Deep Functional Profiling of Wild Animal Microbiomes Reveals Probiotic Bacillus pumilus Strains with a Common Biosynthetic Fingerprint

The biodiversity of microorganisms is maintained by intricate nets of interactions between competing species. Impaired functionality of human microbiomes correlates with their reduced biodiversity originating from aseptic environmental conditions and antibiotic use. Microbiomes of wild animals are free of these selective pressures. Microbiota provides a protecting shield from invasion by pathogens in the wild, outcompeting their growth in specific ecological niches. We applied ultrahigh-throughput microfluidic technologies for functional profiling of microbiomes of wild animals, including the skin beetle, Siberian lynx, common raccoon dog, and East Siberian brown bear. Single-cell screening of the most efficient killers of the common human pathogen Staphylococcus aureus resulted in repeated isolation of Bacillus pumilus strains. While isolated strains had different phenotypes, all of them displayed a similar set of biosynthetic gene clusters (BGCs) encoding antibiotic amicoumacin, siderophore bacillibactin, and putative analogs of antimicrobials including bacilysin, surfactin, desferrioxamine, and class IId cyclical bacteriocin. Amicoumacin A (Ami) was identified as a major antibacterial metabolite of these strains mediating their antagonistic activity. Genome mining indicates that Ami BGCs with this architecture subdivide into three distinct families, characteristic of the B. pumilus, B. subtilis, and Paenibacillus species. While Ami itself displays mediocre activity against the majority of Gram-negative bacteria, isolated B. pumilus strains efficiently inhibit the growth of both Gram-positive S. aureus and Gram-negative E. coli in coculture. We believe that the expanded antagonistic activity spectrum of Ami-producing B. pumilus can be attributed to the metabolomic profile predetermined by their biosynthetic fingerprint. Ultrahigh-throughput isolation of natural probiotic strains from wild animal microbiomes, as well as their metabolic reprogramming, opens up a new avenue for pathogen control and microbiome remodeling in the food industry, agriculture, and healthcare.

Biosurfactant from endophytic Bacillus pumilus 2A: physicochemical characterization, production and optimization and potential for plant growth promotion

BACKGROUND

Microbial surfactants called biosurfactants, thanks to their high biodegradability, low toxicity and stability can be used not only in bioremediation and oil processing, but also in the food and cosmetic industries, and even in medicine. However, the high production costs of microbial surfactants and low efficiency limit their large-scale production. This requires optimization of management conditions, including the possibility of using waste as a carbon source, such as food processing by-products. This papers describes the production and characterization of the biosurfactant obtained from the endophytic bacterial strain Bacillus pumilus 2A grown on various by-products of food processing and its potential applications in supporting plant growth. Four different carbon and nitrogen sources, pH, inoculum concentration and temperature were optimized within Taguchi method.

RESULTS

Optimization of bioprocess within Taguchi method and experimental analysis revealed that the optimal conditions for biosurfactant production were brewer's spent grain (5% w/v), ammonium nitrate (1% w/v), pH of 6, 5% of inoculum, and temperature at 30 °C, leading to 6.8 g/L of biosurfactant. Based on gas chromatography-mass spectrometry and Fourier transform infrared spectroscopy analysis produced biosurfactant was determined as glycolipid. Obtained biosurfactant has shown high and long term thermostability, surface tension of 47.7 mN/m, oil displacement of 8 cm and the emulsion index of 69.11%. The examined glycolipid, used in a concentration of 0.2% significantly enhanced growth of Phaseolus vulgaris L. (bean), Raphanus L. (radish), Beta vulgaris L. (beetroot).

CONCLUSIONS

The endophytic Bacillus pumilus 2A produce glycolipid biosurfactant with high and long tem thermostability, what makes it useful for many purposes including food processing. The use of brewer's spent grain as the sole carbon source makes the production of biosurfactants profitable, and from an environmental point of view, it is an environmentally friendly way to remove food processing by products. Glycolipid produced by endophytic Bacillus pumilus 2A significantly improve growth of Phaseolus vulgaris L. (bean), Raphanus L. (radish), Beta vulgaris L. (beetroot). Obtained results provide new insight to the possible use of glycolipids as plant growth promoting agents.

A novel feruloyl esterase with high rosmarinic acid hydrolysis activity from Bacillus pumilus W3

A novel feruloyl esterase (BpFae12) with rosmarinic acid (RA) hydrolysis activity was isolated from Bacillus pumilus W3 and expressed in Escherichia coli BL21 (DE3). With RA as a substrate, the optimal pH and temperature of BpFae12 were pH 8.0 and 50 °C, respectively. The specific enzyme activity was 12.8 U·mg-1. BpFae12 showed the highest activity and substrate affinity toward RA (Vmax of 13.13 U·mg-1, Km of 0.41 mM). Moreover, it also presented strong hydrolysis performance against chlorogenic acid (190.17 U·mg-1). RA was effectively Hydrolyzed into more bioactive caffeic acid and 3,4-dihydroxyphenyllactic acid by BpFae12, which have potential applications in the food industry.

Bacillus pumilus SE5 originated PG and LTA tuned the intestinal TLRs/MyD88 signaling and microbiota in grouper (Epinephelus coioides)

The normal microbiota plays a key role in the health of host, but little is known of how the fish immune system recognizes and responds to indigenous bacteria/probiotics. Our previous studies have showed that heat-inactivated indigenous Bacillus pumilus SE5 activate the TLR2 signaling pathways and modulate the intestinal microbiota in grouper (Epinephelus coioides), suggesting microbial-associated molecular patterns (MAMPs) involved. In this study, whole cell wall (CW) and two possible MAMPs, peptidoglycan (PG) and lipoteichoic acid (LTA) have been extracted from B. pumilus SE5 and their effects on intestinal immune related genes expression and microbiota were evaluated in a 60 days feeding trial. Significantly elevated expression of TLR1, TLR2, TLR5 and MyD88 was observed in fish fed the CW, PG and LTA containing diets, and the highest expression was observed in groups PG and LTA. At the same time, significantly upregulated expression of antimicrobial effectors, such as antimicrobial peptides (epinecidin-1, hepcidin-1 and β-defensin), C-type Lectin and IgM was observed in fish fed PG and LTA containing diets. This induced activation of intestinal immunity was consistent with the microbiota data showing that CW, PG and LTA originated from SE5 modulated the overall structure of intestinal microbiota, and the relative abundance of potentially pathogenic Vibrio decreased significantly while beneficial Lactobacillus increased significantly in fish fed PG and LTA. In conclusion, both the PG and LTA originated from B. pumilus SE5 could activate TLRs/MyD88 signaling and expression of wide-ranging antibacterial effectors, and therefore shape the intestinal microbiota in grouper.

Enhancing the activity and stability of Mn-superoxide dismutase by one-by-one ligation to catalase

Dismutation of superoxide by superoxide dismutase (SOD) generates hydrogen peroxide, which may be reduced to hydroxyl radical. The generated H₂O₂ during the catalysis can have an oxidative damage to SOD. Hydrogen peroxide decomposition by catalase (CAT) can help circumvent the problem. Mn-superoxide dismutase (herein referred to as SOD) and CAT are dimeric and tetrameric proteins, respectively. Herein, through intein-mediated in vivo subunit splicing, the C-terminus of the CAT subunit (CAT^S) has been specifically ligated to the N-terminus of the SOD subunit (SOD^S) with a peptide bond. Thus, the splicing product SOD&CAT combines the superoxide anion (•O₂^-) scavenging ability and the ability of decomposing H₂O₂. The in vivo subunit splicing has little effect on the secondary structures of the enzymes as confirmed by circular dichroism (CD) spectra. Fluorescence spectra showed that the splicing product SOD&CAT has a higher stability than SOD. In the splicing product SOD&CAT, the SOD subunits are in close proximity to the CAT subunits, facilitating immediate transfer of H₂O₂ between the enzymes and enabling efficient decomposition of H₂O₂. SOD&CAT exhibited a superoxide anion (•O₂^-) scavenging ability 244% higher than that of SOD and 46% higher than that of the mixed enzymes SOD+CAT.

The parasporal crystals of Bacillus pumilus strain 15.1: a potential virulence factor?

Bacillus pumilus strain 15.1 was previously found to cause larval mortality in the Med-fly Ceratitis capitata and was shown to produce crystals in association with the spore. As parasporal crystals are well-known as invertebrate-active toxins in entomopathogenic bacteria such as Bacillus thuringiensis (Cry and Cyt toxins) and Lysinibacillus sphaericus (Bin and Cry toxins), the B. pumilus crystals were characterized. The crystals were composed of a 45 kDa protein that was identified as an oxalate decarboxylase by peptide mass fingerprinting, N-terminal sequencing and by comparison with the genome sequence of strain 15.1. Synthesis of crystals by a plasmid-cured derivative of strain 15.1 (produced using a novel curing strategy), demonstrated that the oxalate decarboxylase was encoded chromosomally. Crystals spontaneously solubilized when kept at low temperatures, and the protein produced was resistant to trypsin treatment. The insoluble crystals produced by B. pumilus 15.1 did not show significant toxicity when bioassayed against C. capitata larvae, but once the OxdD protein was solubilized, an increase of toxicity was observed. We also demonstrate that the OxdD present in the crystals has oxalate decarboxylate activity as the formation of formate was detected, which suggests a possible mechanism for B. pumilus 15.1 activity. To our knowledge, the characterization of the B. pumilus crystals as oxalate decarboxylase is the first report of the natural production of parasporal inclusions of an enzyme.

Integration of Bacterial Expansin on Agarolytic Complexes to Enhance the Degrading Activity of Red Algae by Control of Gelling Properties

Expansin act by loosening hydrogen bonds in densely packed polysaccharides. This work characterizes the biological functions of expansin in the gelling and degradation of algal polysaccharides. In this study, the bacterial expansin BpEX from Bacillus pumilus was fused with the dockerin module of a cellulosome system for assembly with agarolytic complexes. The assembly of chimeric expansin caused an indicative enhancement in agarase activity. The enzymatic activities on agar substrate and natural biomass were 3.7-fold and 3.3-fold higher respectively than that of agarase as a single enzyme. To validate the effect on the agar degradation, the regulation potential of parameters related to gel rheology by bacterial expansin was experimentally investigated to indicate that the bacterial expansin lowered the gelling temperature and viscosity of agar. Thus, these results demonstrated the possibility of advancing more efficient strategies for utilizing agar as oligo sugar source in the biorefinery field that uses marine biomass as feedstocks.

Efficacy of viable Bacillus pumilus isolated from farmed fish on immune responses and increased disease resistance in Nile tilapia (Oreochromis niloticus): Laboratory and on-farm trials

Applications of viable Bacillus pumilus AQAHBS01 isolated from Nile tilapia farms as probiotics were studied in both laboratory and farm conditions. In the laboratory, feeding fish (approximately 50 g) with feed containing viable B. pumilus at concentrations of 1 × 10⁷-10⁹ colony forming units (CFU)/kg elevated fish immune responses, as indicated by their phagocytic activity and superoxide anion levels, and led to more effective disease resistance against Streptococcus agalactiae. However, when these concentrations were applied to Nile tilapia cultures growing in cage culture systems, only B. pumilus AQAHBS01 at concentrations of 1 × 10⁸ and 10⁹ CFU/kg diet could effectively enhance disease resistance against S. agalactiae during the critical period of early to middle April when the temperature reached 33 °C, whereas control fish and fish that consumed B. pumilus AQAHBS01 at concentrations of 1 × 10⁷ CFU/kg showed very rapid streptococcosis-induced mortality. However, in late April, massive levels of organic matter-containing water flowed into the culture areas, causing all fish groups to become infected with Flavobacterium columnare. Moreover, the dissolved oxygen levels in the river declined to critical levels of approximately 1.0-1.5 mg/L, causing anorectic effects in fish for long periods of time. This effect may have also gradually killed the cultured fish until the end of the experiment. This information strongly demonstrates the effective application of B. pumilus as a probiotic for streptococcosis resistance in both laboratory and field culture conditions. For on-farm cage culture practices, however, fluctuations in water quality remain a significant constraint for probiotic application, as they usually induce negative effects on fish health. This decline in health makes fish more fragile and more susceptible to problems from both infectious and non-infectious diseases, which farmers must consider carefully.

Production of spore laccase from Bacillus pumilus W3 and its application in dye decolorization after immobilization

Given that spore laccase from the Bacillus genus is heat- and alkali-resistant, it is more suitable for industrial applications than fungal laccase. To determine the optimal culture conditions for spore laccase production, the effects of Cu²⁺ concentration, oxygen content, and culture time on spore laccase production from Bacillus pumilus W3 were investigated. The optimal production parameters were 0.2 mM of Cu²⁺, 200 rpm shaking speed, 100 mL liquid loading, and 5 days of cultivation. Spore laccase was efficiently immobilized on amino-functionalized celite. When used in dye decolorization, the immobilized spore laccase removed 84.15% of methyl green and 69.70% of acid red 1 after 48 h of treatment. Moreover, the immobilized spore laccase retained 87.04% of its initial decolorization activity after six cycles in the decolorization of acid red 1. These insights into the culture conditions and immobilization of spore laccases should be useful in the development of spore laccase as a biocatalyst in the treatment of textile wastewater.

1-Acyl-3-0-[β-glucopyranosyl-(1"-+ 6')-β-glucopyranosyl]-glycerols and Cordycedipeptides B and C, New Metabolites from Bacillus pumilus

Four 1-monoacyl-3-0-[β-glucopyranosyl-( ->6)-β-glucopyranosyl]-glycerols (1) and four 1,2-diacyl-3-0-[p-glucopyranosyl-(1->6)-p-glucopyranosyl]- glycerols (2a) with acyl residues consisting of 1:1 mixtures of 1-iso-pentadecanoyl- and 1 -anteiso-pentadecanoyl residues and the respective heptadecanoic acid isomers s as main components, have been characterized in the extracts of Bacillus pumilus strain DKS 1. Twenty-seven further metabolites, among them the diketopiperazines cordycedipeptide A (3), B (4), and C (5), were obtained. All compounds were elucidated by NMR and MS techniques and fully characterized and tested for antimicrobial activity against Legionella pneumophila.