Populations Of Bacteria Research Articles

A targeted approach to enrich host-associated bacteria for metagenomic sequencing.

Multicellular eukaryotic organisms are hosts to communities of bacteria that reside on or inside their tissues. Often the eukaryotic members of the system contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes, targeting (i) Endozoicomonas spp, and (ii) all other bacteria. NovaSeq sequencing resulted in 67-91M reads per sample, 55%-90% of which were identified as bacterial. Most reads were taxonomically assigned to the key coral-associated family, Endozoicomonadaceae, with Vibrionaceae also abundant. Endozoicomonadaceae were 5x more abundant in the 'Endozoicomonas' population, highlighting the success of the dual-labelling approach. This method effectively enriched coral samples for bacteria with <1% contamination from host and algal symbionts. The application of this method will allow researchers to decipher the functional potential of coral-associated bacteria. This method can also be adapted to accommodate other host-associated communities.

Biodegradation of low-density polyethylene by plasma-activated Bacillus strain

Plastic biodegradation by microorganisms is an eco-friendly and sustainable method without any ramifications. Herein, we used a cultivation method and 16S rRNA sequencing to screen bacteria that can efficiently colonize and degrade low-density polyethylene (LDPE) from various plastic wastes. We identified Bacillus safensis BS-10L through whole-genome sequencing analysis and verified its LDPE-degradation ability. However, the decomposition mechanism of the isolated bacteria was unclear and the decomposition efficiency was insufficient, so low-temperature plasma was used to increase the decomposition efficiency of the bacteria. The population and viability of bacteria treated with cold plasma increased. Plasma-activated bacteria could induce cracks, holes, and roughness on the surface of LDPE films over 90 days, and over 30 days; the LDPE film lost 13.40 ± 0.013% and 27.78 ± 0.014% of its mass by BS-10L and plasma-treated BS-10L, respectively. Fourier-transform infrared spectroscopic analysis identified new peaks of the C=O and C-O groups in the plasma-treated LDPE film, exhibiting high transmittance in the LDPE film that was inoculated with bacteria. X-ray photoelectron spectroscopic analysis showed that C-O bonds were generated by BS-10L strain, and relatively strong C=O bonds were generated in the film inoculated with plasma-treated BS-10L strain. Plasma treatment increased the colonization of the BS-10L strain and changed the chemical bonding of the LDPE film, suggesting that plasma-activated BS-10L could accelerate decomposition by oxidation by increasing the carbonyl group of the PE film. Therefore, plasma technology may be effective for enhancing the plastic-degrading ability of microorganisms.

POPULASI BAKTERI DAN RESPIRASI MIKROBA TANAH PADA RHIZOSFER TANAMAN JAGUNG ( Zea mays L.) YANG DIBERI PUPUK TERPADU DAN BIOCHAR SEKAM PADI PADA MASA VEGETATIF MAKSIMUM

This study aims to determine the Bacterial Population and Microbial Respiration in the rhizosphere of corn plants due to the application of integrated fertilizers and rice husk biochar soil amendments during the maximum vegetative period. This research was conducted using an experimental method with polybag experiments in a greenhouse from July to September 2021. The experiment was arranged using a completely randomized design (CRD) with 7 treatment combinations P0 (control treatment), P1 (Urea + phonska administration), P2 ( Giving Urea + Phonska + Biochar), P3 (Giving Urea + Phonska + BPF), P4 (Giving Urea + Phonska + Biochar + BPF), P5 (Giving Urea + Phonska + BPF + Compost), P6 (Giving Urea + Phonska + Biochar) + BPF + Compost). Each treatment was repeated 3 times, so as many as 21 units of experimental polybags were obtained. Parameters measured were total bacterial population, population of phosphate solubilizing bacteria, soil microbial respiration, pH, cation exchange capacity, and C-Organic. The results showed that the application of integrated fertilizers (inorganic, compost and biological-BPF) and rice husk biochar had a significant effect. on the total bacterial population, BPF and soil microbial respiration in the corn plant rhizosphere observed at the maximum vegetative period. From this study, it was concluded that the combination of inorganic fertilizer + organic fertilizer + bpf and biochar was the best combination in increasing the total population of bacteria, phosphate solubilizing bacteria and soil microbial respiration.

Optimizing corn silage quality during hot summer conditions of the tropics: investigating the effect of additives on in-silo fermentation characteristics, nutrient profiles, digestibility and post-ensiling stability

Corn crop grown and ensiled at high temperature have lower water soluble carbohydrates (WSC), epiphytic lactic acid bacteria (LAB) population, lactic acid concentration, fermentation quality and aerobic stability. This study systematically investigated the effects of heterofermentative LAB (hetLAB), homofermentative LAB (homLAB), molasses and their mixture (MIX) on in-silo fermentation characteristics, chemical profiles, Cornell Net Carbohydrate and Protein System (CNCPS) carbohydrate subfractions, in vitro digestibility (DMD), microbial count, and post-ensiling aerobic stability of whole crop corn silage during hot summer (30 to 45°C) condition. Corn hybrids (P30K08 and DK6789) were ensiled at targeted dry matter (DM) of 330 g/kg for 0, 3, 7, 21, and 150 days in 3 L silos, without additive (CCS) or treated with hetLAB (4×106 cfu/g Lactobacillus buchneri), homLAB (1×106 cfu/g of L. plantarum), molasses (3% of fresh forage) or MIX (half of individual doses of homLAB, hetLAB and molasses) additives. The CCS, homLAB, hetLAB, molasses, or MIX treated chopped material of each hybrid were ensiled in 16 replicate silos at a density of 260 kg of DM/m3. Compared to CCS, the additives significantly improved silage nutritional and fermentation quality, DM digestibility (in vitro), count of LAB, DM recovery and aerobic stability, and decreased counts of yeast and mold. Among the inoculants, the homLAB and MIX inoculated silages had greatest improvement in fermentation quality and nutritional value. The homLAB produced corn silage with the highest (P &amp;lt; 0.05) content of lactic acid, and soluble carbohydrates, and lowest contents of acetic acid, NH3-N and pH, demonstrating desirable and restricted in silo fermentation. On the other hand, the hetLAB inoculated silages had the greatest (P &amp;lt; 0.05) value of acetic acids, highlighting greater aerobic stability. Interestingly, the MIX silages followed the hetLAB in acetic acid value and homLAB in lactic acid value. Notably, without additive stable pH was not achieved during 21 days, with application of molasses, hetLAB and the MIX inoculants stable pH was achieved during 7 days, and with homLAB stable pH was achieved during the first 3 days of ensiling. The greatest numbers of viable LAB were recorded in homLAB (8.13 log cfu/g) and MIX (7.89 log cfu/g) inoculated silages, while the lowest for CCS (6.29 log cfu/g). The lowest yeast (1.48 log cfu/g) and mold (0.22 log cfu/g) were recorded for hetLAB inoculated silage. The greatest (P &amp;lt; 0.05) DM recovery was recorded for hetLAB (97.3%) and MIX (96.9%), and the lowest for the control silage (92.9%). All additives significantly improved the aerobic stability of corn silage, and the greatest value of &amp;gt;72 h was recorded for hetLAB and MIX inoculats, and the lowest for CSC (25 h). In conclusion, additives application can improve fermentation quality, nutritional value, DM recovery and aerobic stability of whole crop corn silage under hot summer conditions of the tropics. The MIX inoculant showed potential to improve in-silo fermentation, and aerobic stability at the same time, however, further investigation are required, particularly with respect of dose rate.

Global transcriptomic analysis of breast cancer and normal mammary epithelial cells infected with Borrelia burgdorferi.

The bacterial spirochete Borrelia burgdorferi, the causative agent of Lyme Disease, can disseminate and colonize various tissues and organs, orchestrating severe clinical symptoms including arthritis, carditis, and neuroborreliosis. Previous research has demonstrated that breast cancer tissues could provide an ideal habitat for diverse populations of bacteria, including B. burgdorferi, which is associated with a poor prognosis. Recently, we demonstrated that infection with B. burgdorferi enhances the invasion and migration of triple-negative MDA-MB-231 cells which represent a type of breast tumor with more aggressive cancer traits. In this study, we hypothesized that infection by B. burgdorferi affects the expression of cancer-associated genes to effectuate breast cancer phenotypes. We applied the high-throughput technique of RNA-sequencing on B. burgdorferi-infected MDA-MB-231 breast cancer and normal-like MCF10A cells to determine the most differentially expressed genes (DEG) upon infection. Overall, 142 DEGs were identified between uninfected and infected samples in MDA-MB-231 while 95 DEGs were found in MCF10A cells. A major trend of the upregulation of C-X-C and C-C motif chemokine family members as well as genes and pathways was associated with infection, inflammation, and cancer. These genes could serve as potential biomarkers for pathogen-related tumorigenesis and cancer progression which could lead to new therapeutic opportunities.

Gut microbiota of Suncus murinus, a naturally obesity-resistant animal, improves the ecological diversity of the gut microbiota in high-fat-diet-induced obese mice.

The global population of obese individuals is increasing, affecting human health. High-fat diets are a leading cause of this epidemic, and animal models, such as mice, are often used in related research. Obese individuals have a different gut microbiota composition from non-obese ones, characterized by a sizeable population of certain bacteria associated with fat storage. The gut microbiome plays a significant role in regulating human physiological and metabolic functions. Links between obesity, high-fat diets and gut microbiota have become hot topics of discussion. Recently, research on the modulation of the gut microbiota has focused on fecal microbiota transplantation (FMT), which has been recognized as an effective method of studying the function of gut microbiota. The purpose of this study was to investigate how the gut microbiota of Suncus murinus, a naturally obesity-resistant animal, through FMT, affected the ecology of the gut microbiota of high-fat diet induced obese mice. In this study, Suncus murinus was used as a donor for FMT. High-fat diet induced C57BL/6NCrSIc mice were used as recipients, the body weight changes were measured and changes in their gut flora were analyzed using a 16S rRNA gene analysis. The study found that, after the FMT procedure, the FMT group tended to have a lower body weight than the control group. At the phylum level, the most predominant phyla in all groups were Firmicutes and Proteobacteria, while Deferribacteres was not detected in the FMT or antibiotic administration groups, and Bacteroidetes was not present in the antibiotic administration group. At the genus level, the FMT group had significantly lower OTU richness than the control group but greater diversity than the control group. These results indicate that FMT from Suncus murinus can help reorganize and improve the gut microbiota of mice in a balanced and diverse ecosystem.

Airborne bacteria viability and air quality: a protocol to quantitatively investigate the possible correlation by an atmospheric simulation chamber

Abstract. Biological particulate matter or bioaerosol are a subset of atmospheric aerosol. They influence climate, air quality, and health via several mechanisms which often are poorly understood. In particular, the quantitative study of possible relationship between bioaerosol viability and air quality or meteorological conditions is an open and relevant issue. The difficulty of retrieving such possible correlations by analyses of data collected during in-field campaigns can benefit of targeted experiments conducted in well-controlled conditions inside atmospheric simulation chambers (ASCs). ChAMBRe (Chamber for Aerosol Modelling and Bio-aerosol Research) is an ASC in Genoa (Italy) designed and built to perform experimental research on bioaerosol. In this article, we focus on bacteria viability. A multi-step protocol was developed and thoroughly tested to cultivate a suitable bacteria population (E. coli), nebulize and inject in a chamber of viable cells, expose and monitor the viability variation inside ChAMBRe, hold at selected conditions, and finally incubate and count the concentration of viable bacteria. The whole procedure showed an estimated lifetime of total (T) and viable (V) E. coli of about 153 and 32 min, respectively and a V : T lifetime ratio of 40±5 min when ChAMBRe is held in a reference baseline condition. The coefficient of variation of 13 % shows how sensitive the protocol is also to changes in viability when the bacteria are exposed to other (e.g. polluted) conditions. First results showing a viability reduction observed exposing the E. coli strain to NOx concentrations and solar irradiation are presented and discussed. The present results pave the way for systematic studies aimed at the definition of dose–effect relationship for several bacteria strains under different conditions of atmospheric pollutants.

Evaluation of bigel systems as potential substitutes to partially replace pork backfat in semi-dry sausages

Bigels prepared with olive oil oleogels admixed with κ-carrageenan or κ-carrageenan and gelatin hydrogels (BG1 and BG2, respectively) were characterized with respect to microstructure and textural properties and were used as pork backfat alternatives in semi-dry sausages. Stable oleogel-in-hydrogel type bigels were formed, with BG2 having higher hardness values. Control sausages (CF) were formulated with 20% pork backfat and sausage treatments B1F and B2F had 50% of the pork backfat substituted by BG1 and BG2 bigels, respectively. Moisture, water activity, texture, microbial counts, sensorial and nutritional attributes of the resulting sausages were assessed during fermentation and after pasteurization and storage. Substituted sausages had increased weight loss, moisture, and water activity. Color evaluation revealed that the treatments with bigels exhibited the same trend in color formation and no differences were recorded in L* and a* values of the sausages. Total viable counts and lactic acid bacteria populations were not affected by the addition of bigel systems. Regarding the texture parameters, B2F semi-dry sausages exhibited similar values of hardness and cohesiveness to CF. Sausages formulated with bigels exhibited a reduction in energy (20%), fat (27%), saturated fatty acids (30%) and cholesterol (∼6%) content. B2F sausages had similar liking scores with CF, and they did not show any undesirable sensory attributes. The results demonstrate that bigels are a promising fat alternative to manufacture semi-dry meat products with lower fat content and a better nutritional profile.

A skin microbiome model with AMP interactions and analysis of quasi-stability vs stability in population dynamics

The skin microbiome plays an important role in the maintenance of a healthy skin. It is an ecosystem, composed of several species, competing for resources and interacting with the skin cells. Imbalance in the cutaneous microbiome, also called dysbiosis, has been correlated with several skin conditions, including acne and atopic dermatitis. Generally, dysbiosis is linked to colonization of the skin by a population of opportunistic pathogenic bacteria. Treatments consisting in non-specific elimination of cutaneous microflora have shown conflicting results. In this article, we introduce a mathematical model based on ordinary differential equations, with 2 types of bacteria populations (skin commensals and opportunistic pathogens) and including the production of antimicrobial peptides to study the mechanisms driving the dominance of one population over the other. By using published experimental data, assumed to correspond to the observation of stable states in our model, we reduce the number of parameters of the model from 13 to 5. We then use a formal specification in quantitative temporal logic to calibrate our model by global parameter optimization and perform sensitivity analyses. On the time scale of 2 days of the experiments, the model predicts that certain changes of the environment, like the elevation of skin surface pH, create favorable conditions for the emergence and colonization of the skin by the opportunistic pathogen population, while the production of human AMPs has non-linear effect on the balance between pathogens and commensals. Surprisingly, simulations on longer time scales reveal that the equilibrium reached around 2 days can in fact be a quasi-stable state followed by the reaching of a reversed stable state after 12 days or more. We analyze the conditions of quasi-stability observed in this model using tropical algebraic methods, and show their non-generic character in contrast to slow-fast systems. These conditions are then generalized to a large class of population dynamics models over any number of species.

Gut butyrate-producers confer post-infarction cardiac protection

The gut microbiome and its metabolites are increasingly implicated in several cardiovascular diseases, but their role in human myocardial infarction (MI) injury responses have yet to be established. To address this, we examined stool samples from 77 ST-elevation MI (STEMI) patients using 16 S V3-V4 next-generation sequencing, metagenomics and machine learning. Our analysis identified an enriched population of butyrate-producing bacteria. These findings were then validated using a controlled ischemia/reperfusion model using eight nonhuman primates. To elucidate mechanisms, we inoculated gnotobiotic mice with these bacteria and found that they can produce beta-hydroxybutyrate, supporting cardiac function post-MI. This was further confirmed using HMGCS2-deficient mice which lack endogenous ketogenesis and have poor outcomes after MI. Inoculation increased plasma ketone levels and provided significant improvements in cardiac function post-MI. Together, this demonstrates a previously unknown role of gut butyrate-producers in the post-MI response.

Effect of Three Different Preservatives on the Microbiota of Shalgam, a Traditional Lactic Acid Fermented Beverage.

Shalgam is a traditional Turkish beverage derived from the natural fermentation of purple carrots (Daucus carota) that boasts valuable antioxidant and prebiotic properties. These features of shalgam increase efforts to enhance its shelf life and ensure safe consumption. In this study, the effects of three different preservatives (sodium benzoate, potassium sorbate, or natamycin) on the physicochemical and microbiological properties of shalgam produced at laboratory scale and stored at room temperature for six months were investigated. Each preservative was used in four different concentrations (25, 100, 400, and 800 mg/L) to assess their impacts on the population of lactic acid bacteria (LAB) and yeast. After determining the total acidity and pH of the samples, colorimetric measurements were performed. The isolated LAB were defined using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) method. The addition of preservatives did not significantly affect the pH of the shalgam samples (3.44-3.52) compared to the control sample (3.43). However, a slight increase was observed in the total acidity of preservative-treated samples, with the highest level (5.61 g/L lactic acid) recorded in samples containing 100 mg/L sodium benzoate. Lacticaseibacillus paracasei subsp. paracasei, which has the potential to impart probiotic properties to shalgam, was the predominant LAB species in both non-treated and preservative-treated samples. The use of preservatives significantly reduced the total number of yeasts, which may cause spoilage in shalgam. The results indicate that using sodium benzoate at a concentration of 100 mg/L is the optimum method for shalgam production, resulting in the highest total acidity value obtained. Overall, the findings provide a significant contribution to prolonging the shelf life of shalgam, a beverage with immense production and consumption potential worldwide.

Eco-evolutionary dynamics of experimental Pseudomonas aeruginosa populations under oxidative stress.

Within-host environments are likely to present a challenging and stressful environment for opportunistic pathogenic bacteria colonizing from the external environment. How populations of pathogenic bacteria respond to such environmental challenges and how this varies between strains is not well understood. Oxidative stress is one of the defences adopted by the human immune system to confront invading bacteria. In this study, we show that strains of the opportunistic pathogenic bacterium Pseudomonas aeruginosa vary in their eco-evolutionary responses to hydrogen peroxide stress. By quantifying their 24 h growth kinetics across hydrogen peroxide gradients we show that a transmissible epidemic strain isolated from a chronic airway infection of a cystic fibrosis patient, LESB58, is much more susceptible to hydrogen peroxide than either of the reference strains, PA14 or PAO1, with PAO1 showing the lowest susceptibility. Using a 12 day serial passaging experiment combined with a mathematical model, we then show that short-term susceptibility controls the longer-term survival of populations exposed to subinhibitory levels of hydrogen peroxide, but that phenotypic evolutionary responses can delay population extinction. Our model further suggests that hydrogen peroxide driven extinctions are more likely with higher rates of population turnover. Together, these findings suggest that hydrogen peroxide is likely to be an effective defence in host niches where there is high population turnover, which may explain the counter-intuitively high susceptibility of a strain isolated from chronic lung infection, where such ecological dynamics may be slower.

Effects of dietary supplementation with Radix Isatidis polysaccharide on egg quality, immune function, and intestinal health in hens

This study aimed to investigate the effects of supplementing laying hen diets with Radix Isatidis Polysaccharide (RIPS) on egg quality, immune function, and intestinal health. The research was conducted using 288 Hyland Brown hens, which were randomly assigned to four dietary treatments: control (without RIPS), low dose (200 g/t), medium dose (500 g/t), and high dose (1000 g/t) of RIPS. Each dietary treatment was administered to eight replicates of nine hens for nine weeks. The results revealed that RIPS inclusion in diets significantly improved egg quality parameters such as egg shape index, yolk color, haugh unit, and protein height (P < 0.05). Additionally, RIPS supplementation enhanced immune function as evidenced by an alteration in serum biochemical parameters, an increase in the spleen index, and a decrease in the liver index. Further, an evaluation of intestinal health showed that RIPS fortified the intestinal barrier, thus increasing the population of beneficial intestinal bacteria and reducing the abundance of harmful ones. Such mechanisms promoted intestinal health, digestion, and nutrient absorption, ultimately leading to enhanced egg quality. In conclusion, supplementing laying hen diets with RIPS has been demonstrated to improve egg quality by boosting immunity and optimizing intestinal digestion and absorption.

PSXIII-24 Effect of Inclusion of Hay and Concentrate Containing Monensin and Methionine on in Vitro Methane Production

Abstract The objective of this study was to evaluate the effect of the inclusion of hay and Suplemento Total concentrate as a substitute for corn on gas production and methane concentration in vitro. The experiment was conducted under anaerobic conditions using bottles that simulate the ruminal environment (ANKOM Gas Pressure Monitor) containing artificial saliva, rumen liquid, and two g of substrates from each treatment: (MI) Control, 1.62 g of corn containing 9% of crude protein and 0.38 g of mineral mix and; (FMM) 1.02 g of Tifton 85 hay and 0.98 g of Suplemento Total concentrate (Suplemento Nutrição Animal) containing 13.5% of crude protein, 0.32% of monensin and 0.63% of methionine. Duplicate substrates and duplicate blanks were fermented for each treatment in two runs, with a total of four repetitions per treatment. The accumulated pressure resulting from the fermentation was measured automatically over 48 h using the Gas Monitor software connected to the ANKOM modules of each bottle. The conversion of the pressure to gas volume was calculated as follows: Volume (mL) = 2.3932 + 3.4053 × pressure (R2 = 0.9146; n = 1.151). At the end of each run, a gas sample was collected from each bottle to measure methane concentration using gas chromatography. To obtain the methane production for every 100 mL of gas produced, the total volume of methane produced was multiplied by 100 and divided by the total gas production. Data were analyzed in a completely randomized design using analysis of variance (ANOVA) at α = 0.05. Was observed 23.86% of increase in gas production (64.79 vs 80.25 mL, P = 0.0072), 45.53% reduction in total methane production (46.50 vs 25.33 mL, P &amp;lt; 0.001), and 56.07% reduction in methane production for every 100 mL of gas produced (71.96 vs 31.61 mL, P &amp;lt; 0.001) in the FMM treatment compared with the MM, respectively (Table 1). Improvement in the quality of the diet, as well as the use of monensin and methionine, increases the fermentation rate, which explains the increase in gas production. Linked to this, there is also a reduction in methane production by reducing the population of gram-positive bacteria, which are precursors of methanogenesis. Therefore, the inclusion of hay and Suplemento Total concentrate containing 0.32 percent of monensin and 0.63 percent of methionine in place of corn with mineral mixture increased gas production and reduced methane production in vitro.

Non-starter lactic acid bacteria and citrate fermenting bacteria in milk supply chain: Are they easily controlled?

The frequency and possible sources of non-starter lactic acid bacteria (NSLAB) and citrate fermenting bacteria (CFB) at four points of a milk supply chain were evaluated. The relationship between the distance from farms (G1 and G2) to industry with NSLAB, CFB and psychrotrophic bacteria populations was also evaluated. A positive correlation between psychrotrophic and CFB was verified, which points to the need for the correct use of good milking practices to control these bacteria. NSLAB showed a significant increase in the population in raw milk samples collected in industrial silos (4.4 log cfu mL−1). CFB populations showed a significant increase in milk from tank trucks (4 log cfu mL−1). There was no difference between G1 and G2 in microorganisms counts. Even after the pasteurisation process, NSLAB and CFB populations remained high, which points to the occurrence of post-heat treatment recontamination, formation of biofilms and/or the presence of thermoduric microbiota.

Assessing differential land use impacts on soil quality: A method based on log-response ratios and polygonal projections

Soil quality indices (SQI) used for assessing soil degradation are often developed using additive scoring functions. However, these SQI may lack reference values for interpreting their outputs and the capacity to differentiate changes in specific variables. To overcome these limitations, this study introduces SQI using Log Response Ratios (LRR) as measures of size effects caused by land use in physical, chemical, and microbiological soil quality indicators. LRR vectors projected 2D polygons with condensed change measures along their perimeters. This method was tested in andosols within the southeastern region of Antioquia, Colombia. These soils were subjected to contrasting stages of degradation determined by the extent of A-horizon removal due to land use practices. This study shows that mining and agriculture have detrimental effects on soil organic carbon and water contents, and that size effects vary significantly between land uses (p < 0.05). Microbiological features also exhibit distinct size effects, such as populations of culturable mesophilic bacteria and fungi, microbial basal respiration, spore density of arbuscular mycorrhizal fungi (AMF), their diversity, and total glomalin-related soil proteins (p < 0.05). The SQI proposed exhibited a negative correlation with SQI computed from scoring additive functions either considering the entire dataset (R2 = 0.87) or a minimum dataset (R2 = 0.90). This approach underscores the utility of using LRR geometrical analysis to assess global soil quality differences among land uses (p < 0.01), offering a visual, quantifiable representation of the effects of each land use over specific soil quality indicators.

Metagenomic analysis of the microbial community in kefir grains from different milk sources

Abstract. Sumarmono J, Kusuma RJ, Rahayu N, Sukarno AS, Wulansari PD. 2023. Metagenomic analysis of the microbial community in kefir grains from different milk sources. Biodiversitas 24: 5302-5308. Kefir is a type of traditional fermented milk made from kefir grains. The quality of kefir grain depends on the milk medium, which impacts microbial diversity and population. This study uses metagenomic analysis to assess the microbial populations of kefir grains prepared from cow's milk and goat milk using the 16s rRNA method. The results revealed that &gt;99% Relative Abundance (RA) of the sample's total bacteria belonged to the phylum Firmicutes and the phylum Bacteroidota, respectively. However, most of the phylum Firmicutes was found in the sample of goat milk kefir. Further investigation revealed that goat milk samples had Lactobacillus, Streptococcus, and Staphylococcus genera, while the cow milk samples contained &gt;99% RA of Lactobacillus, Bacteroides, and Muribaculaceae. Regarding yeast, the family Saccharomycetaceae predominated in cow's milk, while goat milk had 2% of the family Saccharomycetaceae and 97% of unassigned microorganisms. The functional analysis revealed that kefir grains from the two sources had a variety of amino acid metabolisms, secondary metabolite metabolisms, and vitamin production. This metagenomic analysis shows that the type of milk affects the diversity of the population of both bacteria and yeast. This study opens up opportunities to further investigate the potential of kefir as a functional food beverage, a source of probiotics, and an antibacterial agent property.

Physiological changes in broiler chickens subjected to dietary ajwain (trachyspermum ammi l.) essential oil in encapsulated and conventional forms within a wheat-based diet

The aim of this study was to investigate the effects of different diet types, forms, and contents of ajwain essential oil (AEO) on various physiological characteristics of broiler chickens, including cell-mediated immunity responses, intestinal morphology, and microflora. A total of 1500 one-day-old male broiler chickens were allocated to different treatments based on a 2 × 3 × 2 factorial arrangement, considering diet types (corn and corn-wheat), contents of AEO (0, 150, and 300 mg/kg of diet), and forms of AEO (conventional and encapsulated). The results indicated that the broiler chickens fed the diet containing 150 ppm EO demonstrated reduced skin thickness in response to a 2,4-dinitrochlorobenzene challenge, 24 h after injection, compared to those receiving a diet without EO (P < 0.05). Increasing the EO content led to an increase in the villous height to crypt depth ratio in the jejunum of broiler chickens receiving 300 ppm EO (P < 0.05). Moreover, there was a slight improvement in the villous height to crypt depth ratio in the jejunum of broiler chickens fed the corn-wheat diet (P = 0.07). Broiler chickens fed the 300 ppm EO showed a lower total bacterial population compared to those fed the 150 ppm EO (P < 0.05). Finally, the use of EO at a content of 150 ppm improved cellular immune response, while EO at a content of 300 ppm improved the morphology and overall population of intestinal bacteria. Furthermore, the inclusion of wheat-corn diets exhibited enhanced morphological characteristics of the intestines. However, the forms of AEO did not exert any significant influence on the physiological traits.

Does postoperative pulmonary infection correlate with intestinal flora following gastric cancer surgery? - a nested case-control study.

The primary objective of this study was to investigate the potential correlation between gut microbes and postoperative pulmonary infection in gastric cancer patients. Additionally, we aimed to deduce the mechanism of differential functional genes in disease progression to gain a better understanding of the underlying pathophysiology. A nested case-control study design was utilized to enroll patients with gastric cancer scheduled for surgery at West China Hospital of Sichuan University. Patients were categorized into two groups, namely, the pulmonary infection group and the control group, based on the development of postoperative pulmonary infection. Both groups were subjected to identical perioperative management protocols. Fecal samples were collected 24 h postoperatively and upon pulmonary infection diagnosis, along with matched controls. The collected samples were subjected to 16S rDNA and metagenomic analyses, and clinical data and blood samples were obtained for further analysis. A total of 180 fecal specimens were collected from 30 patients in both the pulmonary infection and control groups for 16S rDNA analysis, and 3 fecal samples from each group were selected for metagenomic analysis. The study revealed significant alterations in the functional genes of the intestinal microbiome in patients with postoperative pulmonary infection in gastric cancer, primarily involving Klebsiella, Enterobacter, Ruminococcus, and Collinsella. During postoperative pulmonary infection, gut flora and inflammatory factors were found to be associated with the lipopolysaccharide synthesis pathway and short-chain fatty acid (SCFA) synthesis pathway. The study identified enriched populations of Klebsiella, Escherella, and intestinal bacteria during pulmonary infection following gastric cancer surgery. These bacteria were found to regulate the lipopolysaccharide synthesis pathway, contributing to the initiation and progression of pulmonary infections. Inflammation modulation in patients with postoperative pulmonary infection may be mediated by short-chain fatty acids. The study also revealed that SCFA synthesis pathways were disrupted, affecting inflammation-related immunosuppression pathways. By controlling and maintaining intestinal barrier function, SCFAs may potentially reduce the occurrence of pulmonary infections after gastric cancer surgery. These findings suggest that targeting the gut microbiome and SCFA synthesis pathways may be a promising approach for preventing postoperative pulmonary infections in gastric cancer patients.

Microencapsulation of Mitragyna leaf extracts to be used as a bioactive compound source to enhance in vitro fermentation characteristics and microbial dynamics.

Mitragyna speciosa Korth is traditionally used in Thailand. They have a high level of antioxidant capacities and bioactive compounds, the potential to modulate rumen fermentation and decrease methane production. The aim of the study was to investigate the different levels of microencapsulated-Mitragyna leaves extracts (MMLE) supplementation on nutrient degradability, rumen ecology, microbial dynamics, and methane production in an in vitro study. A completely randomized design was used to assign the experimental treatments, MMLE was supplemented at 0%, 4%, 6%, and 8% of the total dry matter (DM) substrate. The addition of MMLE significantly increased in vitro dry matter degradability both at 12, 24, and 48 h, while ammonia-nitrogen (NH3-N) concentration was improved with MMLE supplementation. The MMLE had the greatest propionate and total volatile fatty acid production when added with 6% of total DM substrate, while decreased the methane production (12, 24, and 48 h). Furthermore, the microbial population of cellulolytic bacteria and Butyrivibrio fibrisolvens were increased, whilst Methanobacteriales was decreased with MMLE feeding. The results indicated that MMLE could be a potential alternative plant-based bioactive compound supplement to be used as ruminant feed additives.