Bacillus fungorum sp. nov., a bacterium isolated from spent mushroom substrate

Status and development of spent mushroom substrate recycling: A review

The edible mushroom industry is the sixth largest after grain, cotton, oil, vegetables and fruits, and the annual production of edible mushrooms in China exceeds 40 million tons. Edible mushroom cultivation produces a class of by-products consisting mainly of mycelium remnants and lignocellulosic waste, known as Spent Mushroom Substrate (SMS) or Spent Mushroom Compost (SMC). SMS/SMC is rich in nutrients and active ingredients and has an extremely high recycling potential. This review paper summarizes SMS recycling strategies from the perspectives of "environmental remediation" and "circular economy", and briefly discusses the legitimacy, possible challenges and future research of SMS recycling. It is hoped that this will assist researchers in related fields and promote the development of the SMS recycling industry, thereby contributing to sustainable environmental and economic development.Implication StatementThe efficient management of SMS is important for many countries around the world, particularly major mushroom producing countries. Traditional disposal methods (incineration, burial, piling) can cause serious damage to the environment and waste resources. The correct disposal method can protect the natural environment and provide certain economic benefits. This study presents the main methods of SMS processing from both an "environmental remediation" and "circular economy" perspective. In general, this paper emphasizes the importance of SMS processing, introduces the current mainstream processing methods and briefly discusses the legality of their processing methods.

Whole Genome Sequencing Reveals Antimicrobial Resistance and Virulence Genes of Both Pathogenic and Non-Pathogenic B. cereus Group Isolates from Foodstuffs in Thailand

Members of the Bacillus cereus group are spore-forming Gram-positive bacilli that are commonly associated with diarrheal or emetic food poisoning. They are widespread in nature and frequently present in both raw and processed food products. Here, we genetically characterized 24 B. cereus group isolates from foodstuffs. Whole-genome sequencing (WGS) revealed that most of the isolates were closely related to B. cereus sensu stricto (12 isolates), followed by B. pacificus (5 isolates), B. paranthracis (5 isolates), B. tropicus (1 isolate), and "B. bingmayongensis" (1 isolate). The most detected virulence genes were BAS_RS06430, followed by bacillibactin biosynthesis genes (dhbA, dhbB, dhbC, dhbE, and dhbF), genes encoding the three-component non-hemolytic enterotoxin (nheA, nheB, and nheC), a gene encoding an iron-regulated leucine-rich surface protein (ilsA), and a gene encoding a metalloprotease (inhA). Various biofilm-associated genes were found, with high prevalences of tasA and sipW genes (matrix protein-encoding genes); purA, purC, and purL genes (eDNA synthesis genes); lytR and ugd genes (matrix polysaccharide synthesis genes); and abrB, codY, nprR, plcR, sinR, and spo0A genes (biofilm transcription regulator genes). Genes related to fosfomycin and beta-lactam resistance were identified in most of the isolates. We therefore demonstrated that WGS analysis represents a useful tool for rapidly identifying and characterizing B. cereus group strains. Determining the genetic epidemiology, the presence of virulence and antimicrobial resistance genes, and the pathogenic potential of each strain is crucial for improving the risk assessment of foodborne B. cereus group strains.

Bacillus dicomae sp. nov., a new member of the Bacillus cereus group isolated from medicinal plant Dicoma anomala

A Gram-stain-positive, endospore-forming endophytic bacterial strain designated MHSD28T was isolated from surface-sterilized leaves of Dicoma anomala collected from Eisleben, Botlokwa, Limpopo Province, South Africa. The phenotypic and phylogenetic characteristics of strain MHSD28T were consistent with those of members within the Bacillus cereus group. Comparative analysis between this strain and its relatives confirmed that it belongs to this group and forms a monophyletic branch. The digital DNA-DNA hybridization values between strain MHSD28T and its relatives were lower than the 70 % threshold for species delineation. To further determine its phylogenetic position, multi-locus sequence analysis (MLSA) based on five concatenated housekeeping gene (gyrB, atpD, DnaK, rpoB and rpoD) sequences, phenotypic analysis, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) biotyper identification, fatty acid and polar lipid profile analyses were carried out. Phenotypic characterization, MLSA, whole genome sequence based analyses and MALDI-TOF results placed strain MHSD28T within the B. cereus group. The major fatty acids were iso-C15 : 0 and summed feature 3 and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The respiratory quinone was menaquinone-7. The cell-wall peptidoglycan structure included meso-diaminopimelic acid. Considering the above results, strain MHSD28T represents a novel species of the B. cereus group, for which the name Bacillus dicomae sp. nov. is proposed. The type strain is MHSD28T (=BD 2262T=LMG 32287T=CECT 30671T).

Regulation of Enterotoxins Associated with Bacillus cereus Sensu Lato Toxicoinfection

Bacillus cereus sensu lato (s.l.) includes foodborne pathogens, as well as beneficial microorganisms, such as bioinsecticides. Some of the beneficial and commercially used B. cereus s.l. strains have been shown to carry enterotoxin genes, the products of which can cause toxicoinfection in humans. Furthermore, recent epidemiological reports indicated that some bioinsecticidal strains have been linked with foodborne illness outbreaks. This demonstrates the need for improved surveillance of B. cereus s.l., which includes characterization of isolates' virulence capacity. However, the prediction of virulence capacity of B. cereus s.l. strains is challenging. Genetic screening for enterotoxin gene presence has proven to be insufficient for accurate discrimination between virulent and avirulent strains, given that nearly all B. cereus s.l. strains carry at least one enterotoxin gene. Furthermore, complex regulatory networks governing the expression of enterotoxins, and potential synergistic interactions between enterotoxins and other virulence factors make the prediction of toxicoinfection based on isolates' genome sequences challenging. In this review, we summarize and synthesize the current understanding of the regulation of enterotoxins associated with the B. cereus s.l. toxicoinfection and identify gaps in the knowledge that need to be addressed to facilitate identification of genetic markers predictive of cytotoxicity and toxicoinfection.

Bacillus arachidis sp. nov., Isolated from Peanut Rhizosphere Soil

A novel facultatively aerobic bacterium designated SY8 was isolated from a peanut rhizosphere soil sample collected in Jiangsu Province, China. Cells are Gram-stain-positive, rod-shaped, and agar colonies are creamy, opaque, and usually rhizoidal. Strain growth occurs at 30 - 45 °C (optimum 30 °C), pH 4.0 - 10.0 (optimum pH 6.0) and 0 - 4% (w/v) NaCl (optimum 2%) in Luria-Bertani medium. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain SY8 forms a distinct lineage in the clade of genus Bacillus and is related to Bacillus pseudomycoides DSM 12442 ^T (99.9%). Phylogenetic analysis of the concatenated gene sequences of 16S rRNA, gryB and rpoD also indicated that strain SY8 forms a distinct lineage in Bacillus. Calculation of the average nucleotide identities and the digital DNA-DNA hybridization values between strain SY8 and the related type Bacillus strains further revealed that strain SY8 represents a distinct species. The predominant cellular fatty acids are iso C_15:0 (28.7%) and summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) (10.3%). The major polar lipids consisted of diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidylinositol, and three unidentified phospholipids. The major menaquinone of SY8 was MK-7. Based on phenotypic, phylogenetic, chemotaxonomic, and genomic features, strain SY8 represents a novel species of the genus Bacillus. The name Bacillus arachidis sp. nov. is proposed with strain SY8^T (= CCTCC AB 2021100 ^T=LMG 32409 ^T) designated as the type strain.

Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking

Members of the Bacillus cereus sensu lato species complex, also known as the B. cereus group, vary in their ability to cause illness but are frequently isolated from foods, including meat products; however, food safety surveillance efforts that use whole-genome sequencing (WGS) often neglect these potential pathogens. Here, we evaluate the surveillance and source tracking potential of WGS as applied to B. cereus sensu lato by (i) using WGS to characterize B. cereus sensu lato strains isolated during routine surveillance of meat products across South Africa (n = 25) and (ii) comparing the genomes sequenced here to all publicly available, high-quality B. cereus sensu lato genomes (n = 2,887 total genomes). Strains sequenced here were collected from meat products obtained from (i) retail outlets, processing plants, and butcheries across six South African provinces (n = 23) and (ii) imports held at port of entry (n = 2). The 25 strains sequenced here were partitioned into 15 lineages via in silico seven-gene multilocus sequence typing (MLST). While none of the South African B. cereus sensu lato strains sequenced here were identical to publicly available genomes, six MLST lineages contained multiple strains sequenced in this study, which were identical or nearly identical at the whole-genome scale (≤3 core single nucleotide polymorphisms). Five MLST lineages contained (nearly) identical genomes collected from two or three South African provinces; one MLST lineage contained nearly identical genomes from two countries (South Africa and the Netherlands), indicating that B. cereus sensu lato can spread intra- and internationally via foodstuffs. IMPORTANCE Nationwide foodborne pathogen surveillance programs that use high-resolution genomic methods have been shown to provide vast public health and economic benefits. However, Bacillus cereus sensu lato is often overlooked during large-scale routine WGS efforts. Thus, to our knowledge, no studies to date have evaluated the potential utility of WGS for B. cereus sensu lato surveillance and source tracking in foodstuffs. In this preliminary proof-of-concept study, we applied WGS to B. cereus sensu lato strains collected via South Africa's national surveillance program of domestic and imported meat products, and we provide strong evidence that B. cereus sensu lato can be disseminated intra- and internationally via the agro-food supply chain. Our results showcase that WGS has the potential to be used for source tracking of B. cereus sensu lato in foods, although future WGS and metadata collection efforts are needed to ensure that B. cereus sensu lato surveillance initiatives are on par with those of other foodborne pathogens.

Bacillus cereus Invasive Infections in Preterm Neonates: an Up-to-Date Review of the Literature

Bacillus cereus group species are widespread, Gram-positive, spore-forming environmental bacteria. B. cereus sensu stricto is one of the major causes of food poisoning worldwide. In high-risk individuals, such as preterm neonates, B. cereus infections can cause fatal infections. It is important to note that the phenotypic identification methods commonly used in clinical microbiology laboratories make no distinction between B. cereus sensu stricto and the other members of the group (Bacillus anthracis excluded). As a result, all the invasive infections attributed to B. cereus are not necessarily due to B. cereus sensu stricto but likely to other closely related species of the B. cereus group. Next-generation sequencing (NGS) should be used to characterize the whole genome of the strains belonging to the B. cereus group. This could confirm whether the strains involved in previously reported B. cereus invasive infections preferentially belong to formerly known or emerging individual species. Moreover, infections related to B. cereus group species have probably been overlooked, since their isolation in human bacteriological samples has for a long time been regarded as an environmental contaminant of the cultures. Recent studies have questioned the emergence or reemergence of B. cereus invasive infections in preterm infants. This review reports our current understanding of B. cereus infections in neonates, including taxonomical updates, microbiological characteristics, bacterial identification, clinical features, host-pathogen interactions, environmental sources of contamination, and antimicrobial resistance.

Three novel species of the Bacillus cereus group isolated from clinical samples in Japan

Three Gram-positive bacterial strains, BML-BC004, BML-BC017 and BML-BC059, isolated from blood samples from three inpatients in Japan, were identified as members of Bacillus cereus using matrix-assisted laser desorption ionization time-of-flight MS. The 16S rRNA gene sequences of these three strains were more than 97.1 % similar to 18 type strains belonging to the B. cereus group. Whole-genome comparisons, using average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), confirmed that the three strains represented three individual distinct species belonging to the B. cereus group. A phylogenetic tree showed that BML-BC004, BML-BC017 and BML-BC059 were located close to B. luti, B. mobilis and B. paramycoides, respectively. Based on these phylogenetic and phenotypic data, including values below the threshold for ANI and dDDH, the three strains should be classified as representing three different novel species of the B. cereus group: Bacillus sanguinis sp. nov., with type strain BML-BC004^T (=DSM 111102^T=JCM 34122^T), Bacillus paramobilis sp. nov., with type strain BML-BC017^T (=DSM 111100^T=JCM 34124^T) and Bacillus hominis sp. nov., with type strain BML-BC059^T (=DSM 111101^T=JCM 34125^T).

Characterization of Bacillus cereus Group Isolates From Human Bacteremia by Whole-Genome Sequencing

Members of the Bacillus cereus group are spore-forming organisms commonly associated with food poisoning and intestinal infections. Moreover, some strains of the group (i.e., B. cereus sensu stricto and Bacillus thuringiensis) can cause bacteremia in humans, mainly in immunocompromised individuals. Here we performed the genetic characterization of 17 human clinical strains belonging to B. cereus group isolated from blood culture. The whole-genome sequencing (WGS) revealed that the isolates were closely related to B. cereus sensu stricto and B. thuringiensis-type strain. Multilocus sequence typing analysis performed on the draft genome revealed the genetic diversity of our isolates, which were assigned to different sequence types. Based on panC nucleotide sequence, the isolates were grouped in the phylogenetic groups III and IV. The NHE, cer, and inhA gene cluster, entA, entFM, plcA, and plcB, were the most commonly detected virulence genes. Although we did not assess the ability to generate biofilm by phenotypic tests, we verified the prevalence of biofilm associated genes using an in silico approach. A high prevalence of pur gene cluster, xerC, clpY, codY, tasA, sipW, sinI, and sigB genes, was found. Genes related to the resistance to penicillin, trimethoprim, and ceftriaxone were identified in most of the isolates. Intriguingly, the majority of these virulence and AMR genes appeared to be evenly distributed among B. cereus s.s. isolates, as well as closely related to B. thuringiensis isolates. We showed the WGS represents a good approach to rapidly characterize B. cereus group strains, being able to give useful information about genetic epidemiology, the presence of virulence and antimicrobial genes, and finally about the potential hazard related to this underestimated risk.

Novel Effective Bacillus cereus Group Species "Bacillus clarus" Is Represented by Antibiotic-Producing Strain ATCC 21929 Isolated from Soil

The B. cereus group comprises numerous closely related lineages with various degrees of pathogenic potential and industrial relevance. Species-level taxonomic classification of B. cereus group strains is important for risk evaluation and communication but remains challenging. Biochemical and phenotypic assays are often used to assign B. cereus group strains to species but are insufficient for accurate taxonomic classification on a genomic scale. Here, we show that antibiotic-producing ATCC 21929 represents a novel lineage within the B. cereus group that, by all metrics used to delineate prokaryotic species, exemplifies a novel effective species. Furthermore, we show that ATCC 21929 is incapable of producing enterotoxins Hbl and Nhe or exhibiting cytotoxic effects on HeLa cells at human body temperature in vitro. These results provide greater insight into the genomic and phenotypic diversity of the B. cereus group and may be leveraged to inform future public health and food safety efforts.

Gram-positive, spore-forming members of the Bacillus cereus group species complex are widespread in natural environments and display various degrees of pathogenicity. Recently, B. cereus group strain Bacillus mycoides Flugge ATCC 21929 was found to represent a novel lineage within the species complex, sharing a relatively low degree of genomic similarity with all B. cereus group genomes (average nucleotide identity [ANI] < 88). ATCC 21929 has been previously associated with the production of a patented antibiotic, antibiotic 60-6 (i.e., cerexin A); however, the virulence potential and growth characteristics of this lineage have never been assessed. Here, we provide an extensive genomic and phenotypic characterization of ATCC 21929, and we assess its pathogenic potential in vitro. ATCC 21929 most closely resembles Bacillus paramycoides NH24A2^T (ANI and in silico DNA-DNA hybridization values of 86.70 and 34.10%, respectively). Phenotypically, ATCC 21929 does not possess cytochrome c oxidase activity and is able to grow at a range of temperatures between 15 and 43°C and a range of pH between 6 and 9. At 32°C, ATCC 21929 shows weak production of diarrheal enterotoxin hemolysin BL (Hbl) but no production of nonhemolytic enterotoxin (Nhe); at 37°C, neither Hbl nor Nhe is produced. Additionally, at 37°C, ATCC 21929 does not exhibit cytotoxic effects toward HeLa cells. With regard to fatty acid composition, ATCC 21929 has iso-C17:0 present in highest abundance. Based on the characterization provided here, ATCC 21929^T (= PS00077A^T = PS00077B^T = PSU-0922^T = BHP^T) represents a novel effective B. cereus group species, which we propose as effective species “Bacillus clarus.”

IMPORTANCE The B. cereus group comprises numerous closely related lineages with various degrees of pathogenic potential and industrial relevance. Species-level taxonomic classification of B. cereus group strains is important for risk evaluation and communication but remains challenging. Biochemical and phenotypic assays are often used to assign B. cereus group strains to species but are insufficient for accurate taxonomic classification on a genomic scale. Here, we show that antibiotic-producing ATCC 21929 represents a novel lineage within the B. cereus group that, by all metrics used to delineate prokaryotic species, exemplifies a novel effective species. Furthermore, we show that ATCC 21929 is incapable of producing enterotoxins Hbl and Nhe or exhibiting cytotoxic effects on HeLa cells at human body temperature in vitro. These results provide greater insight into the genomic and phenotypic diversity of the B. cereus group and may be leveraged to inform future public health and food safety efforts.