Bacterial Fatty Acid Research Articles

Characteristics of Microbial Utilization for Crop Residue-Derived C in Paddy and Upland Soils

Two typical subtropical agricultural soils, a flooded paddy soil and its adjacent upland, were collected and then incubated with or without 13C-labeled crop residue (maize straw) for 40 days. During the incubation, the mineralization rate of the crop residue was monitored, and the 13C incorporated into fungal and bacterial phospholipid fatty acid (PLFA) was quantified. At the early stage (0.25-1 days), the mineralization rate of crop residue was faster in paddy soil than that in upland soil, whereas the opposite trend was observed from 2 to 20 days. At the late stage (21-40 days), the mineralization rate was similar in both soils. At the end of incubation, 11% of the total crop residue was mineralized in paddy soil, which was about half of that in upland soil (20%). Although paddy soil had a higher amount of microbial biomass (indicated by total PLFA), the total amounts of 13C-PLFA were comparable in both soils, and the enrichment ratio (proportion of 13C to total C in PLFA) was lower in paddy soil than that in upland soil. This indicated that the microbial community in paddy soil was less active in the uptake of crop residue C than that in upland soil. During the incubation, the residue-derived 13C was mainly distributed in bacterial PLFA (up to 86% of total 13C-PLFA, including 59% in gram-positive and 27% in gram-negative bacteria) in paddy soil, and up to 75% of total 13C-PLFA distributed in fungal PLFAs was in upland soil. Thus, bacteria dominated the utilization of crop residue in paddy soil versus fungi in upland soil. Compared with that in upland soil, the microbial activity was suppressed in the anaerobic condition caused by flooding in paddy soil, with a stronger inhibition of fungi than bacteria. Considering the discrepancies of life strategies and necromass turnover between bacteria and fungi, the different dominant microbial groups in the utilization of crop residue in water-logged and well-drained conditions could lead to the distinct accumulation and stabilization of microbial-derived organic matter in paddy and upland soils.

Functionalized Concave Cube Gold Nanoparticles as Potent Antimicrobial Agents against Pathogenic Bacteria.

Gold (Au) is an inert metal in a bulk state; however, it can be used for the preparation of Au nanoparticles (i.e., AuNPs) for multidimensional applications in the field of nanomedicine and nanobiotechnology. Herein, monodisperse concave cube AuNPs (CCAuNPs) were synthesized and functionalized with a natural antioxidant lipoic acid (LA) and a tripeptide glutathione (GSH) because different crystal facets of AuNPs provide binding sites for distinct ligands. There was an ∼10 nm bathochromic shift of the UV-vis spectrum when CCAuNPs were functionalized with LA, and the size of the as-synthesized monodisperse CCAu nanoparticles was 76 nm. The LA-functionalized CCAu nanoparticles (i.e., CCAuLA) showed the highest antibacterial activity against Bacillus subtilis. Both fluorescence images and scanning electron microscopy images confirm the damage of the bacterial cell wall as the mode of antibacterial activity of CCAuNPs. CCAuNPs also cause the oxidation of bacterial cell membrane fatty acids to produce reactive oxygen species, which pave the way for the death of bacteria. Both CCAu nanoparticles and their functionalized derivatives showed excellent hemocompatibility (i.e., percentage of hemolysis is <5% at 80 μg of AuNPs) to human red blood cells and very high biocompatibility to HeLa, L929, and Chinese hamster ovary-green fluorescent protein (CHO-GFP) cells. Taken together, LA and GSH enhance the antibacterial activity and biocompatibility, respectively, of CCAu nanoparticles that interact with the bacteria through Coulomb as well as hydrophobic interactions before demonstrating antibacterial propensity.

Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes

Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.

Microbial community composition of translocated ancient woodland soil: a case study

Soil translocation is an ecological habitat restoration technique, which consists of moving the entire topsoil from a donor site to a chosen receptor site. We investigated soil chemistry and microbiology changes three growing seasons after the salvage of semi‐ancient woodland soil (0.94 ha) to a nearby receptor pasture due to road widening works (Kent, United Kingdom). We sampled (1) Intact woodland soils adjacent to the area of soils that was translocated to represent the lost donor site; (2) The soil from three growing seasons after it had been translocated; and (3) Grassland soils adjacent to the translocated soil to represent the original receptor site. The intention was to ascertain if shifts in soil chemistry and microbial community composition (phospholipid fatty acid analysis, PLFA) occurred due to soil translocation. PLFA signature biomarkers demonstrated the overall microbial community profile of the translocated and woodland soils were similar; however, salvaged soils had a 40% increase in the arbuscular mycorrhizal fungi bioindicator fatty acid 16:1ω5, a 10% decrease in the Gram‐positive bacterial fatty acids, and increased pH (5.01–5.77) compared to the original donor woodland soil. Microbial community composition (PLFA) correlated well with soil pH across all sites. Considering that pH increases with soil depth in this location, it is likely that mixing of soil horizons during translocation increased the topsoil pH causing changes in the soil microbial communities. We concluded that after three growing seasons, the chemical and microbial properties of the salvaged soil were characteristic of a woodland soil but showed signs of disturbance.

FabR senses long-chain unsaturated fatty acids to control virulence in pathogen Edwardsiella piscicida.

Long-chain unsaturated fatty acids (UFAs) can serve as nutrient sources or building blocks for bacterial membranes. However, little is known about how UFAs may be incorporated into the virulence programs of pathogens. A previous investigation identified FabR as a positive regulator of virulence gene expression in Edwardsiella piscicida. Here, chromatin immunoprecipitation-sequencing coupled with RNA-seq analyses revealed that 10 genes were under the direct control of FabR, including fabA, fabB, and cfa, which modulate the composition of UFAs. The binding of FabR to its target DNA was facilitated by oleoyl-CoA and inhibited by stearoyl-CoA. In addition, analyses of enzyme mobility shift assay and DNase I footprinting with wild-type and a null mutant (F131A) of FabR demonstrated crucial roles of FabR in binding to the promoters of fabA, fabB, and cfa. Moreover, FabR also binds to the promoter region of the virulence regulator esrB for its activation, facilitating the expression of the type III secretion system (T3SS) in response to UFAs. Furthermore, FabR coordinated with RpoS to modulate the expression of T3SS. Collectively, our results elucidate the molecular machinery of FabR regulating bacterial fatty acid composition and virulence in enteric pathogens, further expanding our knowledge of its crucial role in host-pathogen interactions.

DHA-Rich Aurantiochytrium Biomass, a Novel Dietary Supplement, Resists Degradation by Rumen Microbiota without Disrupting Microbial Activity

We first sought to evaluate the effect of dietary supplementation with the docosahexaenoic acid (DHA)-rich microalgae, Aurantiochytrium limacinum (AURA), on rumen fermentation and the resistance of DHA to degradation and biohydrogenation by rumen microbes through ex vivo fermentation experiments. Subsequently, we sought to quantify the diet-derived DHA content of milk and the impact of AURA on microbial composition and metabolism in a pilot feeding trial with rumen-cannulated dairy cows. To achieve our aims, rumen fluid from cannulated cows was used as inoculum, and the effect of AURA inclusion on fermentation ex vivo was examined. At doses corresponding to the amount of AURA recommended for commercial production animals, only ~10% of DHA was degraded or biohydrogenated by rumen microorganisms. The results show that feeding with AURA had no effect on either total bacterial density or short-chain fatty acid production. Real-time quantitative PCR analysis of the rumen fluid samples collected during a seven-week in vivo trial revealed that microbes related to lactic acid metabolism and methanogenesis were significantly suppressed by the AURA-supplemented diet. The DHA concentration in milk increased over 25-fold with the AURA-supplemented diet and dropped by 30–40% within one week of washout. The addition of A. limacinum biomass to dairy cow diets resulted in positive effects on rumen microbial composition with no adverse effect on fermentation activity. AURA-derived DHA was stable, with only modest degradation in the rumen, and was successfully deposited in milk. This is the first study to investigate the effect of supplementing the diet of dairy cows with a protist-based biomass, namely, on important rumen fermentation parameters and on DHA deposition in milk, using a combination of ex vivo and in vivo approaches.

Multiple bacterial partners in symbiosis with the nudibranch mollusk Rostanga alisae

The discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host’s ecology. Of particular interest are nudibranchs that unprotected by a shell and feed mainly on sponges. The symbiotic association of the nudibranch Rostanga alisae with bacteria was supported by ample evidence, including an analysis of cloned bacterial 16S rRNA genes and a fluorescent in situ hybridization analysis, and microscopic observations. A total of 74 clones belonging to the phyla α-, β-, γ-Proteobacteria, Actinobacteria, and Cyanobacteria were identified. FISH confirmed that bacteriocytes were packed with Bradyrhizobium, Maritalea, Labrenzia, Bulkholderia, Achromobacter, and Stenotrophomonas mainly in the foot and notum epidermis, and also an abundance of Synechococcus cyanobacteria in the intestinal epithelium. An ultrastructural analysis showed several bacterial morphotypes of bacteria in epidermal cells, intestine epithelium, and in mucus layer covering the mollusk body. The high proportion of typical bacterial fatty acids in R. alisae indicated that symbiotic bacteria make a substantial contribution to its nutrition. Thus, the nudibranch harbors a high diversity of specific endo- and extracellular bacteria, which previously unknown as symbionts of marine invertebrates that provide the mollusk with essential nutrients. They can provide chemical defense against predators.

Identification of zooplankton carbon sources using fatty acid biomarkers in lakes and reservoirs at different trophic states in Nanjing and surrounding areas

脂肪酸在生物的摄食活动中相对稳定，可用于辨别消费者的食物来源.不同营养水平的湖泊与水库中浮游动物的碳源组成有差异，因而可能具有不同的脂肪酸组成特征.本研究对南京市及其周边21个湖库的颗粒有机物（POM）、浮游动物的脂肪酸组成进行了对比分析.结果表明，南京市及其周边湖库21个湖库由中营养、轻富营养、中富营养、重富营养共4个营养水平组成.中营养湖库总氮（TN）、总磷（TP）、叶绿素a（Chl.a）、浮游植物生物量均低于富营养湖库，透明度（SD）则相反.中营养湖库中POM脂肪酸的必需脂肪酸（EFA）平均浓度低于富营养湖库；而细菌特征脂肪酸∑C15+∑C17含量高于富营养湖库.随着湖库富营养化，POM中多不饱和脂肪酸（PUFA）浓度逐渐增大，单不饱和脂肪酸（MUFA）浓度则逐渐减少.中营养湖库中浮游动物PUFA浓度普遍低于富营养湖库，∑C15+∑C17含量高于富营养湖库；且浮游动物体内主要来源于藻类的必需脂肪酸EFA/C16：0比值与细菌源脂肪酸（∑C15+∑C17）/C16：0比值均大于其他湖库，表明中营养湖库中浮游动物摄食了较多细菌.随着湖库营养水平升高，浮游动物饱和脂肪酸（SFA）逐渐增多，MUFA浓度逐渐减少，EFA浓度增多，表明浮游动物主要摄食藻类，而外源碳对浮游动物的碳源贡献较小.冗余分析（RDA）结果显示，EFA/C16：0、（∑C15+∑C17）/C16：0与透明度呈正相关，与Chl.a、总磷、磷酸盐呈高度负相关，表明透明度较高、营养水平相对较低的湖库中，浮游动物可能利用较多的藻类与细菌碳；此外，陆源碳转化指标∑C24/C16：0与TN、硝态氮呈正相关性，表明随着营养水平升高，陆源碳对浮游动物碳源贡献呈增加趋势.总体而言，浮游动物更倾向于利用高质量的内源碳，但在内源碳不足以供给水生生物生长需求的中营养水体中，外源碳对生态系统的物质循环和能量流动会产生重要作用.;Fatty acids are relatively stable in the feeding activities of organisms and can be used to identify consumers' food sources. The carbon source composition of zooplankton in lakes and reservoirs with different nutrient levels is different, so they may have different fatty acid composition characteristics. This study compared the fatty acid composition of POM (particulate organic matter) and zooplankton in 21 lakes and reservoirs in Nanjing and its surrounding areas. The results show that the 21 lakes and reservoirs are composed of four nutritional levels:medium nutrition, light eutrophication, medium eutrophication, and heavy eutrophication. The total nitrogen (TN), total phosphorus (TP), chlorophyll-a (Chl.a), and phytoplankton biomass of mesotrophic lakes and reservoirs are lower than those of eutrophic lakes and reservoirs, while the transparency (SD) is the opposite. The average concentration of essential fatty acids (EFA) of POM fatty acids in mesotrophic lakes was lower than that of eutrophic lakes, while the content of bacterial characteristic fatty acids ∑C15+∑C17 was higher than that of eutrophic lakes. With nutrient increase, the concentration of polyunsaturated fatty acids (PUFA) in POM gradually increases, while the concentration of monounsaturated fatty acids (MUFA) gradually decreases. The PUFA of zooplankton in mesotrophic lakes and reservoirs is generally lower than that of eutrophic lakes and reservoirs, and the content of ∑C15+∑C17 is higher than that of eutrophic lakes and reservoirs; and the ratio of essential fatty acids EFA/C16:0, which are mainly derived from algae, and bacterial fatty acids in zooplankton (The ratio of ∑C15+∑C17)/C16:0 is larger than that of other lakes and reservoirs, indicating that zooplankton in the middle-nutrition lakes and reservoirs ingested more bacteria. As nutrient increases, zooplankton saturated fatty acids (SFA) gradually increase, MUFA gradually decreases, and EFA content increases, indicating that zooplankton mainly feeds on algae, while exogenous carbon contributes little to the carbon source of zooplankton. Redundancy analysis (RDA) show that EFA/C16:0, (∑C15+∑C17)/C16:0 are positively correlated with SD, and highly negatively correlated with Chl.a, TP, and phosphate, suggesting that zooplankton consumed more algal and bacterial carbon; and ∑C24/C16:0 is positively correlated with TN, nitrate nitrogen, indicating that zooplankton utilized more terrestrial carbon. In general, zooplankton is more inclined to use high-quality endogenous carbon, but in mesotrophic water bodies where endogenous carbon is not sufficient to supply the growing needs of aquatic organisms. Exogenous carbon plays an important role in the material circulation and energy flow of the ecosystem.

Pull the trigger: interplay between benthic and pelagic cues driving the early recruitment of a natural bivalve assemblage

AbstractLarval settlement and recruitment are crucial phases in the benthic‐pelagic life cycle of marine benthic invertebrates that controls population dynamic and habitat connectivity. Our study investigated potential triggers driving the settlement of bivalve larvae in a highly dynamic intertidal coarse sand habitat. The early recruitment rate of five dominant bivalve families and abiotic conditions, particulate (&lt;20 µm) organic matter and sediment organic matter, were monitored from May to October 2014. Pelagic particulate organic matter (&lt;20 µm) was dominated by picoplankton throughout the sampling period, with a substantial diatom bloom in spring. Sediment was characterized by fresh organic matter in spring, as suggested by the dominant contribution of polyunsaturated fatty acids, and by a higher proportion of bacterial fatty acid markers during late summer. Different dynamics were also observed in early bivalve recruitment rates, with four different patterns observed over the sampling period. Multiple regression analysis on selected bivalve families showed species‐specific responses to trophic settlement triggers. Indeed, the larva recruitment rate of Mytilidae paralleled pelagic concentration of picoeucaryotes, with the peak early recruitment rate occurring in spring. Surprisingly, the early recruitment rate of Mactridae larvae showed a significant relation to bacterial concentration in the surficial sediment at the end of summer. While the Mytilidae results in such a eutrophic system confirmed those of a previous study in oligotrophic lagoons, therefore supporting the trophic settlement trigger hypothesis, more work is needed to understand the potential role of bacteria in the early recruitment of Mactridae. These results highlight for the first‐time inter‐specific differences in trophic cues that potentially trigger primary settlement in natural bivalve assemblages.

Fatty Acid Synthase Inhibitor Platensimycin Intervenes the Development of Nonalcoholic Fatty Liver Disease in a Mouse Model.

Non-alcoholic fatty liver disease (NAFLD) is a chronic liver disease affecting about 25% of world population, while there are still no approved targeted therapies. Although platensimycin (PTM) was first discovered to be a broad-spectrum antibiotic, it was also effective against type II diabetes in animal models due to its ability to inhibit both bacterial and mammalian fatty acid synthases (FASN). Herein, we report the pharmacological effect and potential mode of action of PTM against NAFLD in a Western diet/CCI4-induced mouse model and a free fatty acids (FFAs)-induced HepG2 cell model. The proper dose of PTM and its liposome-based nano-formulations not only significantly attenuated the Western diet-induced weight gain and the levels of plasma total triglycerides and glucose, but reduced liver steatosis in mice according to histological analyses. Western blotting analysis showed a reduced protein level of FASN in the mouse liver, suggesting that PTM intervened in the development of NAFLD through FASN inhibition. PTM reduced both the protein and mRNA levels of FASN in FFAs-induced HepG2 cells, as well as the expression of several key proteins in lipogenesis, including sterol regulatory element binding protein-1, acetyl-CoA carboxylase, and stearoyl-CoA desaturase. The expression of lipid oxidation-related genes, including peroxisome proliferator activated receptor α and acyl-CoA oxidase 1, was significantly elevated. In conclusion, our study supports the reposition of PTM to intervene in NAFLD progression, since it could effectively inhibit de novo lipogenesis.

Gut Microbiota Composition and Predicted Microbial Metabolic Pathways of Obesity Prone and Obesity Resistant Outbred Sprague-Dawley CD Rats May Account for Differences in Their Phenotype.

Like humans, outbred Sprague-Dawley CD rats exhibit a polygenic pattern of inheritance of the obese phenotype and not all individuals exposed to a high calorie intake develop obesity. We hypothesized that differences in gut microbiota composition account for phenotype differences between obese prone (OP) and obese resistant (OR) rats. We studied the gut microbiota composition of OPand OR rats after a high fat (HF) diet and how they respond to fermentation of resistant starch (RS). In phase 1 of the study 28 OP and 28 OR rats were fed a HF diet. In order to determine causal role of microbiota on phenotypes, In phase 2, a microbiota transplant between the two phenotypes was performed before switching all rats to a HF diet supplemented with 20% RS. We determined microbiota composition by 16S sequencing and predicted microbiota function by PICRUSt2. Despite a similar calorie intake, in phase 2 OP rats gained more weight and accumulated more abdominal fat in both phase 1 and 2 compared to OR rats (P < 0.001; n = 6). The OP rats fermented RS more robustly compared with OR rats with an increase in total bacteria, short chain fatty acids, and increased weight of the cecum, but microbiota of OP rats had much lower alpha diversity and evenness. The microbiota of OP rats, had higher amounts of bacteria from order Bacteroidales, specifically family Muribaculaceae (S24-7), which is known to possess several starch degrading enzymes and was reported in previous studies to increase with fermentation of RS. The OR rats fermented RS less but had higher bacterial diversity and evenness and had significantly higher bacterial counts from phylum Firmicutes particularly order Clostridiales, genus Clostridium and an uncultured bacterium of the genus Akkermansia. The microbiota of OR rats had enhanced bacterial chemotaxis, phosphotransferase system (PTS), and fatty acid biosynthesis compared to OP rats whose microbiota had higher glycan degradation and LPS biosynthesis pathways. The microbiota transplant did not change obesity phenotype or microbiota composition. In conclusion, a higher alpha-diversity and evenness of the microbiota and higher proportions of Clostridiales and Akkermansia in OR rats were associated with a better metabolic phenotype with lower body fat. However, robust RS fermentation caused a lower diversity and evenness and did not result in a leaner phenotype.

Malonyl-acyl carrier protein decarboxylase activity promotes fatty acid and cell envelope biosynthesis in Proteobacteria

Bacterial fatty acid synthesis in Escherichia coli is initiated by the condensation of an acetyl-CoA with a malonyl-acyl carrier protein (ACP) by the β-ketoacyl-ACP synthase III enzyme, FabH. E. coli ΔfabH knockout strains are viable because of the yiiD gene that allows FabH-independent fatty acid synthesis initiation. However, the molecular function of the yiiD gene product is not known. Here, we show the yiiD gene product is a malonyl-ACP decarboxylase (MadA). MadA has two independently folded domains: an amino-terminal N-acetyl transferase (GNAT) domain (MadAN) and a carboxy-terminal hot dog dimerization domain (MadAC) that encodes the malonyl-ACP decarboxylase function. Members of the proteobacterial Mad protein family are either two domain MadA (GNAT-hot dog) or standalone MadB (hot dog) decarboxylases. Using structure-guided, site-directed mutagenesis of MadB from Shewanella oneidensis, we identified Asn45 on a conserved catalytic loop as critical for decarboxylase activity. We also found that MadA, MadAC, or MadB expression all restored normal cell size and growth rates to an E. coli ΔfabH strain, whereas the expression of MadAN did not. Finally, we verified that GlmU, a bifunctional glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase that synthesizes the key intermediate UDP-GlcNAc, is an ACP binding protein. Acetyl-ACP is the preferred glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase substrate, in addition to being the substrate for the elongation-condensing enzymes FabB and FabF. Thus, we conclude that the Mad family of malonyl-ACP decarboxylases supplies acetyl-ACP to support the initiation of fatty acid, lipopolysaccharide, peptidoglycan, and enterobacterial common antigen biosynthesis in Proteobacteria.

Distribution and sources of fatty acids in surface sediments of mangrove ecosystems in the Northern Kerala Coast, India

Fatty acids and bulk geochemical proxies were employed to understand the sources and transformation of sedimentary organic matter from surface sediments of major five mangrove systems in the northern Kerala coast. Texture, tidal rhythm and the proximity to the south eastern Arabian Sea were the main factors influencing distribution and accumulation of the organic matter in these systems. A total of 118 fatty acids were quantified and grouped into short-chain (SCFA), long-chain (LCFA), monounsaturated (MUFA), polyunsaturated (PUFA) and branched-chain (BrFA) fatty acids, hydroxy fatty acids, cyclic fatty acids, and dicarboxylic acids. The distribution of fatty acid groups was in the order SCFA > BrFA > MUFA > LCFA > PUFA. Total fatty acids (TFA) concentration exhibited profound seasonal variations and ranged from 6.25 to 580.49 μg/g (pre-monsoon > post-monsoon > monsoon except in Kadalundi which follows the reverse order). The sedimentary fatty acids in the study region reveal a wide spectrum of inputs from terrestrial, planktonic (preponderance of diatom followed by dinoflagellates along with brown algae, cyanobacteria, red algae) and bacterial sources (e.g., Desulfobulbus-type bacteria, sulfur-reducing bacteria, Sulfur-oxidizing bacteria). Significant concentrations of bacterial fatty acids suggest the functioning of an effective microbial loop and various biogeochemical pathways operating in these sediments (sulfate reduction, iron and manganese oxide reduction, etc.).

Comparative soft-tissue preservation in Holocene-age capelin concretions.

Determining how soft tissues are preserved and persist through geologic time are continuing challenge because decay begins immediately after senescence while diagenetic transformations generally progress over days to millions of years. However, in recent years, carbonate concretions containing partially-to-fully decayed macroorganisms have proven to be remarkable windows into the diagenetic continuum revealing insights into the fossilization process. This is because most concretions are the result of biologically induced mineral precipitation caused by the localized decay of organic matter, which oftentimes preserves a greater biological signal relative to their host sediment. Here we present a comparative lipid biomarker study investigating processes associated with soft-tissue preservation within Holocene-age carbonate concretions that have encapsulated modern capelin (Mallotus villosus). We focus on samples collected from two depositional settings that have produced highly contrasting preservation end-members: (1) Kangerlussuaq, Greenland: a marine environment, which, due to isostatic rebound, has exposed strata containing concretions exhibiting exceptional soft-tissue preservation (6-7kya), and (2) Greens Creek, Ottawa, Canada: a paleo brackish-to-freshwater marine excursion containing concretions exhibiting skeletal remains (~11kya). Lipid biomarker analysis reveals endogenous capelin tissues and productive waters at Kangerlussuaq that are in sharp contrast to Greens Creek concretions, which lack appreciable capelin and environmental signals. Comparable distributions of bacterial fatty acids and statistical analyses suggest soft-tissue preservation within concretions is agnostic to specific heterotrophic decay communities. We, therefore, interpret preservation within carbonate concretions may represent a race between microbially induced authigenic precipitation and decay. Namely, factors resulting in exceptional preservation within concretions likely include: (1) organic matter input, (2) rate of decay, (3) carbonate saturation, (4) porewater velocity, and (5) rate of authigenic (carbonate) precipitation resulting in arrested decay/bacterial respiration due to cementing pore spaces limiting the diffusion of electron acceptors into the decay foci.

Lead derivatization of ethyl 6-bromo-2-((dimethylamino)methyl)-5-hydroxy-1-phenyl-1H-indole-3-carboxylate and 5-bromo-2-(thiophene-2-carboxamido) benzoic acid as FabG inhibitors targeting ESKAPE pathogens

Our previous studies on FabG have identified two compounds 5-bromo-2-(thiophene-2-carboxamido) benzoic acid (A) and ethyl 6-bromo-2-((dimethylamino)methyl)-5-hydroxy-1-phenyl-1H-indole-3-carboxylate(B) as best hits with allosteric mode of inhibition. FabG is an integral part of bacterial fatty acid biosynthetic system FAS II shown to be an essential gene in most ESKAPE Pathogens. The current work is focussed on lead expansion of these two hit molecules which ended up with forty-three analogues (twenty-nine analogues from lead compound A and fourteen compounds from lead compound B). The enzyme inhibition studies revealed that compound 15 (effective against EcFabG, AbFabG, StFabG, MtFabG1) and 19 (inhibiting EcFabG and StFabG) had potency of broad-spectrum inhibition on FabG panel.

Consistent gut bacterial and short-chain fatty acid signatures in hypoabsorptive bariatric surgeries correlate with metabolic benefits in rats.

The study aimed at comparing how changes in the gut microbiota are associated to the beneficial effects of the most clinically efficient hypoabsorptive bariatric procedures, namely Roux-en-Y gastric bypass (RYGB), biliopancreatic diversion with duodenal switch (BPD-DS) and single anastomosis duodeno-ileal bypass with sleeve gastrectomy (SADI-S). Diet-induced obese (DIO) male Wistar rats were divided into seven groups. In addition to the groups subjected to RYGB, BPD-DS and SADI-S, the following four control groups were included: SHAM-operated rats fed a high-fat diet (SHAM HF), SHAM fed a low-fat diet (SHAM LF), SHAM HF-pair-weighed to BPD-DS (SHAM HF-PW) and sleeve-gastrectomy (SG) rats. Body weight, food intake, glucose tolerance, insulin sensitivity/resistance, and L-cell secretion were assessed. The gut microbiota (16 S ribosomal RNA gene sequencing) as well as the fecal and cæcal contents of short-chain fatty acids (SCFAs) were also analyzed prior to, and after the surgeries. The present study demonstrates the beneficial effect of RYGB, BPD-DS and SADI-S on fat mass gain and glucose metabolism in DIO rats. These benefits were proportional to the effect of the surgeries on food digestibility (BPD-DS > SADI-S > RYGB). Notably, hypoabsorptive surgeries led to consonant microbial signatures characterized by decreased abundance of the Ruminococcaceae (Oscillospira and Ruminococcus), Oscillospiraceae (Oscillibacter) and Christensenellaceae, and increased abundance of the Clostridiaceae (Clostridium), Sutterellaceae (Sutterella) and Enterobacteriaceae. The gut bacteria following hypoabsorptive surgeries were associated with higher fecal levels of propionate, butyrate, isobutyrate and isovalerate. Increases in the fecal SCFAs were in turn positively and strongly correlated with the levels of peptide tyrosine-tyrosine (PYY) and with the beneficial effects of the surgery. The present study emphasizes the consistency with which the three major hypoabsorptive bariatric procedures RYGB, BPD-DS and SADI-S create a gut microbial environment capable of producing a SCFA profile favorable to the secretion of PYY and to beneficial metabolic effects.

Dietary Supplementation With Lactobacillus plantarum Ameliorates Compromise of Growth Performance by Modulating Short-Chain Fatty Acids and Intestinal Dysbiosis in Broilers Under Clostridium perfringens Challenge.

Clostridium perfringens is an important zoonotic pathogen associated with food contamination and poisoning, gas gangrene, necrotizing enterocolitis or necrotic enteritis in humans and animals. Dysbacteriosis is supposedly associated with the development of C. perfringens infection induced necrotic enteritis, but the detailed relationship between intestinal health, microbiome, and C. perfringens infection-induced necrotic enteritis remains poorly understood. This research investigated the effect of probiotics on the growth performance and intestinal health of broilers, and the involved roles of intestinal microbiota and microbial metabolic functions under C. perfringens infection. Results showed that subclinical necrotic enteritis was successfully induced as evidenced by the significant lower body weight (BW), suppressed feed conversion ratio (FCR), decreased ileal villus height and mucosal barrier function, and increased ileal histopathological score and bursal weight index. Lactobacillus plantarum or Paenibacillus polymyxa significantly attenuated C. perfringens-induced compromise of growth performance (BW, FCR) and ileal mucosa damage as illustrated by the increased ileal villus height and villus/crypt ratio, the decreased ileal histopathological score and the enhanced ileal mucosal barrier function. L. plantarum also significantly alleviated C. perfringens-induced enlarged bursa of fabricius and the decreased levels of ileal total SCFAs, acetate, lactate, and butyrate. Furthermore, dietary L. plantarum improved C. perfringens infection-induced intestinal dysbiosis as evidenced by significantly enriched short-chain fatty acids-producing bacteria (Lachnospiraceae, Ruminococcaceae, Oscillospira, Faecalibacterium, Blautia), reduced drug-resistant bacteria (Bacteroides, Alistipes) and enteric pathogens (Escherichia coli, Bacteroides fragilis) and bacterial metabolic dysfunctions as illustrated by significantly increased bacterial fatty acid biosynthesis, decreased bacterial lipopolysaccharide biosynthesis, and antibiotic biosynthesis (streptomycin and vancomycin). Additionally, the BW and intestinal SCFAs were the principal factors affecting the bacterial communities and microbial metabolic functions. The above findings indicate that dietary with L. plantarum attenuates C. perfringens-induced compromise of growth performance and intestinal dysbiosis by increasing SCFAs and improving intestinal health in broilers.

Effects of high hydrostatic pressure (HHP) and storage temperature on bacterial counts, color change, fatty acids and non-volatile taste active compounds of oysters (Crassostrea ariakensis)

The effects of HHP and storage temperature on bacterial counts, color, fatty acids and flavor compounds of oysters Crassostrea ariakensis were investigated. Counts of Vibrio vulnificus and Vibrio parahaemolyticus decreased to undetectable levels in ≥ 400 MPa-treated oysters. Storage at −20 °C significantly restrained microbial growth compared to 4 °C (P < 0.05). L* values of HHP-treated oysters significantly increased compared to raw oysters (P < 0.05). Storage slightly affected the color according to total color difference (ΔE*) values. Fatty acid profiles and betaine contents in 400 and 600 MPa-treated oysters at 0 and 15 d were almost the same as raw samples. Contents of total free amino acids (FAAs), Na+ and Ca2+ were significantly higher in 400 and 600 MPa-treated oysters than those in raw oysters at 0 d (P < 0.05), while the opposite results were observed in 5′-adenosine monophosphate (AMP), 5′-guanosine monophosphate (GMP), citric acid, succinic acid, K+ and PO43− (P < 0.05). At 400 and 600 MPa, FAAs significantly decreased after 15-d storage at 4 °C and −20 °C (P < 0.05), while no significant changes were observed in nucleotides, organic acids and inorganic ions.

Adhesion behavior of silica nanoparticles with bacteria: Spectroscopy measurements based on kinetics, and molecular docking

Nanoparticles are intriguing researchers due to their unique properties. In this study, the Stöber method was used to obtain white particles. Through scanning electron microscopy (SEM), X-ray diffraction (XRD) and Fourier transform infrared (FTIR) analysis, the spherical nano-scale particles were confirmed to be nano-silica. Bacteria adsorption experiment displayed that nano-silica could be accumulated on the surface of bacteria. The ultraviolet and fluorescence spectroscopy were used to explain the interaction between silica nanoparticles and recombinant protein A (S. aureus membrane protein) under simulated physiological conditions. The results of UV–vis and fluorescence experiments showed that the quenching mechanism between silica nanoparticles and recombinant protein A was static quenching. The key enzymes in bacterial cell wall synthesis (β-lactamase) and fatty acid biosynthesis (FabI and FabH) pathways were selected, and the molecular docking results explained that silica nanoparticles adhered to the surface of E. coli and S. aureus through forming hydrogen bond with amino acid residue.

Nanoparticle-Hydrogel Systems Containing Platensimycin for Local Treatment of Methicillin-Resistant Staphylococcus aureus Infection.

Skin and soft tissue infections require effective and sustained topical administration. Platensimycin (PTM) is a natural drug lead that targets bacterial fatty acid synthases and has a great potential to treat infections caused by methicillin-resistant Staphylococcus aureus (MRSA). To facilitate the use of PTM against local MRSA infections, we prepared polyacrylamide hydrogels containing polyamidoamine (PAMAM)/PTM nanoparticles (NP-gel(PTM)) for the controlled release of PTM. NP-gel(PTM) can continuously inhibit the growth of MRSA and its biofilm formation in simulated drug flow models in vitro. In situ implantation of NP-gel(PTM) could treat MRSA-infected subcutaneous soft tissues without toxicity. For MRSA-infected skin wounds, NP-gel(PTM) not only showed strong anti-MRSA activity but also accelerated more wound healing than the widely used antibiotic mupirocin. Collectively, PTM is expected to be used in this safe and effective NP-gel delivery platform for the treatment of local infections, which might help to alleviate the current antibiotic resistance crisis.