Fatty acids of the genus Bacillus: an example of branched-chain preference

Strategies for improving fengycin production: a review

Fengycin is an important member of the lipopeptide family with a wide range of applications in the agricultural, food, medical and cosmetic industries. However, its commercial application is severely hindered by low productivity and high cost. Therefore, numerous studies have been devoted to improving the production of fengycin. We summarize these studies in this review with the aim of providing a reference and guidance for future researchers. This review begins with an overview of the synthesis mechanism of fengycin via the non-ribosomal peptide synthetases (NRPS), and then delves into the strategies for improving the fengycin production in recent years. These strategies mainly include fermentation optimization and metabolic engineering, and the metabolic engineering encompasses enhancement of precursor supply, application of regulatory factors, promoter engineering, and application of genome-engineering (genome shuffling and genome-scale metabolic network model). Finally, we conclude this review with a prospect of fengycin production.

Research advances in the identification of regulatory mechanisms of surfactin production by Bacillus: a review

Surfactin is a cyclic hexalipopeptide compound, nonribosomal synthesized by representatives of the Bacillus subtilis species complex which includes B. subtilis group and its closely related species, such as B. subtilis subsp subtilis, B. subtilis subsp spizizenii, B. subtilis subsp inaquosorum, B. atrophaeus, B. amyloliquefaciens, B. velezensis (Steinke mSystems 6: e00057, 2021) It functions as a biosurfactant and signaling molecule and has antibacterial, antiviral, antitumor, and plant disease resistance properties. The Bacillus lipopeptides play an important role in agriculture, oil recovery, cosmetics, food processing and pharmaceuticals, but the natural yield of surfactin synthesized by Bacillus is low. This paper reviews the regulatory pathways and mechanisms that affect surfactin synthesis and release, highlighting the regulatory genes involved in the transcription of the srfAA-AD operon. The several ways to enhance surfactin production, such as governing expression of the genes involved in synthesis and regulation of surfactin synthesis and transport, removal of competitive pathways, optimization of media, and fermentation conditions were commented. This review will provide a theoretical platform for the systematic genetic modification of high-yielding strains of surfactin.

The metabolites of light: Untargeted metabolomic approaches bring new clues to understand light-driven acclimation of intertidal mudflat biofilm

The microphytobenthos (MPB), a microbial community of primary producers, play a key role in coastal ecosystem functioning, particularly in intertidal mudflats. These mudflats experience challenging variations of irradiance, forcing the micro-organisms to develop photoprotective mechanisms to survive and thrive in this dynamic environment. Two major adaptations to light are well described in literature: the excess of light energy dissipation through non-photochemical quenching (NPQ), and the vertical migration in the sediment. These mechanisms trigger considerable scientific interest, but the biological processes and metabolic mechanisms involved in light-driven vertical migration remain largely unknown. To our knowledge, this study investigates for the first time metabolomic responses of a migrational mudflat biofilm exposed for 30 min to a light gradient of photosynthetically active radiation (PAR) from 50 to 1000 μmol photons m-2 s-1. The untargeted metabolomic analysis allowed to identify metabolites involved in two types of responses to light irradiance levels. On the one hand, the production of SFAs and MUFAs, primarily derived from bacteria, indicates a healthy photosynthetic state of MPB under low light (LL; 50 and 100 PAR) and medium light (ML; 250 PAR) conditions. Conversely, when exposed to high light (HL; 500, 750 and 1000 PAR), the MPB experienced light-induced stress, triggering the production of alka(e)nes and fatty alcohols. The physiological and ecological roles of these compounds are poorly described in literature. This study sheds new light on the topic, as it suggests that these compounds may play a crucial and previously unexplored role in light-induced stress acclimation of migrational MPB biofilms. Since alka(e)nes are produced from FAs decarboxylation, these results thus emphasize for the first time the importance of FAs pathways in microphytobenthic biofilms acclimation to light.

Dietary sources of branched-chain fatty acids and their biosynthesis, distribution, and nutritional properties

Branched-chain fatty acids (BCFAs) consist of a wide variety of fatty acids with alkyl branching of methyl group. The most common BCFAs are the types with one methyl group (mmBCFA) on the penultimate carbon (iBCFA) or the antepenultimate carbon (aiBCFA). Long-chain mmBCFAs are widely existing in animal fats, milks and are mostly derived from bacteria in the diet or animal digestive system. Recent studies show that BCFAs benefit human intestinal health and immune homeostasis, but the connection between their content, distribution in the human and their nutritional functions are not well established. In this paper, we reviewed BCFAs from various dietary sources focused on their molecular species. The BCFAs biosynthesis in bacteria, Caenorhabditis elegans, mammals and their distribution in human tissues are summarized. This paper also discusses the nutritional properties of BCFAs including influences on intestinal health, immunoregulatory effects, anti-carcinoma, and anti-obesity activities, by highlighting the most recent research progress.

Branched-Long-Chain Monomethyl Fatty Acids: Are They Hidden Gems?

Branched-long-chain monomethyl fatty acids (BLCFA) are consumed daily in significant amounts by humans in all stages of life. BLCFA are absorbed and metabolized in human intestinal epithelial cells and are not only oxidized for energy. Thus far, BLCFA have been revealed to possess versatile beneficial bioactivities, including cytotoxicity to cancer cells, anti-inflammation, lipid-lowering, reducing the risk of metabolic disorders, maintaining normal β cell function and insulin sensitivity, regulation of development, and mitigating cerebral ischemia/reperfusion injury. However, compared to other well-studied dietary fatty acids like eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), BLCFA has received disproportionate attention despite their potential importance. Here we outlined the major food sources, estimated intake, absorption, and metabolism in human cells, and bioactive properties of BLCFA with a focus on the bioactive mechanisms to advocate for an increased commitment to BLCFA investigations. Humans were estimated to absorb 6-5000 mg of dietary BLCFA daily from fetus to adult. Notably, iso-15:0 inhibited the growth of prostate cancer, liver cancer and T-cell non-Hodgkin lymphomas in rodent models at the effective doses of 35-105 mg/kg/day, 70 mg/kg/day, and 70 mg/kg/day, respectively. Feeding formula prepared with 20% w/w BLCFA mixture to neonatal rats with enterocolitis mitigated the intestine inflammation. Iso-15:0 at doses of 10, 40, and 80 mg/kg relieved brain ischemia/reperfusion injury in rats. In the future, it is crucial to conduct research to establish the epidemiology of BLCFA intake and their impacts on health outcomes in humans as well as to fully uncover the underlying mechanisms for their bioactivities.

Spatiotemporal variation of microbial communities in surficial sediments of Cochin estuary, southwest coast of India

Microorganisms play a major role in the degradation of organic matter in sediments. However, the spatiotemporal variation and factors affecting these communities are not clearly understood. At the same time, conventional hydrographic and geochemical parameters do not offer an accurate assessment of transitional ecosystems. PLFA biomarkers which are specific to different taxonomic groups of microorganisms are able to provide a detailed assessment of the community composition in an environment and reflect a more direct assessment of the biological health of transitional ecosystems. We, therefore, conducted a comparison of PLFA biomarkers at four stations (Barmouth, B; Vaduthala, V; Munambam, M; and Arookutty, A) during three seasons (pre-monsoon, PRE; monsoon, MON; and post-monsoon, POST) in the Cochin estuary (CE). Each of the stations represented either a reference point (B), high pollution (V), high salinity (M), or low pollution (A). The communities determined using PLFA profiles could be categorized into six major groups with each group capable of reflecting the state of the ecosystem which correlated with the conventional parameters. The six groups were: G + ve Bacillota (formerly Firmicutes) and G-ve anaerobes (G-I), G-ve aerobic prokaryotes (G-II), ectomycorrhizal fungi (G-III), arbuscular mycorrhizae (G-IV), type-I methanotrophs (G-V), and microeukaryotes (G-VI). The prokaryotes were predominant in sediments amounting to over 78% of the total PLFAs detected, followed by the microeukaryotes. The freshwater-influenced stations were partially anaerobic in nature during PRE and MON and were mainly affected by both marine and terrestrial organic matter inputs, at times prominent in sewage matter. During POST season, CE behaves uniformly, especially in station M. Salinity and DO of BW and texture and organic matter of the sediment were the driving forces for microbial community structure. The reduced presence of cyclopropane fatty acids suggested that the CE was not under any stress during the study period. Our results using PLFA-based community profiling not only provide the fundamental information required to quickly access the impact of stress and other environmental inputs on the CE but also offer a more robust and realistic assessment of the nature of microbial communities in the ecosystem. A periodic and systemic assessment of PLFA profiles at these stations in CE throughout the year will enable the generation of enough metadata enabling a better understanding of this ecosystem and its efficient management in the long term.

Supplementing branched-chain volatile fatty acids in dual-flow cultures varying in dietary forage and corn oil concentrations. III: Protein metabolism and incorporation into bacterial protein

Some cellulolytic bacteria cannot transport branched-chain AA (BCAA) and do not express complete synthesis pathways, thus depending on cross-feeding for branched-chain volatile fatty acid (BCVFA) precursors for membrane lipids or for reductive carboxylation to BCAA. Our objective was to assess BCVFA uptake for BCAA synthesis in continuous cultures administered high forage (HF) and low forage (LF) diets without or with corn oil (CO). We hypothesized that BCVFA would be used for BCAA synthesis more in the HF than in LF diets. To help overcome bacterial inhibition by polyunsaturated fatty acids in CO, BCVFA usage for bacterial BCAA synthesis was hypothesized to decrease when CO was added to HF diets. The study was an incomplete block design with 8 dual-flow fermenters used in 4 periods with 8 treatments (n = 4) arranged as a 2 × 2 × 2 factorial. The factors were: HF or LF (67 or 33% forage, 33:67 alfalfa:orchardgrass pellets), without or with supplemental CO (3% of dry matter), and without or with 2.15 mmol/d (5 mg/d 13C) each of isovalerate, isobutyrate, and 2-methylbutyrate for one combined BCVFA treatment. The flow of bacterial BCAA increased by 10.7% by supplementing BCVFA and 9.14% with LF versus HF; similarly, dosing BCVFA versus without BCVFA increased BCAA by 1.98% in total bacterial AA, whereas LF increased BCAA by 1.92% versus HF. Additionally, BCVFA supplementation increased bacterial AA flow by 16.6% when supplemented in HF - CO and 12.4% in LF + CO diets, but not in the HF + CO (-1.5%) or LF - CO (+6.7%) diets (Diet × CO × BCVFA interaction). The recovery of 13C in bacterial AA flow was 31% lower with LF than with HF. Of the total 13C recovered in bacteria, 13.8, 17.3, and 30.2% were recovered in Val, Ile, and Leu, respectively; negligible 13C was recovered in other AA. When fermenters were dosed with BCVFA, nonbacterial and total effluent flows of AA, particularly of alanine and proline, suggest decreased peptidolysis. Increased ruminal outflow of bacterial AA, especially BCAA, but also nonbacterial AA could potentially support postabsorptive responses from BCVFA supplementation to dairy cattle.

Bacillus Subtilis (BG01-4TM) Improves Self-Reported Symptoms for Constipation, Indigestion, and Dyspepsia: A Phase 1/2A Randomized Controlled Trial

BACKGROUND

Functional gastrointestinal disorders (FGIDs) are common, difficult-to-manage conditions. Probiotics are emerging as a dietary component that influence gastrointestinal (GI) health. We conducted a double-blinded randomised controlled trial of a proprietary strain of deactivated Bacillus subtilis (BG01-4™) high in branched-chain fatty acids (BCFA) to treat self-reported FGID.

METHODS

Participants (n = 67) completed a four-week intervention of BG01-4™ (n = 34) or placebo (n = 33). The Gastrointestinal Symptom Rating Scale (GSRS) served as the outcome measure, collected prior to, at two weeks, and at four weeks after completion of the intervention.

RESULTS

At four weeks, one of three primary outcomes, constipation in the experimental group, was improved by 33% compared to placebo (15%); both other primary outcomes, Total GSRS and diarrhoea, were significantly improved in both the experimental and placebo groups (32%/26% and 20%/22%, respectively). The pre-planned secondary outcome, indigestion, was improved at four weeks (32%) but compared to the placebo (21%) was not significant (p = 0.079). Exploratory analysis, however, revealed that clusters for constipation (18% improvement, p < 0.001), indigestion (11% improvement, p = 0.04), and dyspepsia (10% improvement, p = 0.04) were significantly improved in the intervention group compared to the placebo.

CONCLUSIONS

These initial findings suggest that in people with self-reported FGID, BG01-4™ improves specific symptoms of constipation and related GI dysfunction. Longer-term confirmatory studies for this intervention are warranted.

TRIAL REGISTRATION

This study was registered prospectively (25 October 2021) at the Australian New Zealand Clinical Trials Registry (ACTRN12621001441808p).

Bacillus pfraonensis sp. nov., a new strain isolated from a probiotic feed additive with low cytotoxicity and antimicrobial activity

Probiotic products containing living microorganisms are gaining popularity, increasing the importance of their taxonomic status. A Bacillus-like isolate, 70 b, cultured from a probiotic feed additive, was ambiguity in taxonomic assignment and could be a novel member of Bacillus cereus group. The results of colony and cellular morphology, physiological and biochemical analysis mainly including growth performance, carbon source utilization, and rMLST and MLST were not conclusive. Fatty acids profile and molecular genetic analysis especially ANI, DDH, and core genome SNPs-based phylogenetic tree confirmed 70 b as one novel species of B. cereus group and proposed as Bacillus pfraonensis sp. nov. Comparative genomic analysis revealed the genetic differences between 70 b and other species of B. cereus group. Pseudomycoicidin was identified in 70 b. 70 b was active against multidrug-resistant pathogenic strains MRSA. The findings support 70 b is a novel species with low cytotoxicity and antimicrobial activity, and provides a better understanding of its unique characteristics and probiotic potential, and exploration of bioactive potential.

Stereoselective synthesis of S-norvaline and related amino acids through a common intermediate

A divergent, enantioselective synthetic strategy is reported to produce the non-proteinogenic, biologically active natural amino acids norvaline, 5-hydroxy-4-oxo-L-norvaline, and ɣ-oxonorvaline. These were synthesized in good yields (45-75%) from the common starting material (S)-allylglycine obtained by asymmetric transfer allylation of glycine Schiff base using the Corey catalyst derived from cinchonidine in more than 97% enantiomeric excess.

Attempts to limit sporulation in the probiotic strain Bacillus subtilis BG01-4TM through mutation accumulation and selection

The use of bacterial spores in probiotics over viable loads of bacteria has many advantages, including the durability of spores, which allows spore-based probiotics to effectively traverse the various biochemical barriers present in the gastrointestinal tract. However, the majority of spore-based probiotics developed currently aim to treat adults, and there is a litany of differences between the adult and infant intestinal systems, including the immaturity and low microbial species diversity observed within the intestines of infants. These differences are only further exacerbated in premature infants with necrotizing enterocolitis (NEC) and indicates that what may be appropriate for an adult or even a healthy full-term infant may not be suited for an unhealthy premature infant. Complications from using spore-based probiotics for premature infants with NEC may involve the spores remaining dormant and adhering to the intestinal epithelia, the out-competing of commensal bacteria by spores, and most importantly the innate antibiotic resistance of spores. Also, the ability of Bacillus subtilis to produce spores under duress may result in less B. subtilis perishing within the intestines and releasing membrane branched-chain fatty acids. The isolate B. subtilis BG01-4^TM is a proprietary strain developed by Vernx Biotechnology through accumulating mutations within the BG01-4^TM genome in a serial batch culture. Strain BG01-4^TM was provided as a non-spore-forming B. subtilis , but a positive sporulation status for BG01-4^TM was confirmed through in vitro testing and suggested that selection for the sporulation defective genes could occur within an environment that would select against sporulation. The durability of key sporulation genes was ratified in this study, as the ability of BG01-4^TM to produce spores was not eliminated by the attempts to select against sporulation genes in BG01-4^TM by the epigenetic factors of high glucose and low pH. However, a variation in the genes in isolate BG01-4-8 involved in the regulation of sporulation is believed to have occurred during the mutation selection from the parent strain BG01-4^TM. An alteration in selected sporulation regulation genes is expected to have occurred from BG01-4^TM to BG01-4-8, with BG01-4-8 producing spores within 24 h, ~48 h quicker than BG01-4^TM.

Facilitating flip-flop: Structural tuning of molecule-membrane interactions in living bacteria

The first barrier that a small molecule must overcome before trespassing into a living cell is the lipid bilayer surrounding the intracellular content. It is imperative, therefore, to understand how the structure of a small molecule influences its fate in this region. Through the use of second harmonic generation, we show how the differing degrees of ionic headgroups, conjugated system, and branched hydrocarbon tail disparities of a series of four styryl dye molecules influence the propensity to "flip-flop" or to be further organized in the outer leaflet by the membrane. We show here that initial adsorption experiments match previous studies on model systems; however, more complex dynamics are observed over time. Aside from probe molecule structure, these dynamics also vary between cell species and can deviate from trends reported based on model membranes. Specifically, we show here that the membrane composition is an important factor to consider for headgroup-mediated small-molecule dynamics. Overall, the findings presented here on how structural variability of small molecules impacts their initial adsorption and eventual destinations within membranes in the context of living cells could have practical applications in antibiotic and drug adjuvant design.

Effects of direct-fed Bacillus subtilis and Bacillus licheniformis on production performance and milk fatty acid profile in dairy cows

The aim of the study was to determine the effect of a Bacillus-based direct-fed microbial on performance of mid-lactating Holstein dairy cows and on their milk fatty acid composition. Six multiparous cows fitted with a rumen cannula were used in a randomized replicated crossover design. Cows received 200 g/d of either whey powder as a control or BioPlus 2B (Chr. Hansen), a commercial direct-fed microbial providing Bacillus subtilis and Bacillus licheniformis, representing a daily dose of 6.4 × 10¹¹ cfu, and using whey powder as a carrier. The 2 experimental periods lasted 14 d and were separated by a 7-d washout interval. Samples were collected on d 0, 13, and 14 of each period. Data from d 0 were used as covariate. Significance was declared at P ≤ 0.05 and tendency at 0.05 <P ≤ 0.10. There was a 10-fold increase in the relative concentration of bacteria from the Bacillus subtilis group in the rumen when feeding direct-fed Bacillus compared with control. Treatment did not affect ruminal pH, NH₃-N, or concentrations of acetate, propionate, and butyrate. However, direct-fed Bacillus increased ruminal concentrations of isovalerate and isobutyrate (tendency). Treatments did not affect lactation performance. Supplying direct-fed Bacillus enhanced milk relative concentration of anteiso 13:0 by 27.3% and of anteiso 15:0 by 6.5% and tended to increase concentrations of iso 14:0 (+41.8%) relative to control. When expressed on a yield basis, direct-fed Bacillus increased the secretion of anteiso 13:0 and decreased that of 11:0, 15:0, 17:0 (tendency), and cis-9 17:1. These variations, although limited in magnitude, indicate that milk branched-chain fatty acid composition is sensitive to ruminal microbiota modifications without changes in chemical composition of the diet.

Improved chemical and isotopic labeling of biomembranes in Bacillus subtilis by leveraging CRISPRi inhibition of beta-ketoacyl-ACP synthase (fabF)

Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure—and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct in vivo structural studies of the cell membrane in the Gram-positive bacterium, Bacillus subtilis, using small-angle neutron scattering. This was accomplished through a genetic inhibition of fatty acid (FA) degradation (ΔfadN) and a chemical inhibition of FA biosynthesis using cerulenin, an irreversible inhibitor of type II fatty acid synthases. Here, we improve upon the previous system by introducing a dCas9/sgRNA-fabF complex that blocks transcription of the essential fabF gene when under xylose induction. This leads to greater sensitivity to cerulenin in the mutant strain (JEBS102) and more robust cell growth when supplementary FAs are introduced to the culture medium. A subtle change in FA uptake is noted when compared to the prior labeling strategy. This is seen in the gas chromatography/mass spectrometry (GC/MS) data as a higher ratio of n16:0 to a15:0, and manifests in an apparent increase in the membrane thickness determined via neutron scattering. This represents an improved method of isotopic labeling for the cell membrane of Bacillus subtilis; enabling improved investigations of cellular uptake and utilization of FAs, cell membrane structure and organization as a phenotypic response to metabolic and environmental changes.

Bacterial diet modulates tamoxifen-induced death via host fatty acid metabolism

Tamoxifen is a selective estrogen receptor (ER) modulator that is used to treat ER-positive breast cancer, but that at high doses kills both ER-positive and ER-negative breast cancer cells. We recapitulate this off-target effect in Caenorhabditis elegans, which does not have an ER ortholog. We find that different bacteria dramatically modulate tamoxifen toxicity in C. elegans, with a three-order of magnitude difference between animals fed Escherichia coli, Comamonas aquatica, and Bacillus subtilis. Remarkably, host fatty acid (FA) biosynthesis mitigates tamoxifen toxicity, and different bacteria provide the animal with different FAs, resulting in distinct FA profiles. Surprisingly these bacteria modulate tamoxifen toxicity by different death mechanisms, some of which are modulated by FA supplementation and others by antioxidants. Together, this work reveals a complex interplay between microbiota, FA metabolism and tamoxifen toxicity that may provide a blueprint for similar studies in more complex mammals.

Here, Diot et al. use the nematode Caenorhabditis elegans as a model to identify off-target toxicity mechanisms for tamoxifen, and find that these include fatty acid metabolism and cell death, which can be modulated by different bacterial species.

Oleic acid based experimental evolution of Bacillus megaterium yielding an enhanced P450 BM3 variant

Background

Unlike most other P450 cytochrome monooxygenases, CYP102A1 from Bacillus megaterium (BM3) is both soluble and fused to its redox partner forming a single polypeptide chain. Like other monooxygenases, it can catalyze the insertion of oxygen unto the carbon-hydrogen bond which can result in a wide variety of commercially relevant products for pharmaceutical and fine chemical industries. However, the instability of the enzyme holds back the implementation of a BM3-based biocatalytic industrial processes due to the important enzyme cost it would prompt.

Results

In this work, we sought to enhance BM3’s total specific product output by using experimental evolution, an approach not yet reported to improve this enzyme. By exploiting B. megaterium’s own oleic acid metabolism, we pressed the evolution of a new variant of BM3, harbouring 34 new amino acid substitutions. The resulting variant, dubbed DE, increased the conversion of the substrate 10-pNCA to its product p-nitrophenolate 1.23 and 1.76-fold when using respectively NADPH or NADH as a cofactor, compared to wild type BM3.

Conclusions

This new DE variant, showed increased organic cosolvent tolerance, increased product output and increased versatility in the use of either nicotinamide cofactors NADPH and NADH. Experimental evolution can be used to evolve or to create libraries of evolved BM3 variants with increased productivity and cosolvent tolerance. Such libraries could in turn be used in bioinformatics to further evolve BM3 more precisely. The experimental evolution results also supports the hypothesis which surmises that one of the roles of BM3 in Bacillus megaterium is to protect it from exogenous unsaturated fatty acids by breaking them down.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12896-022-00750-w.

Chiral analysis of glycerol phosphates - can bacteria biosynthesize heterochiral phospholipid membranes?

Phosphatidylglycerol (1,2-diacyl-sn-glycero-3-phospho-glycerol) (PG) is one of the most abundant lipids in bacteria. However, the chirality of the carbon atom on glycerol phosphate is different between the three kingdoms, Archaea, Bacteria, and Eukarya. Archaea membranes consist of phospholipids with glycerol-1-phosphate (G1P) in the S configuration, whereas phospholipids of the other two kingdoms contain glycerol-3-phosphate (G3P) having R stereochemistry. In the present study, GC/MS and LC/MS methods sensitively detected G3P and G1P from four bacterial strains (Bacillus amyloliquefaciens, B. subtilis, Clavibacter michiganensis, and Geobacillus stearothermophilus). Strain selection was carried out based on a GenBank search that revealed bacterial sequences associated with both enzymes involved in glycerol-phosphate synthesis, i.e., glycerol-3-phosphate dehydrogenase and glycerol-1-phosphate dehydrogenase. The detection of G1P and G3P was made by comparing the retention times of synthetic standards with those of analyzed samples. The structures of both glycerol phosphates were confirmed by selected ion monitoring (SIM) at m/z 171.006. The total concentration of G3P and G1P was around 30 µM, with a ratio of G3P to G1P of 4:1. We showed that PG was the most abundant phospholipid in all four bacteria by using the following analytical techniques and chromatographic modes: hydrophilic interaction liquid chromatography (HILIC), reversed-phase high-performance liquid chromatography high-resolution electrospray ionization tandem mass spectrometry (RP-HPLC/HR-ESI tandem MS) in negative and positive ionization modes, and an enzymatic cleavage by phospholipase C. By using chiral chromatography, the presence of both enantiomers in the glycerol backbone of some molecular species of PG was revealed. These results allow us to conclude that the bacteria examined here produce both enantiomer glycerol phosphates.

Activity of Ancillary Heterotrophic Community Members in Anaerobic Methane-Oxidizing Cultures

Consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria mediate the anaerobic oxidation of methane (AOM) in marine sediments. However, even sediment-free cultures contain a substantial number of additional microorganisms not directly related to AOM. To track the heterotrophic activity of these community members and their possible relationship with AOM, we amended meso- (37°C) and thermophilic (50°C) AOM cultures (dominated by ANME-1 archaea and their partner bacteria of the Seep-SRB2 clade or Candidatus Desulfofervidus auxilii) with L-leucine-3-¹³C (¹³C-leu). Various microbial lipids incorporated the labeled carbon from this amino acid, independent of the presence of methane as an energy source, specifically bacterial fatty acids, such as iso and anteiso-branched C_15:0 and C_17:0, as well as unsaturated C_18:1ω9 and C_18:1ω7. In natural methane-rich environments, these bacterial fatty acids are strongly ¹³C-depleted. We, therefore, suggest that those fatty acids are produced by ancillary bacteria that grow on ¹³C-depleted necromass or cell exudates/lysates of the AOM core communities. Candidates that likely benefit from AOM biomass are heterotrophic bacterial members of the Spirochetes and Anaerolineae—known to produce abundant branched fatty acids and present in all the AOM enrichment cultures. For archaeal lipids, we observed minor ¹³C-incorporation, but still suggesting some ¹³C-leu anabolism. Based on their relatively high abundance in the culture, the most probable archaeal candidates are Bathyarchaeota, Thermoplasmatales, and Lokiarchaeota. The identified heterotrophic bacterial and archaeal ancillary members are likely key players in organic carbon recycling in anoxic marine sediments.

Quantitative analyses for several nutrients and volatile components during fermentation of soybean by Bacillus subtilis natto

This study is to reveal the variation of five pivotal substances, including polysaccharides, proteins, isoflavones, fatty acids and volatile components during the soybean fermentation process by Bacillus subtilis natto. After 96 h of soybean fermentation, the polysaccharide contents were significantly decreased, and the glucose and galactose contents showed the greatest decline in all the monosaccharide components. Moreover, isoflavone glycoside levels were decreased, while the isoflavone aglycone levels were increased following the fermentation. In addition, the SCFAs contents were also significantly increased in comparison with the unfermented soybean. Furthermore, 16 amino acids and 36 volatile components were detected in the fermented soybean. Finally, 21 key compounds were identified through PCA and OPLS-DA analysis of total compounds in the fermentation process. These findings demonstrated that Bacillus subtilis natto had a significant influence on the biochemical profiles of soybean fermentation and consequently contributed to its unique quality.

Low membrane fluidity triggers lipid phase separation and protein segregation in living bacteria

All living organisms adapt their membrane lipid composition in response to changes in their environment or diet. These conserved membrane-adaptive processes have been studied extensively. However, key concepts of membrane biology linked to regulation of lipid composition including homeoviscous adaptation maintaining stable levels of membrane fluidity, and gel-fluid phase separation resulting in domain formation, heavily rely upon in vitro studies with model membranes or lipid extracts. Using the bacterial model organisms Escherichia coli and Bacillus subtilis, we now show that inadequate in vivo membrane fluidity interferes with essential complex cellular processes including cytokinesis, envelope expansion, chromosome replication/segregation and maintenance of membrane potential. Furthermore, we demonstrate that very low membrane fluidity is indeed capable of triggering large-scale lipid phase separation and protein segregation in intact, protein-crowded membranes of living cells; a process that coincides with the minimal level of fluidity capable of supporting growth. Importantly, the in vivo lipid phase separation is not associated with a breakdown of the membrane diffusion barrier function, thus explaining why the phase separation process induced by low fluidity is biologically reversible.

Bioinformatics Modelling and Metabolic Engineering of the Branched Chain Amino Acid Pathway for Specific Production of Mycosubtilin Isoforms in Bacillus subtilis

Mycosubtilin belongs to the family of lipopeptides. Different isoforms with various antifungal activities can be obtained according to the length and the isomery of the fatty acid. In this work, the activities of the mycosubtilin isoforms were first studied against the pathogen Aspergillus niger, revealing the high activity of the anteiso-C17 isoform. Modification of the mycosubtilin isoform patterns during cultures of the natural strain Bacillus subtilis ATCC 6633 was then investigated through amino acid feeding experiments. In parallel, single-gene knockouts and single-gene overexpression, leading to the overproduction of the anteiso-C15 fatty acid chains, were predicted using informatics tools which provide logical reasoning with formal models of reaction networks. In this way, it was in silico predicted that the single overexpression of the ilvA gene as well as the single knockout of the codY gene may lead to the overproduction of anteiso-C15 fatty acid chains. For the first time, it has been demonstrated that overexpression of ilvA helps to enhance the furniture of odd anteiso fatty acids leading to a favored mycosubtilin anteiso-C17 production pattern (+41%). Alternatively, a knock-out codY mutant led to a higher furniture of even iso fatty acids, leading to a favored mycosubtilin iso-C16 production pattern (+180%). These results showed that increased selective synthesis of particular isoforms of mycosubtilin through metabolic engineering is feasible, disclosing the interest of these approaches for future development of lipopeptide-producing strains.

Potential of Prebiotic D-Tagatose for Prevention of Oral Disease

Recent studies have shown phenotypic and metabolic heterogeneity in related species including Streptococcus oralis, a typical oral commensal bacterium, Streptococcus mutans, a cariogenic bacterium, and Streptococcus gordonii, which functions as an accessory pathogen in periodontopathic biofilm. In this study, metabolites characteristically contained in the saliva of individuals with good oral hygiene were determined, after which the effects of an identified prebiotic candidate, D-tagatose, on phenotype, gene expression, and metabolic profiles of those three key bacterial species were investigated. Examinations of the saliva metabolome of 18 systemically healthy volunteers identified salivary D-tagatose as associated with lower dental biofilm abundance in the oral cavity (Spearman’s correlation coefficient; r = -0.603, p = 0.008), then the effects of D-tagatose on oral streptococci were analyzed in vitro. In chemically defined medium (CDM) containing D-tagatose as the sole carbohydrate source, S. mutans and S. gordonii each showed negligible biofilm formation, whereas significant biofilms were formed in cultures of S. oralis. Furthermore, even in the presence of glucose, S. mutans and S. gordonii showed growth suppression and decreases in the final viable cell count in a D-tagatose concentration-dependent manner. In contrast, no inhibitory effects of D-tagatose on the growth of S. oralis were observed. To investigate species-specific inhibition by D-tagatose, the metabolomic profiles of D-tagatose-treated S. mutans, S. gordonii, and S. oralis cells were examined. The intracellular amounts of pyruvate-derived amino acids in S. mutans and S. gordonii, but not in S. oralis, such as branched-chain amino acids and alanine, tended to decrease in the presence of D-tagatose. This phenomenon indicates that D-tagatose inhibits growth of those bacteria by affecting glycolysis and its downstream metabolism. In conclusion, the present study provides evidence that D-tagatose is abundant in saliva of individuals with good oral health. Additionally, experimental results demonstrated that D-tagatose selectively inhibits growth of the oral pathogens S. mutans and S. gordonii. In contrast, the oral commensal S. oralis seemed to be negligibly affected, thus highlighting the potential of administration of D-tagatose as an oral prebiotic for its ability to manipulate the metabolism of those targeted oral streptococci.

Profiles of Odd- and Branched-Chain Fatty Acids and Their Correlations With Rumen Fermentation Parameters, Microbial Protein Synthesis, and Bacterial Populations Based on Pure Carbohydrate Incubation in vitro

The objectives of this study were to evaluate changes in profiles of odd- and branched-chain fatty acids (OBCFA), including pentadecanoic acid (C15:0), 13-methyltetradecanoic acid (iso-C15:0), 12-methyltetradecanoic acid (anteiso-C15:0), 14-methylpentadecanoic acid (iso-C16:0), heptadecanoic acid (C17:0), 15-methylhexadecanoic acid (iso-C17:0), and 14-methylhexadecanoic acid (anteiso-C17:0) during in vitro fermentation of pure carbohydrates mixtures in the buffer-rumen fluid. The second objective was to correlate the changes in the OBCFA profile to the corresponding changes in ruminal fermentation parameters, microbial crude protein (MCP) synthesis, and bacterial populations. Five pure carbohydrates mixtures containing different cellulose: starch (C:S) ratios, i.e., 0:100, 25:75, 50:50, 75:25, and 100:0, were incubated for 6, 12, 18, and 24 h in vitro. The results showed that there was significant interaction (P < 0.05) between C:S and incubation time for changes in all OBCFA profiles, except iso-C17:0. The highest concentration of total OBCFA (3.94 mg/g dry matter; DM) was observed in the residues after 24 h of fermentation when the C:S was 0:100, while the lowest concentration of OBCFA (1.65 mg/g DM) was produced after 6 h of incubation when the C:S was 50:50. The correlation analysis revealed that the concentration of iso-C16:0 might be a potential marker for the estimation of total volatile fatty acids (ρ = 0.78) and MCP synthesis (ρ = 0.82) in the rumen. Compared to starch degrading bacteria, cellulolytic bacteria had stronger correlations with OBCFA concentrations, and the strongest correlation was found between the population of Ruminococcus flavefaciens with C15:0 concentration (ρ = 0.70). Notably, this is the first paper reporting relationship between OBCFA with rumen fermentation products and microbial protein synthesis based on fermentation of pure carbohydrates mixtures in vitro, and thus avoid confounding interference from dietary protein and fat presence in the in vivo studies. However, more in-depth experiments are needed to substantiate the current findings.

Monomethyl branched-chain fatty acid mediates amino acid sensing upstream of mTORC1

Animals have developed various nutrient-sensing mechanisms for survival under fluctuating environmental conditions. Although extensive cell-culture-based analyses have identified diverse mediators of amino acid sensing upstream of mTOR, studies using animal models to examine intestine-initiated amino acid sensing mechanisms under specific physiological conditions are lacking. Here, we developed a Caenorhabditis elegans model to examine the impact of amino acid deficiency on development. We discovered a leucine-derived monomethyl branched-chain fatty acid and its downstream metabolite, glycosphingolipid, which critically mediates the overall amino acid sensing by intestinal and neuronal mTORC1, which in turn regulates postembryonic development at least partly by controlling protein translation and ribosomal biogenesis. Additional data suggest that a similar mechanism may operate in mammals. This study uncovers an amino-acid-sensing mechanism mediated by a lipid biosynthesis pathway.

Short-Chain and Unsaturated Fatty Acids Increase Sequentially From the Lag Phase During Cold Growth of Bacillus cereus

Fatty acids of two mesophilic and one psychrotrophic strains of the foodborne pathogen Bacillus cereus were analyzed by gas chromatography coupled to mass spectrometry during growth at cold (10 and 12°C) vs. optimal (30°C) temperatures and during the whole growth process (6–7 sampling times) from lag to stationary phase. In all these strains, a sequential change of fatty acids during cold growth was observed. Fatty acids were modified as soon as the end of lag, with an increase of the short-chain fatty acids (less than 15 carbons), particularly i13. These short-chain fatty acids then reached a maximum at the beginning of growth and eventually decreased to their initial level, suggesting their importance as a rapid cold adaptation mechanism for B. cereus. In a second step, an increase in Δ^5,10 di-saturated fatty acids and in monounsaturated fatty acids in Δ⁵ position, at the expense of unsaturation in Δ¹⁰, started during exponential phase and continued until the end of stationary phase, suggesting a role in growth consolidation and survival at cold temperatures. Among these unsaturated fatty acids, those produced by unsaturation of n16 increased in the three strains, whereas other unsaturated fatty acids increased in some strains only. This study highlights the importance of kinetic analysis of fatty acids during cold adaptation.

Branched-chain fatty acids in the vernix caseosa and meconium of infants born at different gestational ages

The functional lipid components found in breast milk, vernix caseosa, and meconium are Branched-chain Fatty Acids (BCFA). The goal of this study was to establish the existence of BCFA in vernix and meconium in infants born at different gestational ages. TLC plates and GC-MS were examined for the lipids in vernix caseosa and meconium. The results indicated that there were nine BCFA in vernix caseosa, including iso-12:0, anteiso-13:0, iso-14:0, iso-15:0, anteiso-15:0, iso-16:0, anteiso-17:0, iso-18:0, and iso-20:0. Five BCFA (iso-12:0, anteiso-13:0, iso-14:0, iso-15:0, and anteiso-15:0) were not contained in the meconium, suggesting that some of the BCFA may be digested and consumed by infants. In the vernix caseosa, the content of BCFA in triacylglycerol (TAG) and free fatty acid (FFA) was 15.59% and 11.82%, respectively. The vernix caseosa's wax ester fraction contained the highest content of BCFA, reaching up to 16.81%. The carbon chain length of fatty acids (FA) ranged from 12 to 24 in the vernix caseosa and 14 to 22 in meconium samples. The gestational age was likely to affect BCFA concentrations, with the vernix caseosa and meconium BCFA content being significantly higher in full-term infants than in preterm infants (p < .001). Further research is required into the relationship between BCFA and gut microbiotas.

Chemoenzymatic Generation of Phospholipid Membranes Mediated by Type I Fatty Acid Synthase

The de novo formation of lipid membranes from minimal reactive precursors is a major goal in synthetic cell research. In nature, the synthesis of membrane phospholipids is orchestrated by numerous enzymes, including fatty acid synthases and membrane-bound acyltransferases. However, these enzymatic pathways are difficult to fully reproduce in vitro. As such, the reconstitution of phospholipid membrane synthesis from simple metabolic building blocks remains a challenge. Here, we describe a chemoenzymatic strategy for lipid membrane generation that utilizes a soluble bacterial fatty acid synthase (cgFAS I) to synthesize palmitoyl-CoA in situ from acetyl-CoA and malonyl-CoA. The fatty acid derivative spontaneously reacts with a cysteine-modified lysophospholipid by native chemical ligation (NCL), affording a noncanonical amidophospholipid that self-assembles into micron-sized membrane-bound vesicles. To our knowledge, this is the first example of reconstituting phospholipid membrane formation directly from acetyl-CoA and malonyl-CoA precursors. Our results demonstrate that combining the specificity and efficiency of a type I fatty acid synthase with a highly selective bioconjugation reaction provides a biomimetic route for the de novo formation of membrane-bound vesicles.

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. I: Comparison with branched-chain amino acids and forage source in ruminal batch cultures

Three experiments assessed branched-chain volatile fatty acid (BCVFA) stimulation of neutral detergent fiber (NDF) disappearance after 24 h of incubation in batch cultures derived from ruminal fluid inocula that were enriched with particulate-phase bacteria. In experiment 1, a control was compared with 3 treatments with isomolar doses of all 3 BCVFA (plus valerate), all 3 branched-chain AA (BCAA), or half of each BCVFA and BCAA mix with either alfalfa or grass hays (50%) and ground corn grain (50%). A portion of the BCAA and BCVFA doses were enriched with ¹³C, and valerate (also enriched with ¹³C) was added with BCVFA. Although BCAA yielded a similar production of BCVFA compared with dosing BCVFA, equimolar substitution of BCVFA for BCAA decreased the percentage of N in bacterial pellets when alfalfa hay was fed but increased N when grass hay was fed. Substituting BCVFA for BCAA increased total fatty acid (FA) concentration with alfalfa hay. Dosing of BCAA or BCVFA did not affect total branched-chain FA, iso-FA, or anteiso-FA percentages in bacterial total FA, whereas numerous individual FA isomers and their ¹³C enrichments were affected by these treatments. Increasing recovery of the ¹³C dose from respective labeled BCVFA primers indicated facilitated BCVFA uptake and incorporation into FA compared with BCAA, whereas increased recovery of ¹³C from labeled BCAA in the bacteria pellet but not in the FA fraction suggested direct assimilation into bacterial protein. The BCVFA and valerate were dosed in varying combinations that either summed to 4 mM (experiment 2) or had only 1 mM no matter what combination (experiment 3). In general, grass hay was more responsive to stimulation in NDF digestibility by BCVFA than was alfalfa hay, which was attributed to the higher degradable protein in the latter. The net production of the BCVFA (after subtracting dose) was affected by source and combination of BCVFA. Isovalerate dosing tended to increase its own net production; in contrast, isobutyrate seemed to be used more when it was added alone, but 2-methylbutyrate seemed to be preferred over isobutyrate when 2-methylbutyrate was added. Results supported potential interactions, including potential feedback in production from feed BCAA or increased concentration-dependent competition for dosed BCVFA into cellular products. Under our conditions, the BCVFA appear to be more readily available than BCAA, probably because of regulated BCAA transport and metabolism. Valerate consistently provided no benefit. Using nonparametric ranking, all 3 BCVFA or either isovalerate or isobutyrate (both yielding iso-FA) should be combined with 2-methylbutyrate (yielding anteiso-FA) as a potential opportunity to improve NDF digestibility when rumen-degraded BCAA are limited in diets to decrease environmental impact from N in waste.

Characterization of fecal branched-chain fatty acid profiles and their associations with fecal microbiota in diarrheic and healthy dairy calves

Branched-chain fatty acids (BCFA) have recently been reported to play a role in human gut health during early life. However, little information is available on the fecal BCFA profiles in young ruminants and whether they are associated with the development of neonatal calf diarrhea. The objectives of this study were to (1) characterize BCFA profiles in feces collected from young calves, (2) compare the fecal BCFA composition between diarrheic and nondiarrheic dairy calves, and (3) explore the potential relationships between BCFA and microbiota in the feces. A total of 32 male Holstein dairy calves (13 ± 3 d old) with the same diet management were grouped as diarrheic (n = 16) or healthy (n = 16) based on fecal score (determined by liquid fecal consistency with some solid particles); diarrhea cases were defined as fecal score ≥2 for at least 2 d. Fecal samples were collected on the seventh day after calf arrival, and the fecal BCFA and microbial profiles were assessed using gas chromatograph and amplicon sequencing, respectively. In total, 7 BCFA were detected in the feces of all dairy calves; however, the concentrations of fecal BCFA differed between diarrheic and nondiarrheic calves. Specifically, the concentrations of iso-C16:0, iso-C17:0, anteiso-C17:0, and total even-chain BCFA were significantly higher in the feces of diarrheic calves. When the associations between BCFA and bacteria were studied, the relative abundance of Eggerthella was positively correlated with the concentrations of iso-C16:0 (ρ = 0.67), iso-17:0 (ρ = 0.77), anteiso-C17:0 (ρ = 0.73), and iso-C18:0 (ρ = 0.65), whereas the relative abundance of Subdoligranulum was positively correlated with the concentrations of iso-C14:0 (ρ = 0.62), iso-C15:0 (ρ = 0.78), and anteiso-C15:0 (ρ = 0.63). Use of random forest algorithm showed that BCFA such as anteiso-C15:0, iso-C16:0, iso-C17:0, iso-C18:0, and total even-chain BCFA could be used as biomarkers to differentiate diarrheic calves from healthy ones. Our findings generated fundamental knowledge on the potential roles of BCFA in neonatal calf gut health. Follow-up studies with larger animal populations are warranted to validate the feasibility of using BCFA as indicators of health status in neonatal calves.

Detailed analysis of the fatty acid composition of six plant-pathogenic bacteria

Bacteria show distinct and characteristic fatty acid (FA) patterns which can be modified by environmental conditions. In this study, we cultivated six plant-pathogenic bacteria of agricultural concern and performed a detailed analysis of the fatty acid composition. The study covered four strains of the gram-negative Xanthomonas campestris pathovar (pv) campestris (Xcc), Xanthomonas perforans (Xp), Acidovorax citrulli (Ac) and Pseudomonas syringae pv. tomato (Pst), and two strains of the gram-positive Clavibacter michiganensis subsp. michiganensis (Cmm) and Streptomyces scabies (Ssc). After cultivation, freeze-dried bacteria samples were transesterified and analysed by gas chromatography with mass spectrometry in full scan and selected ion monitoring (SIM) modes. Altogether, 44 different FAs were detected in the six strains with individual contributions of 0.01-43.8% to the total FAs. The variety in the six strains ranged between 12 and 31 individual FAs. The FA composition of Xcc, Xp, Cmm and Ssc were dominated by iso- and anteiso-fatty acids (especially i15:0, a15:0, i16:0), which is typical for most bacteria. In contrast to this, Ac and Pst showed only saturated and monounsaturated FAs. Four of the six bacteria showed similar FA patterns as reported before in the literature. Differences were observed in the case of Cmm where many more FAs were detected in the present study. In addition, to the best of our knowledge, the FA pattern of Xp was presented for the first time.

Polyphasic characterization and identification of the bioremediation agent Bacillus sp. SFC 500-1E

Bacillus sp. SFC 500-1E is used for the effective treatment of tannery effluents since it consistently removes hexavalent chromium from diverse contaminated matrices. The aim of the present study was to complete identification of the strain through a polyphasic characterization, which included the pattern of carbohydrate utilization, fatty acids profile, multilocus sequence analysis, multiplex PCR profile and the analysis of the complete genome sequence. Morpho-physiological and biochemical characterization results and analysis of 16S rRNA sequences were not conclusive. The strain formed a monophyletic clade with B. toyonensis BCT-7112, B. thuringiensis MC28 and B. cereus Rock 1-3. However, genomic comparisons with type strains of B. cereus and B. thuringiensis showed that the isolated belonged to a different species. Results of this study highlight the relevance of the genome sequence of this strain, identified as Bacillus toyonensis SFC 500-1E, to expand knowledge of its bioremediation potential and to explore unknown decontamination activities.

Reclassification of Brevibacterium frigoritolerans DSM 8801T as Bacillus frigoritolerans comb. nov. Based on Genome Analysis

16S rRNA gene sequence analysis showed that the type strain Brevibacterium frigoritolerans DSM 8801^T had the highest similarity (99.7%) with the reference strain Bacillus simplex NBRC 15720^T, followed by Bacillus muralis DSM 16288^T (99.6%), Bacillus butanolivorans DSM 18926^T (99.5%), and Bacillus loiseleuriae FJAT-27997^T (97.9%). This relationship is confirmed by the phylogenetic analysis indicating that Bre. frigoritolerans DSM 8801^T fell in the genus Bacillus group and formed a clade with the closely related Bacillus species. Average nucleotide identity and in silico DNA-DNA hybridization (isDDH) values between strain DSM 8801^T and the most closed reference strain Bac. simplex NBRC 15720^T were both much lower than species definition threshold values of 95% and 70%, respectively, which indicated strain DSM 8801^T should not be affiliated to one of the validly named Bacillus species. The percentage of conserved protein (POCP) values between the strain DSM 8801^T and the type strains of the above species were 80.7%, 69.2%, 72.2%, 53.6%, and 50.0%, respectively, higher than the genus definition threshold value of 50%. The main isoprenoid quinone of strain DSM 8801^T was MK-7, the main polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidyl ethanolamine (PE), and the major fatty acids were anteiso-C_15:0 and iso-C_15:0. On the basis of the phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, Bre. frigoritolerans DSM 8801^T should belong to the genus Bacillus, and be proposed to reclassify as Bacillus frigoritolerans comb. nov., with the type strain DSM 8801^T (=ATCC 25097^T = CCUG 43489^T= CIP 67.20^T= JCM 11681^T).

Relations of Ruminal Fermentation Parameters and Microbial Matters to Odd- and Branched-Chain Fatty Acids in Rumen Fluid of Dairy Cows at Different Milk Stages

Simple Summary

The objective of this study was to determine the relationships between milk odd- and branched-chain fatty acids (OBCFAs) and ruminal fermentation parameters, microbial populations, and base contents. Significant relationships existed between the concentrations of C11:0, iso-C15:0, anteiso-C15:0, C15:0, and anteiso-C17:0 in rumen and milk. The total OBCFA content in milk was positively related to the acetate molar proportion but negatively correlated with isoacid levels. The adenine/N ratio was negatively related to milk OBCFA content but positively associated with the iso-C15:0/iso-C17:0 ratio.

Abstract

The purpose of this research was to evaluate whether relationships exist between odd- and branched-chain fatty acids (OBCFAs) originating from milk fat and the corresponding data of ruminal fermentation parameters, microbial populations, and base contents that were used to mark microbial protein in rumen. Nine lactating Holstein dairy cows with similar body weights and parity were selected in this study, and the samples of rumen and milk were collected at the early, middle, and late stages, respectively. The rumen and milk samples were collected over three consecutive days from each cow, and the ruminal and milk OBCFA profiles, ruminal fermentation parameters, bacterial populations, and base contents were measured. The results showed that the concentrations of OBCFAs, with the exception of C11:0 and C15:0, were significantly different between milk and rumen (p < 0.05). The concentrations of anteiso-fatty acids in milk were higher than those in rumen, and the contents of linear odd-chain fatty acids were higher than those of branched-chain fatty acids in both milk and rumen. Significant relationships that existed between the concentrations of C11:0, iso-C15:0, anteiso-C15:0, C15:0, and anteiso-C17:0 in rumen and milk (p < 0.05). The total OBCFA content in milk was positively related to the acetate molar proportion but negatively correlated with isoacid contents (p < 0.05). The populations of Ruminococcus albus, R. flavefacients, and Eubacterium ruminantium were significantly related to milk C13:0 contents (p < 0.05). The adenine/N ratio was negatively related to milk OBCFA content (p < 0.05) but positively associated with the iso-C15:0/iso-C17:0 ratio (p < 0.05). Milk OBCFAs were significantly correlated with ruminal fermentation parameters, ruminal bacterial populations, and base contents. Milk OBCFAs had the potential to predict microbial nitrogen flow, and the prediction equations for ruminal microbial nitrogen flow were established for OBCFAs in dairy milk.

Substrate characteristic bacterial fatty acid production based on amino acid assimilation and transformation in marine sediments

Polar lipid-derived fatty acids (PLFAs) and their stable carbon isotopes are frequently combined to characterize microbial populations involved in the degradation of organic matter, offering a link to biogeochemical processes and carbon sources used. However, PLFA patterns derive from multiple species and may be influenced by substrate types. Here, we investigated such dependencies by monitoring the transformation of position-specifically 13C-labeled amino acids (AAs) in coastal marine sediments dominated by heterotrophic bacteria. Alanine was assimilated into straight-chain FAs, while valine and leucine incorporation led to the characteristic production of even- and odd-numbered iso-series FAs. This suggests that identical microbial communities adjust lipid biosynthesis according to substrate availability. Transformation into precursor molecules for FA biosynthesis was manifested in increased 13C recoveries of the corresponding volatiles acetate, isobutyrate and isovalerate of up to 39.1%, much higher than for PLFAs (<0.9%). A significant fraction of 13C was found in dissolved inorganic carbon (up to 37.9%), while less was recovered in total organic carbon (up to 17.3%). We observed a clear discrimination against the carboxyl C, whereby C2 and C3 positions were preferentially incorporated into PLFAs. Therefore, position-specific labeling is an appropriate tool for reconstructing the metabolic fate of protein-derived AAs in marine environments.

Identification of an amphipathic peptide sensor of the Bacillus subtilis fluid membrane microdomains

Regions of increased fluidity are newly found bacterial membrane microdomains that are composed of short, unsaturated and branched fatty acyl chains in a fluid and disordered state. Currently, little is known about how proteins are recruited and localized to these membrane domains. Here, we identify a short amphipathic α-peptide in a previously unreported crystal structure and show that it is responsible for peripheral localization of the phosphate acyltransferase PlsX to the fluid microdomains in Bacillus subtilis. Mutations disrupting the amphipathic interaction or increasing the nonpolar interaction are found to redistribute the protein to the cytosol or other part of the plasma membrane, causing growth defects. These results reveal a mechanism of peripheral membrane sensing through optimizing nonpolar interaction with the special lipids in the microdomains. This finding shows that the fluid membrane microdomains may take advantage of their unique lipid environment as a means of recruiting and organizing proteins.

Insights Into the Microbiology of the Chaotropic Brines of Salar de Atacama, Chile

Microbial life inhabiting hypersaline environments belong to a limited group of extremophile or extremotolerant taxa. Natural or artificial hypersaline environments are not limited to high concentrations of NaCl, and under such conditions, specific adaptation mechanisms are necessary to permit microbial survival and growth. Argentina, Bolivia, and Chile include three large salars (salt flats) which globally, represent the largest lithium reserves, and are commonly referred to as the Lithium Triangle Zone. To date, a large amount of information has been generated regarding chemical, geological, meteorological and economical perspectives of these salars. However, there is a remarkable lack of information regarding the biology of these unique environments. Here, we report the presence of two bacterial strains (isolates LIBR002 and LIBR003) from one of the most hypersaline lithium-dominated man-made environments (total salinity 556 g/L; 11.7 M LiCl) reported to date. Both isolates were classified to the Bacillus genera, but displayed differences in 16S rRNA gene and fatty acid profiles. Our results also revealed that the isolates are lithium-tolerant and that they are phylogenetically differentiated from those Bacillus associated with high NaCl concentration environments, and form a new clade from the Lithium Triangle Zone. To determine osmoadaptation strategies in these microorganisms, both isolates were characterized using morphological, metabolic and physiological attributes. We suggest that our characterization of bacterial isolates from a highly lithium-enriched environment has revealed that even at such extreme salinities with high concentrations of chaotropic solutes, scope for microbial life exists. These conditions have previously been considered to limit the development of life, and our work extends the window of life beyond high concentrations of MgCl2, as previously reported, to LiCl. Our results can be used to further the understanding of salt tolerance, most especially for LiCl-dominated brines, and likely have value as models for the understanding of putative extra-terrestrial (e.g., Martian) life.

Enhancing surfactin production by using systematic CRISPRi repression to screen amino acid biosynthesis genes in Bacillus subtilis

Background

Surfactin is a cyclic lipopeptide that is of great industrial use owing to its extraordinary surfactant power and antimicrobial, antiviral, and antitumor activities. Surfactin is synthesized by a condensation reaction in microbes, which uses fatty acids and four kinds of amino acids (l-glutamate, l-aspartate, l-leucine and l-valine) as precursors. Surfactin biosynthesis could be improved by increasing the supply of fatty acids; however, the effect of the regulation of amino acid metabolism on surfactin production was not yet clear.

Results

In this study, we aimed to improve surfactin production in B. subtilis by repressing the genes on the branch metabolic pathways of amino acid biosynthesis using CRISPRi technology. First, 20 genes were inhibited individually, resulting in 2.5- to 627-fold decreases in transcriptional level as determined by RT-qPCR. Among the 20 recombinant strains, 16 strains obtained higher surfactin titres than that produced by the parent BS168NU-Sd strain (the surfactin production of BS168NU-Sd with only dCas9 but no sgRNA expression was 0.17 g/L). In particular, the strains in which the yrpC, racE or murC genes were inhibited individually produced 0.54, 0.41, or 0.42 g/L surfactin, respectively. All three genes are related to the metabolism of l-glutamate, whose acylation is the first step in the surfactin condensation reaction. Furthermore, these three genes were repressed in combination, and the strain with co-inhibition of yrpC and racE produced 0.75 g/L surfactin, which was 4.69-fold higher than that of the parent strain. In addition, the inhibition of bkdAA and bkdAB, which are related to the metabolism of l-leucine and l-valine, not only improved surfactin production but also increased the proportion of the C₁₄ isoform.

Conclusions

This study, to the best of our knowledge for the first time, systematically probed the regulatory effect of increasing the supply of amino acids on surfactin production. It provided an effective strategy and a new perspective for systematic studies on surfactin and other amino acid-derived chemicals.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1139-4) contains supplementary material, which is available to authorized users.

Decoding the Fatty Acid Profile of Bacillus licheniformis I89 and Its Adaptation to Different Growth Conditions to Investigate Possible Biotechnological Applications

Bacillus licheniformis I89 is a Gram-positive bacterium, a producer of the lantibiotic lichenicidin. No information is available on its fatty acid (FA) composition. Bacillus species are rich in branched FA (BrFA), claimed to be beneficial to human health and to treat diseases. Herein, the FA profile of B. licheniformis I89 was evaluated under different growth conditions: at two growth temperatures (37 and 50 °C) and at different growth phases (lag, exponential, and stationary), using gas chromatography-mass spectrometry. The FA profile revealed predominant BrFA of the iso-series and anteiso-series (i-15:0, ai-15:0, i-16:0, i-17:0, and ai-17:0) and low amounts of saturated FA (14:0, 16:0, and 18:0). Comparing the FA profiles at different temperatures, in the lag phase, at 50 °C, there was a decrease of ai-17:0 and a decrease of i-15:0 in the exponential phase, in comparison with 37 °C. In all growth phases, there was a decrease of ai-15:0 and an increase of i-17:0. From the lag to the stationary phase, at 50 °C, there was a decrease of ai-17:0 and i-16:0, whereas i-15:0 increased, while at 37 °C, there was an increase of i-15:0 and i-16:0, and a decrease in ai-15:0 and ai-17:0. B. licheniformis I89 can adapt its FA profile, at moderate temperatures, by changing the iso-FA and anteiso-FA composition and the iso/anteiso ratio. This nonpathogenic bacterium species can be used as a source of BrFA with putative beneficial health effects for gut protection and with reported antitumor properties, foreseeing its use for producing compounds with biotechnological applications.

Rational strain improvement for surfactin production: enhancing the yield and generating novel structures

Surfactin, one of the most powerful microbial surfactants, is a lipopeptide-type biosurfactant which combines interesting physicochemical properties and biological activities. However, the high cost caused by its low productivity largely limits the commercial application of surfactin. Hence, many engineered bacterium have also been used to enhance surfactin biosynthesis. This review briefly summarizes the mechanism of surfactin biosynthesis, highlighting the synthesis pathway of N-terminally attached fatty acids, and outlines the main genetic engineering strategies for improving the yield and generating novel structures of surfactin, including promoter engineering, enhancing efflux systems, modifying the transcriptional regulatory genes of surfactin synthase (srfA), genomics and transcriptomics analysis, non ribosomal peptide synthetase (NRPS) domain and combinatorial biosynthesis. Finally, we discuss the future prospects of the research on surfactin.

Antisense RNA-Based Strategy for Enhancing Surfactin Production in Bacillus subtilis TS1726 via Overexpression of the Unconventional Biotin Carboxylase II To Enhance ACCase Activity

The antisense RNA (asRNA) strategy is commonly used to block protein expression and downregulate the contents of metabolites in several microorganisms. Here, we show that the asRNA strategy can also be used to block gfp expression in Bacillus subtilis TS1726, which could further be utilized in the identification of new genes and functions. Via application of this strategy, biotin carboxylase II encoded by yngH (GeneID 939474) was identified to play a more significant role in maintaining acetyl-CoA carboxylase (ACCase) activity and enhancing surfactin synthesis compared to those of other ACCase subunits. The yngH gene was then overexpressed in the engineered strain B. subtilis TS1726(yngH). The surfactin titer of TS1726(yngH) increased to 13.37 g/L in a flask culture, representing a 43% increase compared to that of parental strain TS1726. This strategy opens the door to achieving large-scale production and broad application of surfactin.

High levels of branched chain fatty acids in nātto and other Asian fermented foods

The mean intake (500 mg/day) of branched chain fatty acids (BCFA) in western countries is from dairy products and beef. We hypothesized that Asian countries with low dairy consumption have an alternative source of BCFA and report the characterization of nātto and selected fermented foods for BCFA content. Nātto BCFA averaged 0.6 (range 0.21-1.43) mg BCFA per g natto (wet weight) and was highly variable. Nātto major BCFA are C14-17 iso- and anteiso-BCFA similar to fluid milk. BCFA concentrations were 1.00 ± 0.64%, 1.63 ± 0.72% and 0.65 ± 0.07%, of total fatty acids in nātto, shrimp paste and fish sauce, respectively. In contrast, saturates, monounsaturates, and major polyunsaturates were more constant (coefficient of variation = 21%, 26% and 4% compared to 64% for nātto BCFA). Detection of fatty acid ethyl esters were confirmed in miso and found in homemade kimchi. Habitual nātto and/or fermented seafood consumption could support BCFA intakes similar to dairy consumption.

Human meibum chain branching variability with age, gender and meibomian gland dysfunction

NMR spectroscopy was used to measure hydrocarbon chain branching variability in meibum with age, gender and Meibomian gland dysfuction (MGD). A cohort of 65 meibum donors without dry eye and 31 donors with MGD was studied. Heteronuclear 2D NMR was used to confirm CH₃ resonance assignments allowing us to positively identify 23 of the 27 proton resonances of cholesteryl ester and ¹H resonances due to straight chain, iso-branched and anteiso-branched hydrocarbons. Meibum from donors without dry eye contained 57 ± 1% straight-chains, 23 ± 1% iso-branched chains and 20 ± 1% anteiso-branched hydrocarbon chains. Compared with meibum from donors without dry eye, meibum from donors with MGD contained less, 50 ± 2% straight-chains, more, 32 ± 2% iso-branched chains and the same amount, 18.0 ± 0.07%, of anteiso-branched hydrocarbon chains. Meibum hydrocarbon chain branching did not change with age between 22 and 68 years of age, nor was it influenced by gender. Based on previous studies, one would expect anteiso-branched chains would contribute to lowering the phase transition temperature of meibum, decrease the elasticity of the tear film lipid layer and increase the molecular area and spreading of meibum on the surface of the eye. Although we speculate that the observed differences in iso-chain branching do not influence tear film stability or rheology, the speculation has yet to be tested.

Potential of Lentibacillus sp. NS12IITR for production of lipids with enriched branched-chain fatty acids for improving biodiesel properties along with hydrocarbon co-production

Hypersaline environment is inhabited by array of microbes which have the potential to produce industrially important products. This study explored biomass and lipid production potential of the halophilic bacterium, strain NS12IITR which was isolated from Sambhar Lake, Rajasthan. Sequencing and phylogenetic analysis revealed that the bacterium belonged to genus Lentibacillus. The salient feature of the isolate is its ability to accumulate total cellular lipid up to 18.9 ± 0.45% of dry cell weight. In addition, trans-esterification of extracted lipid yielded 77.6 ± 5.56% of total esters as methyl ester of branched-chain fatty acids (BCFAs). To assess the nature of extracted lipid, lipid sample was fractionated on the silicic acid column, which demonstrated that 49.03 ± 1.35% of the total lipids was neutral in nature. Trans-esterification of the neutral lipid fraction yielded 60.62 ± 4.88% of total esters as methyl ester of BCFAs. Methyl esters of BCFAs were present in trans-esterified products of neutral as well as polar lipid fractions. Furthermore, the isolate produced hydrocarbons both extracellularly (C₁₀-C₃₀) and intra-cellularly (C₁₅-C₂₈). The concentration of extracellular hydrocarbon (21.11 ± 0.78 mg/L) synthesized by strain NS12IITR is in close agreement with the yield reported from other hydrocarbon producing bacteria. This is hereby a first report on the co-production of lipids and hydrocarbon from a halophilic bacterium. The production of neutral lipid with high percentage of BCFAs and co-production of hydrocarbons makes the isolate NS12IITR a potential claimant for biofuel production.

Engineered Production of Short-Chain Acyl-Coenzyme A Esters in Saccharomyces cerevisiae

Short-chain acyl-coenzyme A esters serve as intermediate compounds in fatty acid biosynthesis, and the production of polyketides, biopolymers and other value-added chemicals. S. cerevisiae is a model organism that has been utilized for the biosynthesis of such biologically and economically valuable compounds. However, its limited repertoire of short-chain acyl-CoAs effectively prevents its application as a production host for a plethora of natural products. Therefore, we introduced biosynthetic metabolic pathways to five different acyl-CoA esters into S. cerevisiae. Our engineered strains provide the following acyl-CoAs: propionyl-CoA, methylmalonyl-CoA, n-butyryl-CoA, isovaleryl-CoA and n-hexanoyl-CoA. We established a yeast-specific metabolite extraction protocol to determine the intracellular acyl-CoA concentrations in the engineered strains. Propionyl-CoA was produced at 4-9 μM; methylmalonyl-CoA at 0.5 μM; and isovaleryl-CoA, n-butyryl-CoA, and n-hexanoyl-CoA at 6 μM each. The acyl-CoAs produced in this study are common building blocks of secondary metabolites and will enable the engineered production of a variety of natural products in S. cerevisiae. By providing this toolbox of acyl-CoA producing strains, we have laid the foundation to explore S. cerevisiae as a heterologous production host for novel secondary metabolites.

Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane

Lipid extracts are an excellent choice of model biomembrane; however at present, there are no commercially available lipid extracts or computational models that mimic microbial membranes containing the branched-chain fatty acids found in many pathogenic and industrially relevant bacteria. We advance the extract of Bacillus subtilis as a standard model for these diverse systems, providing a detailed experimental description and equilibrated atomistic bilayer model included as Supporting Information to this Letter and at ( http://cmb.ornl.gov/members/cheng ). The development and validation of this model represents an advance that enables more realistic simulations and experiments on bacterial membranes and reconstituted bacterial membrane proteins.

Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure

The cytoplasmic membrane of a prokaryotic cell consists of a lipid bilayer or a monolayer that shields the cellular content from the environment. In addition, the membrane contains proteins that are responsible for transport of proteins and metabolites as well as for signalling and energy transduction. Maintenance of the functionality of the membrane during changing environmental conditions relies on the cell's potential to rapidly adjust the lipid composition of its membrane. Despite the fundamental chemical differences between bacterial ester lipids and archaeal ether lipids, both types are functional under a wide range of environmental conditions. We here provide an overview of archaeal and bacterial strategies of changing the lipid compositions of their membranes. Some molecular adjustments are unique for archaea or bacteria, whereas others are shared between the two domains. Strikingly, shared adjustments were predominantly observed near the growth boundaries of bacteria. Here, we demonstrate that the presence of membrane spanning ether-lipids and methyl branches shows a striking relationship with the growth boundaries of archaea and bacteria.

Digestion of Ceramide 2-Aminoethylphosphonate, a Sphingolipid from the Jumbo Flying Squid Dosidicus gigas, in Mice

Ceramide 2-aminoethylphosphonate (CAEP), a sphingophosphonolipid containing a carbon-phosphorus bond, is frequently found in marine organisms and has a unique triene type of sphingoid base in its structure. CAEP has not been evaluated as a food ingredient, although it is generally contained in Mollusca organisms such as squids and shellfish, which are consumed worldwide. In this study, we aimed to elucidate the effects of CAEP as a food component by evaluating the digestion of CAEP extracted from the skin of the jumbo flying squid Dosidicus gigas. Our results revealed that dietary CAEP was digested to free sphingoid bases via ceramides by the mouse small intestinal mucosa. At pH 7.2, CAEP was hydrolyzed more rapidly than the major mammalian sphingolipid sphingomyelin; however, the hydrolysis of CAEP was similar to that of sphingomyelin at pH 9.0. Thus, the digestion of CAEP may be catalyzed by alkaline spingomyelinase and other enzymes. Our findings provide important insights into the digestion of the dietary sphingophosphonolipid CAEP in marine foods.