibacillus for which the name Ureibacillus aquaedulcis sp. nov. (Type strain, BA0131T = MCC 5284 = JCM 36475) is proposed. Additionally, based on extensive genomic and phylogenetic analyses, we propose reclassification of two species, L. yapensis and L. antri, as U. yapensis comb. nov. (Type strain, ylb-03T = JCM 32871T = MCCC 1A12698T) and U. antri (Type strain, SYSU K30002T = CGMCC 1.13504T = KCTC 33955T).

Evaluation of the Antimicrobial Activity of Phytochemicals from Tea and Agarwood Leaf Extracts against Isolated Bacteria from Poultry and Curd

Antibiotic-resistant bacteria are becoming increasingly common, leading to a global health crisis. The effects of abusing antibiotics not only increase pathogenic resistance but also cause various diseases and syndromes. Gut microbiota contains many beneficial roles for health, while antibiotics kill both pathogens and gut microbiota which is considered one of the major side effects of antibiotics. In fact, new antibiotic compounds are needed in this urgent scenario; phytoremediation is the oldest but most effective method, and research on the antibacterial properties of several types of medicinal plants has already been conducted. Tea and agarwood plants are well known for their economic contribution in both beverage and cosmetic production, as well as for their medicinal value. In this study, tea and agarwood leaf extracts were analyzed for their antimicrobial activity against both pathogenic and beneficial bacteria. Fresh tea (Camellia sinensis) leaves were collected in three varieties, namely, BT-6 from Sylhet, BT-7 from Moulvibazar, and BT-8 from Habiganj; also, green tea (nonfermented tea), black tea (fully fermented tea), and agarwood (Aquilaria malaccensis) were collected from Sylhet region of Bangladesh. Unlike commercial antibiotics, which have side effects on probiotics (beneficiary bacteria), leaf extract activities were analyzed to check if they had positive effects on probiotics that can be found in the gastrointestinal tract as well as dairy products. Potential beneficiary bacteria, Lysinibacillus macroides strain SRU-001 (NCBI accession no. MW665108), and pathogenic bacteria, Aeromonas caviae strain YPLS-62 (NCBI accession no. MW666783), were isolated from the small intestine of poultry and curd, respectively. Tea and agarwood leaves (5 g powder/80 mL methanol) with solvents were kept for seven days at room temperature, and extracts were applied for antimicrobial assays by the disc diffusion assay against the isolated bacteria. 50 µL of each leaf extract was examined against 50 µL of each bacterial culture, where gentamicin was a control. After 24 hours of incubation, tea and agarwood leaf extracts showed an 11-15 mm zone of inhibition against pathogenic A. caviae, while only BT-8 showed 7 mm (disc diameter 6 mm) against probiotic L. macroides. However, compared to leaf extracts, gentamicin showed a 27 mm zone of inhibition against both L. macroides strain SRU-001 and A. caviae strain YPLS-62 bacteria. This research clearly indicates that gentamicin kills both pathogenic and beneficiary bacteria, while leaf extracts from tea and agarwood plants contain antimicrobial activity against only pathogenic A. caviae but no effects on probiotic L. macroides. This outcome indicates not only the potential therapeutic values of tea and agarwood leaves as antibiotics over commercial antibiotics but also the chance of having pathogens in curd and potential beneficial bacteria from the poultry small intestine.

Additive-induced pH determines bacterial community composition and metabolome in traditional mustard seed fermented products

Introduction

Kahudi and Kharoli are unique naturally fermented mustard seed products prepared and consumed in the northeastern region of India. The pre-fermentation processing of mustard seeds (soaking, pan-frying, mixing with alkaline or acidic additives, airtight packaging) renders a stringent fermentation environment. The metabolic activities of fermenting bacterial populations yield a myriad of glucosinolate-derived bioactive components which have not been described earlier.

Methods

This present study employed integrated 16S rRNA amplicon sequencing and LC-MS-based metabolomics to elucidate the bacterial diversity and metabolome of the two fermented mustard seed food products.

Results and Discussion

Univariate and multivariate analyses of metabolomics data revealed differential abundances of a few therapeutically-important metabolites viz., sinapine, indole-3-carbinol, γ-linolenic acid in Kahudi, and metabolites viz., β-sitosterol acetate, 3-butylene glucosinolate, erucic acid in Kharoli. A metagenomic investigation involving the 16S rRNA (V3–V4) amplicon sequencing showed the dominance of Firmicutes (99.1 ± 0.18%) in Kahudi, and Firmicutes (79.6 ± 1.92%) and Proteobacteria (20.37 ± 1.94%) in Kharoli. The most abundant genera were Bacillus (88.7 ± 1.67% in Kahudi; 12.5 ± 1.75% in Kharoli) followed by Lysinibacillus (67.1 ± 2.37% in Kharoli; 10.4 ± 1.74% in Kahudi). Members of both these genera are well known for proteolytic and endospore-forming abilities which could have helped in colonizing and thriving in the stringent fermentation environments.

Analysis of bacterial communities of three cassava-based traditionally fermented Nigerian foods (abacha, fufu and garri)

Globally, cassava is an important food crop that contributes significantly to food security. In Nigeria, cassava can be traditionally processed into abacha (fermented strips), fufu (submerged-fermented porridge) and garri (solid-state fermented farinated granules) for human consumption. Despite the widespread consumption of these foods, there is a major knowledge gap in understanding their core bacterial diversity. This study, therefore, applied next-generation sequencing of 16S rRNA gene to delineate the bacterial diversity in abacha, fufu and garri. Amplicon sequence variants belonging to nine phyla were present in the three foods. Firmicutes dominated the bacterial community of abacha and fufu, whereas, Proteobacteria was the dominant phylum in garri. At genus level taxa, Lactococcus, Lysinibacillus and Pseudomonas dominated the bacterial community in abacha, fufu and garri, respectively. Other dominant phylotypes reported in the foods belonged to Bacillus, Clostridium sensu stricto (cluster 1), Cupriavidus, Enterobacter, Sphingomonas and Staphylococcus. To the best of our knowledge, Clostridium sensu stricto cluster 1 and Lysinibacillus in fufu, and Brevundimonas, Cupriavidus, Sphingomonas and Strenotrophomomas in garri are reported for the first time. Although some potential pathogenic genera were recorded, the foods contained potentially functional species that could be explored to improve artisanal food production, food security and safeguard consumer health.

Fermentation of Palm Oil Mill Effluent in the Presence of Lysinibacillus sp. LC 556247 to Produce Alternative Biomass Fuel

A bacterial strain, identified as Lysinibacillus sp. LC 556247 POME, was isolated from palm oil mill effluent (POME). The present article highlights the potential utilization of POME as a sole fermentation medium by Lysinibacillus sp. LC 556247 to produce biomass fuel via aerobic fermentation. The fermentation was performed in a shake flask with a working volume of 300 mL, agitated at 180 rpm, incubated at 35 ± 2 °C for various fermentation hours, ranging from 1, 2, 3, 4, 24, 48, 72, 96, and 120 h, and was followed by a drying process. Elucidation of the POME characteristics, calorific energy values (CEV), moisture content (MC), oil and grease content, chemical oxygen demand (COD), biochemical oxygen demand (BOD), dissolved oxygen (DO), total suspended solids (TSS), pH, total nitrogen, and the colony-forming unit (CFU) were performed. The results demonstrate that the highest CEV, of 21.25 ± 0.19 MJ/kg, was obtained at 48 h fermentation. High amounts of extractable oil and nitrogen content were retrieved at the highest CEV reading of the fermented and dried POME samples, which were 17.95 ± 0.02% and 12.80 ± 0.08%, respectively. The maximum removal efficiencies for the COD (50.83%), the BOD (71.73%), and the TSS (42.99%) were achieved at 120 h of fermentation, with an operating pH ranging from 4.49–4.54. The XRF analysis reveals that the fermented and dried products consisted of elements that had a high amount of carbon and potassium, and a significantly low amount of silica, which is sufficient for the effective burning of biomass fuel in the boiler.

Bacterial and Fungal Microbiome Profiling in Chilhuacle Negro Chili (Capsicum annuum L.) Associated With Fruit Rot Disease

Chilhuacle negro chili (Capsicum annuum L.) is an ancient Mexican landrace that is deeply linked to the culinary heritage of the country. Because of the high profitability and uniqueness of this crop, the Universidad Autónoma del Estado de Morelos is exploring its production in controlled environments. In the crop cycles of 2018 to 2019, the production of chilhuacle negro plants was seriously affected by an unidentified pathogen causing fruit rot, which reduced its quality, yield, and market value. Therefore, the main objective of this work was to study and characterize the fruit microbiota, which could help reveal the causal agent of this disease. Using DNA metabarcoding coupled with Illumina and nanopore sequencing technologies, we collected and analyzed both healthy and infected chili fruit, along with greenhouse bioaerosols. We also explored the bacterial and fungal microbiota by using microbiological techniques to isolate some of the culturable bacterial and fungal species. Our results suggest that the seedborne fungus Alternaria alternata is activated during the maturation stage of chilhuacle negro fruit, triggering a microbiome imbalance, which may in turn enable the establishment of other opportunistic pathogenic fungi during fruit decay, such as Mucor sp. To our knowledge, this is the first study of the chilhuacle negro chili microbiome, which can shed some light on our understanding of one of the main diseases that affect this valuable crop.

Lysinibacillus agricola sp. nov., isolated from soil

A gram-staining-positive, rod-shaped bacterium, designed strain FJAT-51161^T was isolated from farmland soil collected from Fujian Province, China. Growth was observed at 25-40 °C (optimum 30 °C), pH 7.0-9.0 (optimum 7.0), and NaCl tolerance in the range of 0-7% (w/v), respectively. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain FJAT-51161^T belonged to the genus Lysinibacillus, and had the closest relationship with Lysinibacillus xylanilyticus XDB9^T (99.0% 16S rRNA sequence similarity). The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values based on the genome sequence analysis between strain FJAT-51161^T and the closest reference strain were 38.0% for dDDH and 88.7% for ANI, respectively, lower than the prokaryotic species delineation values. Further analysis showed that strain FJAT-51161^T shared the fatty acid profiles such as iso-C_15:0 (46.7%), iso-C_16:0 (15.8%), C_16:1 ω7c alcohol (14.0%), anteiso-C_15:0 (6.9%) with other members of the genus Lysinibacillus. As the peptidoglycan contained the amino acids alanine, lysine, glycine and aspartic acid, the type A4α was deduced as found in the closest relatives of strain FJAT-51161^T. The peptidoglycan of strain FJAT-51161^T was L-Lys-D-Asp (type A4α). The main quinone was MK-7 and MK-6. The major polar lipids were diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE). The DNA G + C content is 36.6 mol%. Based on the phenotypic characters and taxono-genomics study, strain FJAT-51161^T is considered to represent a novel Lysinibacillus species, for which the name Lysinibacillus agricola sp. nov. is proposed. The type strain is FJAT-51161^T (GDMCC1.2350^T = KCTC 43326^T).

Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures

The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.

Application of LpxC enzyme inhibitor to inhibit some fast-growing bacteria in human gut bacterial culturomics

BACKGROUND

Culturomics can ascertain traces of microorganisms to be cultivated using different strategies and identified by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry or 16S rDNA sequencing. However, to cater to all requirements of microorganisms and isolate as many species as possible, multiple culture conditions must be used, imposing a heavy workload. In addition, the fast-growing bacteria (e.g., Escherichia) surpass the slow-growing bacteria in culture by occupying space and using up nutrients. Besides, some bacteria (e.g., Pseudomonas) suppress others by secreting antibacterial metabolites, making it difficult to isolate bacteria with lower competence. Applying inhibitors to restrain fast-growing bacteria is one method to cultivate more bacterial species from human feces.

RESULTS

We applied CHIR-090, an LpxC enzyme inhibitor that has antibacterial activity against most Gram-negative bacteria, to culturomics of human fresh feces. The antibacterial activity of CHIR-090 was first assessed on five Gram-negative species of bacteria (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus vulgaris, and Bacteroides vulgatus), all of which are commonly isolated from the human gut. Then, we assessed suitable concentrations of the inhibitor. Finally, CHIR-090 was applied in blood culture bottles for bacterial cultivation. In total, 102 species from five samples were identified. Of these, we found one new species, two species not reported previously in the human gut, and 11 species not previously isolated from humans.

CONCLUSIONS

CHIR-090 can suppress E. coli, P. aeruginosa, K. pneumoniae, Pro. vulgaris, but not B. vulgatus. Compared with the non-inhibitor group, CHIR-090 increased bacteria isolation by 23.50%, including four species not reported in humans and one new species. Application of LpxC enzyme inhibitor in culturomics increased the number of species isolated from the human gut.

Isolation and characterization of a novel piezotolerant bacterium Lysinibacillus yapensis sp. nov., from deep-sea sediment of the Yap Trench, Pacific Ocean

A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03^T, with peritrichous flagella was isolated from deep-sea sediment of the Yap Trench at a depth of 4435 m. The bacterium was found to be catalase-positive but oxidase-negative. Growth of this bacterium was observed at 15-50°C (optimum 37°C), pH 5-10.5 (optimum 7), 0-5% NaCl (optimum 1%, w/v) and 0.1-50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YLB-03^T was a member of the genus Lysinibacillus. Strain YLB-03^T was closely related to Lysinibacillus sinduriensis BLB-1^T and Lysinibacillus chungkukjangi 2RL3-2^T (98.4%), Lysinibacillus halotolerans LAM-612^T (98.0%), Lysinibacillus telephonicus KT735049^T (97.5%), Lysinibacillus endophyticus C9^T (97.5%), Lysinibacillus composti NCCP-36^T and Lysinibacillus massiliensis 4400831^T (97.3%). The ANI and the GGDC DNA-DNA hybridization estimate values between strain YLB-03^T and closely related type strains were 73.7-76.3% and 34.7-38.7%, respectively. The principal fatty acids were anteiso-C_15:0 and iso-C_15:0. The G+C content of the chromosomal DNA was 39.6 mol%. The respiratory quinone was determined to be MK-7. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α) and the cell-wall sugars were glucose and xylose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The combined genotypic and phenotypic data showed that strain YLB-03^T represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus yapensis sp. nov. is proposed, with the type strain YLB-03^T (= MCCC 1A12698^T = JCM 32871^T).

Genetic Clearness Novel Strategy of Group I Bacillus Species Isolated from Fermented Food and Beverages by Using Fibrinolytic Enzyme Gene Encoding a Serine-Like Enzyme

Fibrinolytic enzyme gene (fibE) is widely conserved among Bacillus spp. belonging to group I species. This is encoding a serine-like enzyme (FibE) secreted in extracellular medium. This present work aims to assess the molecular usefulness of this novel conserved housekeeping gene among group I Bacillus spp. to identify and discriminate some related strains in traditional fermented food and beverages in Republic of Congo. First of all 155 isolates have been screened for enzymatic activities using caseinolytic assays. PCR techniques and nested PCR method using specific primers and correlated with 16S RNA sequencing were used. Blotting techniques have been performed for deep comparison with molecular methods. As a result B. amyloliquefaciens (1), B. licheniformis (1), B. subtilis (1), B. pumilus (3), B. altitudinis (2), B. atrophaeus (1), and B. safensis (3) have been specifically identified among 155 isolates found in fermented food and beverages. Genetic analysis and overexpression of glutathione S-transferases (GSTs) fused to mature protein of FibE in Escherichia coli BL21 and TOP10 showed 2-fold higher enzymatic activities by comparison with FibE wild type one. Immunodetection should be associated but this does not clearly discriminate Bacillus belonging to group I.

Anti-biofilm Properties of Bacterial Di-Rhamnolipids and Their Semi-Synthetic Amide Derivatives

A new strain, namely Lysinibacillus sp. BV152.1 was isolated from the rhizosphere of ground ivy (Glechoma hederacea L.) producing metabolites with potent ability to inhibit biofilm formation of an important human pathogens Pseudomonas aeruginosa PAO1, Staphylococcus aureus, and Serratia marcescens. Structural characterization revealed di-rhamnolipids mixture containing rhamnose (Rha)-Rha-C10-C10, Rha-Rha-C8-C10, and Rha-Rha-C10-C12 in the ratio 7:2:1 as the active principle. Purified di-rhamnolipids, as well as commercially available di-rhamnolipids (Rha-Rha-C10-C10, 93%) were used as the substrate for the chemical derivatization for the first time, yielding three semi-synthetic amide derivatives, benzyl-, piperidine-, and morpholine. A comparative study of the anti-biofilm, antibacterial and cytotoxic properties revealed that di-Rha from Lysinibacillus sp. BV152.1 were more potent in biofilm inhibition, both cell adhesion and biofilm maturation, than commercial di-rhamnolipids inhibiting 50% of P. aeruginosa PAO1 biofilm formation at 50 μg mL^-1 and 75 μg mL^-1, respectively. None of the di-rhamnolipids exhibited antimicrobial properties at concentrations of up to 500 μg mL^-1. Amide derivatization improved inhibition of biofilm formation and dispersion activities of di-rhamnolipids from both sources, with morpholine derivative being the most active causing more than 80% biofilm inhibition at concentrations 100 μg mL^-1. Semi-synthetic amide derivatives showed increased antibacterial activity against S. aureus, and also showed higher cytotoxicity. Therefore, described di-rhamnolipids are potent anti-biofilm agents and the described approach can be seen as viable approach in reaching new rhamnolipid based derivatives with tailored biological properties.

Description of Lysinibacillus telephonicus sp. nov., isolated from the screen of a cellular phone

A novel bacterial strain, designated S5H2222T, was isolated form the screen of a cellular phone. The cells were Gram-stain-positive, rod-shaped, aerobic and motile, and endospores are formed. S5H2222T grew as pale white colonies on trypticase soy agar and the best growth was observed at 37 °C (10-55 °C) and at pH 7.0 (5.0-9.0). S5H2222T could tolerate up to 10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences placed this strain within the genus Lysinibacillus and it exhibited high 16S rRNA gene sequence similarity to Lysinibacillus halotolerans LAM612T (97.8 %), Lysinibacillus chungkukjangi 2RL3-2T (97.4 %) and Lysinibacillus sinduriensis BLB-1T (97.2 %). The DNA-DNA relatedness of the strain with L. halotolerans JCM 19611T, L. chungkukjangi KACC 16626T and L. sinduriensis KACC 16611T was 57, 64 and 55 % respectively. The genomic DNA G+C content was 39.8 mol%. The major fatty acids of S5H2222T were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. MK-7 was the only menaquinone and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, four unidentified polar lipids were also present. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α). On the basis of the results of the phenotypic and genotypic characterizations, it was concluded that S5H2222T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus telephonicus sp. nov. is proposed. The type strain is S5H2222T (=MCC 3065T=KACC 18714T=LMG 29294T).