Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group

Rheinheimera pleomorphica sp. nov., a Novel Alkali-Tolerant Bacteria Isolated from Chilika Lake, India

A novel Gram-negative gamma-proteobacterium, non-sporulating motile, rod or coccus-shaped bacterium designated as strain PKS7^T was isolated from a sediment sample collected from Chilika Lake, Odisha, India and characterized taxonomically using a polyphasic approach. The major quinone was Q8 and major cellular fatty acids were C_16:0, C_17:0, C_15:1w8c_, C_17:1w8c, C_12:03-OH. The chemotaxonomic features confirmed the isolate to be a member of genus Rheinheimera. 16SrRNA gene sequence of strain PKS7^T was closest in similarity to R. aquimaris SW-353^T (99.36% identity), R. muenzenbergensis E49^T (98.63%), R. nanhaiensis E407-8^T (98.35%), R. japonica KMM 9513^T (98.35%) and R. baltica DSM-14885^T (98.08%). The 16S rRNA gene sequence-based phylogenetic analysis and sequence similarity between the isolated strain and type strains also revealed its affiliation to genus Rheinheimera. DNA-DNA relatedness with closest type strain R. aquimaris SW-353^T was 25.0% (±3.40) and in silico DDH showed values in the range of 17.7-37.1% with the type strains of the genus Rheinheimera for which whole genome sequence are available. Strain PKS7^T was also distinguished by a multi-locus sequence analysis (MLST) by alingning gyrB gene sequences of the closest type strains of Rheinheimera. The draft genome of strain PKS7^T contained 32 contigs of total size 3,963,569 bp comprising of 3763 predicted coding sequences with a G + C content of 50.7 mol%. Comparision of phenotypic and genotypic data with its closest neighbours and closely related species confirm the strain PKS7^T to be recognised as a novel species within the genus Rheinheimera, for which the name Rheinheimera pleomorphica sp. nov. is proposed. The type strain is PKS7^T (= KCTC 42365 = JCM 30460).

Comparison of Six Commercial Meat Starter Cultures for the Fermentation of Yellow Mealworm (Tenebrio molitor) Paste

In this study, six commercial meat starters, each consisting of a pure strain of a lactic acid-fermenting bacterium (including Lactococcus lactis, Lactobacillus curvatus, L. farciminis, L. plantarum, L. sakei, and Pediococcus acidilactici), were tested for their ability to ferment a paste produced from the yellow mealworm (Tenebrio molitor). During fermentation, microbial counts, pH, and the bacterial community composition were determined. In addition, UPLC-MS was applied to monitor the consumption of glucose and the production of glutamic (Glu) and aspartic (Asp) acid. All tested starters were able to ferment the mealworm paste, judged by a pH reduction from 6.68 to 4.60–4.95 within 72 h. Illumina amplicon sequencing showed that all starters were able to colonize the substrate efficiently. Moreover, the introduction of the starter cultures led to the disappearance of Bacillus and Clostridium species, which were the dominant microorganisms in un-inoculated samples. Of the six cultures tested, Lactobacillus farciminis was most promising as its application resulted in the largest increase (±25 mg/100 g of paste) in the content of free glutamic and aspartic acid. These amino acids are responsible for the appreciated umami flavour in fermented food products and might stimulate the acceptance of insects and their consumption.

Biodegradation of Petroleum Hydrocarbons by Bacillus subtilis BL-27, a Strain with Weak Hydrophobicity

The biodegradation of petroleum hydrocarbons has many potential applications and has attracted much attention recently. The hydrocarbon-degrading bacterium BL-27 was isolated from petroleum-polluted soil and was compounded with surfactants to improve biodegradation. Its 16S rDNA and rpoD gene sequences indicated that it was a strain of Bacillus subtilis. Strain BL-27 had extensive adaptability and degradability within a broad range of temperatures (25–50 °C), pH (4.0–10.0) and salinity (0–50 g/L NaCl). Under optimal conditions (45 °C, pH 7.0, 1% NaCl), the strain was able to degrade 65% of crude oil (0.3%, w/v) within 5 days using GC-MS analysis. Notably, strain BL-27 had weak cell surface hydrophobicity. The adherence rate of BL-27 to n-hexadecane was 29.6% with sucrose as carbon source and slightly increased to 33.5% with diesel oil (0.3%, w/v) as the sole carbon source, indicating that the cell surface of BL-27 is relatively hydrophilic. The strain was tolerant to SDS, Tween 80, surfactin, and rhamnolipids at a concentration of 500 mg/L. The cell surface hydrophobicity reduced more with the addition of surfactants, while the chemical dispersants, SDS (50–100 mg/L) and Tween 80 (200–500 mg/L), significantly increased the strain’s ability to biodegrade, reaching 75–80%. These results indicated that BL-27 has the potential to be used for the bioremediation of hydrocarbon pollutants and could have promising applications in the petrochemical industry.

Application of Zearalenone (ZEN)-Detoxifying Bacillus in Animal Feed Decontamination through Fermentation

Zearalenone (ZEN) is an estrogenic mycotoxin which can cause loss in animal production. The aim of this study was to screen Bacillus strains for their ZEN detoxification capability and use a fermentation process to validate their potential application in the feed industry. In the high-level ZEN-contaminated maize (5 mg·kg-1) fermentation test, B2 strain exhibited the highest detoxification rate, removing 56% of the ZEN. However, B2 strain was not the strain with the highest ZEN detoxification in the culturing media. When B2 grew in TSB medium with ZEN, it had higher bacterial numbers, lactic acid, acetic acid, total volatile fatty acids, and ammonia nitrogen. The ZEN-contaminated maize fermented by B2 strain had better fermentation characteristics (lactic acid > 110 mmol·L-1; acetic acid < 20 mmol·L-1; pH < 4.5) than ZEN-free maize. Furthermore, B2 also had detoxification capabilities toward aflatoxins B1, deoxynivalenol, fumonisin B1, and T2 toxin. Our study demonstrated differences in screening outcome between bacterial culturing conditions and the maize fermentation process. This is important for the feed industry to consider when choosing a proper method to screen candidate isolates for the pretreatment of ZEN-contaminated maize. It appears that using the fermentation process to address the ZEN-contaminated maize problem in animal feed is a reliable choice.

Genotypic and phenotypic characterization of Edwardsiella isolates from different fish species and geographical areas in Asia: Implications for vaccine development

The genus Edwardsiella is one of the major causes of fish diseases globally. Herein, we examined 37 isolates from ten different fish species from India, South Korea and Taiwan to gain insight into their phenotypic and genotypic properties, of which 30 were characterized as E. tarda with phenotypic homology estimated at 85.71% based on API-20E biochemical tests. Genotyping using 16S rRNA put all isolates together with E. anguillarum, E. hoshinae, E. tarda, E. piscicida and E. ictaluri reference strains in a monophyletic group. In contrast, the gyrB phylogenetic tree clearly separated E. ictaluri, E. tarda and E. hoshinae reference strains from our isolates and put our isolates into two groups with group I being homologous with the E. anguillarum reference strain while group II was homologous with the E. piscicida reference strain. Hence, our findings point to E. piscicida and E. anguillarum as species infecting different fish species in Asia. Homology of the ompW protein suggested that strains with broad protective coverage could be identified as vaccine candidates. This study underscores the importance of combining genotyping with phenotyping for valid species classification. In addition, it accentuates the importance of phylogenetic comparison of bacterial antigens for identification of potential vaccine candidates.

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.

Phylogenetic diversity of aerobic spore-forming Bacillalles isolated from Brazilian soils

The phylum Firmicutes comprises seven classes where most species are either aerobic or anaerobic endospore former. Inside Firmicutes, species allocated in the genus Bacillus and related genera are collectively named aerobic endospore-forming bacteria (AEFB), and the soil is their major reservoir. AEFB have great importance in health, agriculture, and biotechnology although the more studied species are Bacillus subtilis and the human pathogens Bacillus cereus and Bacillus anthracis. AEFB have great importance in health, agriculture, and biotechnology; although the knowledge about these organisms is based on few species, notably, Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. In this work, we generated partial 16S rRNA gene sequences of both strands of 192 AEFB strains isolated from soils of Distrito Federal, Brazil (SDF strains). The resulting consensus sequences were used to obtain taxonomic assignment and establish the phylogenetic relationships among these strains. Through this approach, we could observe that classified SDF strains were distributed among genera Bacillus (169 strains; 88.02%), Paenibacillus (11; 5.73%), Lysinibacillus (6; 3.13%), Brevibacillus (4; 2.08%), Terribacillus (1; 0.52%), and Rummeliibacillus (1; 0.52%). Phylogenetic trees revealed these 192 SDF strains can be segregated into eight groups spanning families Bacillaceae and Paenibacillaceae belonging to the order Bacillales. To expand the knowledge about the diversity of these SDF strains, further studies regarding characterization with different methodologies are underway.

Molecular Characterization and Toxin Profiles of Bacillus spp. Isolated from Retail Fish and Ground Beef

Bacillus species are common in the environment due to their spore-forming ability and nutritional versatility and cause food contamination. Bacilli play a significant role in foodborne illnesses and food spoilage. In this study, 52 Bacillus isolates from retail fish and ground beef were identified and differentiated based on 16S rRNA, gyrB, and rpoB gene sequencing. The presence of genes encoding emetic toxin (ces), hemolytic enterotoxin hemolysin BL (hbl), nonhemolytic enterotoxin (nhe) and cytotoxin K (cytK1) was assessed in all Bacillus isolates. The ability of the Bacillus isolates to produce several extracellular enzymes that contribute to pathogenicity and food spoilage was investigated. The 16S rRNA, rpoB, and gyrB gene sequence similarities of the Bacillus isolates tested were 96.1%, 83.2%, and 77.5%, respectively. The gyrB gene demonstrated a higher degree of sequence variation than the 16S rRNA and rpoB genes. The prevalence of Bacillus isolates producing at least two of the genes of the HBL and NHE complexes was 23.1% and 15.4%, respectively. Of the B. cereus isolates, 10 (41.7%) possessed two or more enterotoxin genes. None of the isolates carried the ces and cytK1 genes. All isolates were positive for the production of enzymes such as protease, lipase, gelatinase, and DNase. However, only 92.3% of the tested isolates were positive for amylase. In conclusion, our results revealed that the presence of genes involved in toxin production and enzyme production in meat-originated B. cereus and other Bacillus isolates may cause spoilage of food and pose a health risk for consumers. PRACTICAL APPLICATION: Bacillus species can be found in various foods due to their ubiquitous nature. Bacillus spp., especially B. cereus, are associated with food poisoning and other infections in humans. Toxins and many extracellular enzymes produced by Bacillus spp. are the causative agents of foodborne outbreaks, food spoilage, and low-quality food with significantly reduced edibility. This study highlights the characterization of Bacillus spp. and presence of potentially pathogenic Bacillus species in meats.

Underrecognized niche of spore-forming bacilli as a nitrite-producer isolated from the processing lines and end-products of powdered infant formula

Although nitrite in powdered milk formula (PIF) is a recognized health risk for infants, the presence of nitrite in PIF has only been investigated as a chemical contaminant during the inspection of end-products. The risk posed by microbial sources of nitrite during the PIF manufacturing process has not been considered. This is the first study to report the taxonomy and physiological characteristics of nitrite-producing bacteria isolated from PIF processing environments. All isolates identified as nitrite-producers (133 out of 501 strains collected over four years) from work-in-process and end-products of PIF were spore-forming bacilli. Nitrite-producing metabolism under PIF processing conditions was found in not only thermophilic isolates (3 Bacillus, 60 Geobacillus from 63 strains; 100%) but also in mesophilic isolates (65 Bacillus, 1 Anoxybacillus from 70 strains; 65.7%). Geobacillus was the only highly heat-resistant sporeformer and vigorous nitrite-producer exhibiting dramatic increases in nitrite over short periods of incubation (a maximum value within 3 h). High conversions of nitrate to nitrite (up to 88.8%) was also observed, highlighting bacteria as a key source of nitrite in PIF processing lines. Further research into the diversity of metabolic activity observed in this study can facilitate specialized management of nitrite-producers in PIF processing lines.

Thalassospira marina sp. nov., isolated from surface seawater

Two novel marine bacteria, designated strains CSC3H3^T and CSC1P2, were isolated from surface seawater of the South China Sea. Both strains were Gram-negative, oxidase-positive, catalase-positive, curved rods and motile. They grew at 10-40 °C, pH 5-10 and in the presence of 0-15 % (w/v) NaCl. Their 16S rRNA gene sequences were identical to each other. Phylogenetic analysis based on 16S rRNA gene sequences indicated that they belong to the genus Thalassospira, and shared 97.5-98.3 % sequence similarity to all other validly type strains of the genus Thalassospira, and the highest similarity was to the type strain Thalassospira povalilyticaZumi 95^T (98.3 %), followed by Thalassospira australica NP3b2^T (98.2 %). The digital DNA-DNA hybridization value between the two strains was 80.4 %, while the values with T. povalilyticaZumi 95^T and T. australica NP3b2^T were only 20.5-20.7 % and 20.4-20.5 %, respectively. The two strains possess similar major cellular fatty acids including C18 : 1ω7c, C16 : 0, C19 : 0ω8c cyclo, C18 : 1 2-OH and C17 : 0 cyclo. The G+C contents of the chromosomal DNA of strains CSC3H3^T and CSC1P2 were 54.6 and 54.5 mol%, respectively. The major respiratory quinone was ubiquinone 10. Phosphatidylethanolamine, phosphatidylglycerol and several unidentified phospholipids, aminolipid and lipids were present in both strains. Based on phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Thalassospira, for which the name Thalassospira marina sp. nov. is proposed. The type strain is CSC3H3^T (=MCCC 1A11786^T=KCTC 62333^T).

A Novel Oligonucleotide Pair for Genotyping Members of the Pseudomonas Genus by Single-Round PCR Amplification of the gyrB Gene

Pseudomonas is a phylogenetically diverse bacterial genus which is broadly distributed in different ecological niches, and whose taxonomy is continuously under revision. For that purpose, gyrB is one of the housekeeping genes routinely used for multilocus sequence analysis (MLSA). As we noticed that there was not a single primer pair available in the literature suitable for direct sequencing of this gene, we decided to design a unique oligonucleotide pair and to set up a polymerase chain reaction (PCR) protocol to obtain a single amplicon for the entire Pseudomonas genus. Based on the available gyrB sequence from 148 Pseudomonas species, we identified highly conserved regions to design oligonucleotides without fully degenerate positions. We then set up cycling conditions for achieving high specificity and yield of the PCR protocol. Then, we showed that the amplicons produced with this procedure were appropriate for direct sequencing with both primers, obtaining more than 95% of amplicons coverage. Finally, we demonstrated that a PCR-RFLP (restriction fragment length polymorphism) approach served to differentiate among Pseudomonas species, and even between members of the same species.

Bacillus subtilis strain specificity affects performance improvement in broilers

The study reports the effects on broiler performance of a newly isolated Bacillus subtilis strain, which is phylogenetically not closely related to already well-described strains of B. subtilis. In the first experiment, birds were reared in battery cages and exposed to C. perfringens. An increase in growth performance was observed with the strain when compared to the challenged animals. Three additional growth trials were conducted to 35 d of age, in different rearing conditions (genetic breeds, corn-soybean meal-based diet with or without animal proteins, in presence or absence of phytase, on fresh or used litter) to investigate the efficacy and the specificity of this new B. subtilis strain on the improvement of BWG and FCR of broilers in comparison with a B. subtilis-based DFM already used in the field. Whatever the rearing conditions tested, the new B. subtilis strain led to an average 3.2% improvement in feed conversion ratio or bodyweight. Comparatively, the commercial Bacillus strain significantly improved broiler performance in only one trial out of 3 with an average improvement reaching 2%. All these results indicate that this new B. subtilis strain consistently improves broiler performances.

Isolation of bacteria from fermented food and grass carp intestine and their efficiencies in improving nutrient value of soybean meal in solid state fermentation

Background

Soybean meal is an excellent and cost-effective protein source; however, its usage is limited in the piglet due to the presence of anti-nutritional factors and the antigens glycinin and β-conglycinin. The objective of the current study was to screen and select for bacteria that can be efficiently adopted to ferment soybean meal in order to solve this problem.

Results

Bacteria were isolated from fermented soy foods and the grass carp intestine, and strains selected for high protease, cellulase and amylase activities. The isolated bacteria were characterized as Bacillus cereus, Bacillus subtilis and Bacilus amyloliquefacien, respectively. Fermentation with food-derived Isolate-2 and fish-derived F-9 increased crude protein content by 5.32% and 8.27%, respectively; improved the amino acid profile by increasing certain essential amino acids, broke down larger soy protein to 35 kDa and under, eliminated antigenicity against glycinin and β-conglycinin, and removed raffinose and stachyose in the soybean meal following a 24-h fermentation.

Conclusions

Our results suggest these two B. amyloliquefaciens bacteria can efficiently solid state ferment soybean meal and ultimately produce a more utilizable food source for growing healthy piglets.

Versatile Antagonistic Activities of Soil-Borne Bacillus spp. and Pseudomonas spp. against Phytophthora infestans and Other Potato Pathogens

The world potato is facing major economic losses due to disease pressure and environmental concerns regarding pesticides use. This work aims at addressing these two issues by isolating indigenous bacteria that can be integrated into pest management strategies. More than 2,800 strains of Bacillus-like and Pseudomonas-like were isolated from several soils and substrates associated with potato agro-systems in Belgium. Screenings for antagonistic activities against the potato pathogens Alternaria solani, Fusarium solani (BCCM-MUCL 5492), Pectobacterium carotovorum (ATCC 15713), Phytophthora infestans (CRA-W10022) and Rhizoctonia solani (BCCM-MUCL 51929) were performed, allowing the selection of 52 Bacillus spp. and eight Pseudomonas spp. displaying growth inhibition of at least 50% under in vitro conditions, particularly against P. infestans. All 60 bacterial isolates were identified based on 16S rRNA gene sequencing and further characterized for the production of potential bio-active secondary metabolites. The antagonistic activities displayed by the selected strains indicated that versatile metabolites can be produced by the strains. For instance, the detection of genes involved bacilysin biosynthesis was correlated with the strong antagonism of Bacillus pumilus strains toward P. infestans, whereas the production of both bio-surfactants and siderophores might explain the high antagonistic activities against late blight. Greenhouse assays with potato plants were performed with the most effective strains (seven Bacillus spp. and four Pseudomonas spp.) in order to evaluate their in vivo antagonistic effect against P. infestans. Based on these results, four strains (Bacillus amyloliquefaciens 17A-B3, Bacillus subtilis 30B-B6, Pseudomonas brenneri 43R-P1 and Pseudomonas protegens 44R-P8) were retained for further evaluation of their protection index against P. infestans in a pilot field trial. Interestingly, B. subtilis 30B-B6 was shown to significantly decrease late blight severity throughout the crop season. Overall, this study showed that antagonistic indigenous soil bacteria can offer an alternative to the indiscriminate use of pesticide in potato agro-systems.

Complete Genome Sequence of Bacillus velezensis CN026 Exhibiting Antagonistic Activity against Gram-Negative Foodborne Pathogens

We report here the complete genome sequence of Bacillus velezensis strain CN026, a member of the B. subtilis group, which is known for its many industrial applications. The genome contains 3,995,812 bp and displays six gene clusters potentially involved in strain CN026’s activity against Gram-negative foodborne pathogens.

Evaluation of repetitive-PCR and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid strain typing of Bacillus coagulans

In order to establish rapid and accurate typing method for Bacillus coagulans strains which is important for controlling in some canned foods and tea-based beverages manufacturing because of the high-heat resistance of the spores and high tolerance of the vegetative cells to catechins and chemicals, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and repetitive-PCR (rep-PCR) were evaluated. For this purpose, 28 strains of B. coagulans obtained from various culture collections were tested. DNA sequence analyses of the genes encoding 16S rRNA and DNA gyrase classified the test strains into two and three groups, respectively, regardless of their phenotypes. Both MALDI-TOF MS and rep-PCR methods classified the test strains in great detail. Strains classified in each group showed similar phenotypes, such as carbohydrate utilization determined using API 50CH. In particular, the respective two pairs of strains which showed the same metabolic characteristic were classified into the same group by both MALDI-TOF MS and rep-PCR methods separating from the other strains. On the other hand, the other strains which have the different profiles of carbohydrate utilization were separated into different groups by these methods. These results suggested that the combination of MALDI-TOF MS and rep-PCR analyses was advantageous for the rapid and detailed typing of bacterial strains in respect to both phenotype and genotype.

Characterization of garlic endophytes isolated from the black garlic processing

The objectives of this study were to isolate and identify garlic endophytes, and explore the characteristics of dominant strains. Garlic endophytes were studied through phenotypical characterization and comparative sequence analysis of 16S rDNA based on culture‐dependent approaches. Representative strains inferred from 16S rDNA sequencing were selected for further identification by gyrA and rpoB gene loci and phylogenetic analysis based on concateneted house‐keeping sequences. Seven kinds of Bacillus were found from garlic and black garlic, respectively. Further studies demonstrated that the total bacteria and endophytes showed a sharp decrease firstly, followed by a rapid rise, then maintained at a certain level, and finally slowed down during the black garlic processing. B. subtilis, B. methylotrophicus, and B. amyloliquefaciens were the dominant strains. The selected strains were capable of fermenting glucose, lactose, sucrose, and garlic polysaccharide to produce acid but no gas, with a strong ability of heat resistance. The results indicated that there were a certain number of garlic endophytes during the black garlic processing, and Bacillus was the dominant strains under the conventional culture‐dependent methods. This report provided useful information for the presence and type of garlic endophytes during the black garlic processing, which were of great significance to study the formation mechanism and quality improvement of black garlic in the future, as well as the security of garlic powder.

Draft Genome Sequences of Bacillus subtilis Strain DKU_NT_01 Isolated from Traditional Korean Food Containing Soybean (Chung-gook-jang)

Here, we report the whole-genome sequence of Bacillus subtilis strain DKU_NT_01 isolated from traditional Korean food containing soybean (chung-gook-jang). The de novo genome of Bacillus subtilis strain DKU_NT_01 has one contig and G+C content of 55.4%, is 4,954,264 bp in length, and contains 5,011 coding sequences (CDSs).

Production of bioactive hydrolysate using protease, β-glucosidase and α-amylase of Bacillus spp. isolated from kinema

The aim of this study was the production of soybean bioactive hydrolysate using Bacillus spp. isolated from kinema. Totally 251 bacteria isolated from kinema samples, collected at different time period were screened for protease, β-glucosidase and α-amylase activities and further identified by ARDRA based grouping followed by analysis of 16S rRNA gene sequence similarity. The results showed that Bacillus subtilis, Bacillus amyloliquefaciens and Bacillus licheniformis were the major Bacillus species. Twelve fermentative strains belonging to these groups and having high protease, α-amylase and β-glucosidase activity were used for solid state fermentation. The best strains for soybean fermentation that result in production of protein hydrolysates rich in polyphenols that have higher bioactivity were B. subtilis KN12C, B. amyloliquefaciens KN2G and B. licheniformis KN13C. Potential isolates can be applied for the production of soybean hydrolysates and can also find application in production of value added products from by-products of soybean processing industries.

Impact of Mannanase-Producing Bacillus spp. on the Accuracy of the 3M Petrifilm Aerobic Count Method

Consistent deviations of the 3M Petrifilm aerobic counts (AC) from the standard pour plate aerobic plate count (APC) were observed with dehydrated onion and garlic products. A large study was designed to determine the relationship of these two methods and the root cause for the deviations. A total of 3,800 dehydrated onion and garlic samples were analyzed by both the Petrifilm AC and the standard pour plate APC method. Large spreader-like liquefied areas were observed on numerous Petrifilm plates. These liquefied areas made enumeration inaccurate. "Liquefier" microorganisms from Petrifilm plates were isolated and identified to species level by 16S rRNA and gyrB gene sequencing. Enzyme diffusion assay was performed to determine potential enzymatic degradation of guar gum, the gelling agent used in Petrifilm plates. The results indicated that the correlation between Petrifilm AC and standard APC is relatively low. Paired t test results suggested that the Petrifilm AC method produced significantly different results compared with standard APC. The discrepancies were attributable at least partly to a liquefier organism that hydrolyzed guar gum, leading to liquefaction. Liquefaction of Petrifilm plates seems to have two effects on accuracy: (i) liquefied areas may allow motile organisms to move and multiply in the liquefied area during the incubation period, yielding more than one colony from one cell and, as a result, leading to overestimation of the microbial load and (ii) the blurred areas obscure other colonies, leading to potential underestimation. The liquefier organism was identified as Bacillus amyloliquefaciens , a potent mannanase producer and heat-resistant spore former. Enzyme diffusion assay confirmed that mannanase contained in the cell-free supernatant of B. amyloliquefaciens can hydrolyze the 1,4-β-mannopyranosyl bond, the backbone of guar gum. This is the first report of the role of B. amyloliquefaciens in the liquefaction of Petrifilm plates and its negative impact on accuracy.

Introducing the sporobiota and sporobiome

Unrelated spore-forming bacteria share unique characteristics stemming from the presence of highly resistant endospores, leading to similar challenges in health and disease. These characteristics are related to the presence of these highly transmissible spores, which are commonly spread within the environment and are implicated in host-to-host transmission. In humans, spore-forming bacteria contribute to a variety of pathological processes that share similar characteristics, including persistence, chronicity, relapses and the maintenance of the resistome. We first outline the necessity of characterizing the totality of the spore-forming bacteria as the sporobiota based on their unique common characteristics. We further propose that the collection of all genes of spore-forming bacteria be known as the sporobiome. Such differentiation is critical for exploring the cross-talk between the sporobiota and other members of the gut microbiota, and will allow for a better understanding of the implications of the sporobiota and sporobiome in a variety of pathologies and the spread of antibiotic resistance.

Multilocus Genetic Characterization of Lactobacillus fermentum Isolated from Ready-to-Eat Canned Food

The primary mission of the U.S. Food and Drug Administration is to enforce the Food, Drug, and Cosmetic Act and regulate food, drug, and cosmetic products. Thus, this agency monitors the presence of pathogenic microorganisms in these products, including canned foods, as one of the regulatory action criteria and also ensures that these products are safe for human consumption. This study was carried out to investigate the effectiveness of pathogen control and integrity of ready-to-eat canned food containing Black Bean Corn Poblano Salsa. A total of nine unopened and recalled canned glass jars from the same lot were examined initially by conventional microbiologic protocols that involved a two-step enrichment, followed by streaking on selective agar plates, for the presence of gram-positive and gram-negative bacteria. Of the eight subsamples examined for each sample, all subsamples of one of the containers were found positive for the presence of slow-growing rod-shaped, gram-positive, facultative anaerobic bacteria. The recovered isolates were subsequently sequenced at rRNA and gyrB loci. Afterward, multilocus sequence typing (MLST) was performed characterizing 11 additional known MLST loci (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). Analyses of the nucleotide sequences of rRNA, gyrB, and 11 MLST loci confirmed these gram-positive bacteria recovered from canned food to be Lactobacillus fermentum . Thus, the DNA sequencing of housekeeping MLST genes can provide species identification of L. fermentum and can be used in the canned food monitoring program of public health importance.

First complete genome sequence of Bacillus glycinifermentans B-27

The first complete genome sequence of Bacillus glycinifermentans B-27 was determined by SMRT sequencing generating a genome sequence with a total length of 4,607,442 bases. Based on this sequence 4738 protein-coding sequences were predicted and used to identify gene clusters that are related to the production of secondary metabolites such as Lichenysin, Bacillibactin and Bacitracin. This genomic potential combined with the ability of B. glycinifermentans B-27 to grown in bile containing media might contribute to a future application of this strain as probiotic in productive livestock potentially inhibiting competing and pathogenic organisms.

Studies on expression of different virulence genes of Pasteurella multocida

Pasteurella multocida is the causative agent of a wide range of diseases in avian and mammalian hosts. Different adhesin and membrane proteins play role in the pathogenesis of the disease. In the present study, the relative expression of 5 different virulence genes (plpE, ptfA, tbpA, hgbA and fhaB1) from Pasteurella multocida B:2 grown in iron rich and iron limiting media was measured using real time PCR employing SYBR green chemistry. The expression of tbpA, hgbA, plpE and fhaB1 was found to be significantly upregulated by 4, 2.3, 1.3, 2.3 folds, respectively, under iron limiting conditions. In contrast, the expression of gene ptfA was significantly down regulated (0.4 fold) as compared to organism grown in normal medium.

Extracts containing CLPs of Bacillus amyloliquefaciens JN68 isolated from chicken intestines exert antimicrobial effects, particularly on methicillin-resistant Staphylococcus aureus and Listeria monocytogenes

Bacillus amyloliquefaciens JN68, which has been discussed with regards to its antimicrobial activities, was successfully isolated from healthy chicken intestines in the present study. Using the spot-on-the-lawn antagonism method, the preliminary study indicated that a suspension culture of the B. amyloliquefaciens JN68 strain can inhibit the growth of Aspergillus niger and Penicillium pinophilum. Furthermore, the cyclic lipopeptides (CLPs) produced by the B. amyloliquefaciens JN68 strain were further purified through acid precipitation and Bond Elut®C18 chromatography, and their structures were identified using the liquid chromatography‑electrospray ionization‑mass spectrometry (MS)/MS method. Purified CLPs exerted broad spectrum antimicrobial activities on various pathogenic and foodborne bacteria and fungi, as determined using the agar well diffusion method. Listeria monocytogenes can induce listeriosis, which is associated with a high mortality rate. Methicillin‑resistant Staphylococcus aureus (MRSA) is a major pathogenic bacteria that causes nosocomial infections. Therefore, L. monocytogenes and MRSA are currently of great concern. The present study aimed to determine whether B. amyloliquefaciens JN68 extracts could inhibit L. monocytogenes and MRSA. The results indicated that extracts of B. amyloliquefaciens JN68 have CLP components, and can successfully inhibit the growth of L. monocytogenes and MRSA.

Structural differences in gut bacteria communities in developmental stages of natural populations of Lutzomyia evansi from Colombia's Caribbean coast

Background

Lutzomyia evansi, a phlebotomine insect endemic to Colombia’s Caribbean coast, is considered to be the main vector of visceral and cutaneous leishmaniasis in the region. Although insects of this species can harbor pathogenic and non-pathogenic microorganisms in their intestinal microbiota, there is little information available about the diversity of gut bacteria present in Lutzomyia evansi. In this study, conventional microbiological methods and molecular tools were used to assess the composition of bacterial communities associated with Lutzomyia evansi guts in immature and adult stages of natural populations from the department of Sucre (Caribbean coast of Colombia).

Methods

Sand flies were collected from two locations (peri-urban and jungle biotype) in the Department of Sucre (Caribbean coast of Colombia). A total of 752 Lutzomyia evansi intestines were dissected. In this study, 125 bacterial strains were isolated from different culture media (LB Agar, MacConkey Agar). Different methods were used for bacterial identification, including ribosomal intergenic spacer analysis (RISA) and analysis of the 16S rRNA and gyrB gene sequences. The genetic profiles of the bacterial populations were generated and temporal temperature gradient gel electrophoresis (TTGE) was used to compare them with total gut DNA. We also used PCR and DNA sequence analysis to determine the presence of Wolbachia endosymbiont bacteria and Leishmania parasites.

Results

The culture-dependent technique showed that the dominant intestinal bacteria isolated belong to Acinetobacter, Enterobacter, Pseudomonas, Ochrobactrum, Shinella and Paenibacillus in the larval stage; Lysobacter, Microbacterium, Streptomyces, Bacillus and Rummeliibacillus in the pupal stage; and Staphylococcus, Streptomyces, Brevibacterium, Acinetobacter, Enterobacter and Pantoea in the adult stage. Statistical analysis revealed significant differences between the fingerprint patterns of the PCR-TTGE bands in bacterial communities from immature and adult stages. Additionally, differences were found in bacterial community structure in fed females, unfed females, males and larvae. The intestinal bacteria detected by PCR-TTGE were Enterobacter cloacae and Bacillus thuringiensis, which were present in different life stages of Lu. evansi, and Burkholderia cenocepacia and Bacillus gibsonii, which were detected only in the larval stage. Wolbachia and Leishmania were not detected in gut samples of Lutzomyia evansi.

Conclusions

The analyses conducted using microbiological and molecular approaches indicated significant variations in the bacterial communities associated with the gut of Lu. evansi, depending on the developmental stage and food source. We propose that these elements affect microbial diversity in L. evansi guts and may in turn influence pathogen transmission to humans bitten by this insect.

Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57

Bacillus amyloliquefaciens H57 is a bacterium isolated from lucerne for its ability to prevent feed spoilage. Further interest developed when ruminants fed with H57-inoculated hay showed increased weight gain and nitrogen retention relative to controls, suggesting a probiotic effect. The near complete genome of H57 is ~3.96 Mb comprising 16 contigs. Within the genome there are 3,836 protein coding genes, an estimated sixteen rRNA genes and 69 tRNA genes. H57 has the potential to synthesise four different lipopeptides and four polyketide compounds, which are known antimicrobials. This antimicrobial capacity may facilitate the observed probiotic effect.

Molecular analysis of bacterial community dynamics during the fermentation of soy-daddawa condiment

Bacterial community dynamics during soy-daddawa fermentation was investigated using culture-dependent and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) molecular methods. The total titratable acidity (TTA), pH, and bacterial counts (BCs) were monitored daily during a 72-h fermentation period. Bacteria were characterized based on 16S rRNA gene sequencing. TTA ranged from 0.08 to 0.26 mg lactic acid/g, whereas pH ranged from 7.01 to 8.19. BCs increased from 3.9 to 10.61 log CFU/g. Fifty-eight isolates were obtained by culture method and clustered into seven operational taxonomic units (OTUs) at 97% sequence similarity, whereas four OTUs were obtained from the PCR-DGGE method. Taxonomic identification revealed that bacteria belonged to the genera Bacillus, Enterobacter, Enterococcus, and Staphylococcus with B. subtilis being present throughout fermentation. Medically significant isolates, including B. anthracis, Enterococcus casseliflavus, and Enterobacter hormaechei were detected. These results emphasize the need for starter culture utilization and offer a platform for starter culture screening and selection.

Ecology of Bacillaceae

Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.

PCR-denaturing gradient gel electrophoresis analysis of microbial community in soy-daddawa, a Nigerian fermented soybean (Glycine max (L.) Merr.) condiment

Soy-daddawa, a fermented soybean (Glycine max (L.) Merr.) condiment, plays a significant role in the culinary practice of West Africa. It is essential to understand the microbial community of soy-daddawa for a successful starter culture application. This study investigated the microbial community structure of soy-daddawa samples collected from Nigerian markets, by PCR-denaturing gradient gel electrophoresis (DGGE) targeting the V3-V5 region of the 16S rRNA gene of bacteria and internal transcribed spacer 2 (ITS2) region of fungi. Six bacterial and 16 fungal (nine yeasts and seven molds) operational taxonomic units (OTUs)/species were obtained at 97% sequence similarity. Taxonomic assignments revealed that bacterial OTUs belonged to the phyla Firmicutes and Actinobacteria, and included species from the genera Atopostipes, Bacillus, Brevibacterium and Nosocomiicoccus. Densitometric analysis of DGGE image/bands revealed that Bacillus spp. were the dominant OTU/species in terms of population numbers. Fungal OTUs belonged to the phyla Ascomycota and Zygomycota, and included species from the genera, Alternaria, Aspergillus, Candida, Cladosporium, Dokmaia, Issatchenkia, Kodamaea, Lecythophora, Phoma, Pichia, Rhizopus, Saccharomyces and Starmerella. The majority of fungal species have not been previously reported in soy-daddawa. Potential opportunistic human pathogens such as Atopostipes suicloacalis, Candida rugosa, Candida tropicalis, and Kodamaea ohmeri were detected. Variation in soy-daddawa microbial communities amongst samples and presence of potential opportunistic pathogens emphasises the need for starter culture employment and good handling practices in soy-daddawa processing.

Engineering of a Bacillus amyloliquefaciens Strain with High Neutral Protease Producing Capacity and Optimization of Its Fermentation Conditions

The neutral protease has high potential for industrial applications, and attempts to improve enzyme expression level have important application values. In the present study, a neutral protease-encoding gene, Banpr, was cloned from Bacillus amyloliquefaciens strain K11, and a genetic manipulation method specific for this difficult-to-transform strain was developed for the high-level expression of neutral protease. The recombinant plasmid pUB110-Banpr was constructed in Bacillus subtilis strain WB600 and then transformed into strain K11 under optimized conditions. A positive transformant 110N-6 with the highest protease secreting capacity on skim milk plates and great genetic stability for more than 100 generations was selected for further study. Optimization of the fermentation conditions increased the enzyme activity of strain 110N-6 to 8995 ± 250 U/ml in flask culture and 28084 ± 1282 U/ml in 15-l fermentor, which are significantly higher than that of the native strain K11 and industrial strain B. subtilis AS.1398, respectively. The high expression level and extreme genetic stability make B. amyloliquefaciens strain 110N-6 more favorable for mass production of neutral protease for industrial uses.

Assessing the Unseen Bacterial Diversity in Microbial Communities

For both historical and technical reasons, 16S ribosomal RNA has been the most common molecular marker used to analyze the contents of microbial communities. However, its slow rate of evolution hinders the resolution of closely related bacteria—individual 16S-phylotypes, particularly when clustered at 97% sequence identity, conceal vast amounts of species- and strain-level variation. Protein-coding genes, which evolve more quickly, are useful for differentiating among more recently diverged lineages, but their application is complicated by difficulties in designing low-redundancy primers that amplify homologous regions from distantly related taxa. Given the now-common practice of multiplexing hundreds of samples, adopting new genes usually entails the synthesis of large sets of barcoded primers. To circumvent problems associated with use of protein-coding genes to survey microbial communities, we develop an approach—termed phyloTAGs—that offers an automatic solution for primer design and can be easily adapted to target different taxonomic groups and/or different protein-coding regions. We applied this method to analyze diversity within the gorilla gut microbiome and recovered hundreds of strains that went undetected after deep-sequencing of 16S rDNA amplicons. PhyloTAGs provides a powerful way to recover the fine-level diversity within microbial communities and to study stability and dynamics of bacterial populations.