Analysis of the metals and metalloids concentrations and of the bacterial population in sediments of the Red River Delta, Vietnam.

In this study, we discuss for the first time the relationships between the diversity of the bacterial population and of the metals and metalloids concentrations in the sediments of the Red River Delta, Vietnam. The analysis of the 16S rRNA by the Illumina technology revealed a diversified population and a potential of bioremediation by the microorganisms, notably by the Bacilli relatively abundant in the Bach Dang estuary, where high metals and metalloids concentrations were highlighted. This work offers new information on the environmental context of the delta and highlights the potential impact that metals and metalloids may have on the bacterial population. Further investigations on the role of the bacteria in the biogeochemistry of this ecosystem will be of interest for the development of bioremediation processes.

The identification of active compounds and therapeutic properties of fermented and non-fermented red sorghum for the treatment of Alzheimer's dementia.

Sorghum is a promising treatment for Alzheimer's disease (AD), due to its rich antioxidant and anti-inflammatory qualities. Fermentation may also affect nutritional values. Therefore, the purpose of this study was to discover the phenolic and flavonoid chemicals found in both fermented and non-fermented red sorghum, as well as their potential therapeutic uses for AD. L. fermentum, and L. reuteri, and/or L. plantarum and L. casei were used to ferment samples of sorghum. The rats were grouped into five groups, healthy animals, and rats with Alzheimer's receiving 200 mg/kg of saline, non-fermented sorghum, and fermented sorghum fermented with L. fermentum and L. reuteri, as well as L. plantarum and L. casei. Various assessments were conducted, including evaluations of behavioral responses, antioxidant responses, inflammatory responses, acetylcholine levels and acetylcholine esterase, and bacterial populations in stool. P-hydroxybenzoic acid, eriodictyo naringenin, and apigenin were significantly higher in fermented samples, while glycerols were higher in non-fermented samples. The induction of Alzheimer's led to decrease step-through latency, time in target zone, FRAP, acetylcholine levels, Bifidobacterium population and lactobacillus population, while increased escape latency, platform location latency, MDA levels, IL-6, TNF-α, acetylcholine esterase, and coliform population (P = 0.001). The administration of both non-fermented sorghum and fermented sorghum demonstrated the potential to reverse the effects of AD, with a notably higher efficacy observed in the fermented samples compared to the non-fermented ones. In conclusion, fermentation exerted significant effects on the bioactive compounds the administration of fermented sorghum resulted in improved behavioral responses, characterized by a reduction in oxidation, inflammation and microbial population.

Analysis of chlorhexidine, antibiotics and bacterial community composition in water environments from Brazil, Cameroon and Madagascar during the COVID-19 pandemic.

The widespread of chlorhexidine and antibiotics in the water bodies, which grew during the global COVID-19 pandemic, can increase the dispersion of antibiotic resistance. We assessed the occurrence of these pharmaceutical compounds as well as SARS-CoV-2 and analysed the bacterial community structure of hospital and urban wastewaters from Brazil, Cameroon, and Madagascar. Water and wastewater samples (n = 59) were collected between January-June 2022. Chlorhexidine, azithromycin, levofloxacin, ceftriaxone, gentamicin and meropenem were screened by Ultra-High-Performance Liquid Chromatography coupled with mass spectrometer. SARS-CoV-2 was detected based on the nucleocapsid gene (in Cameroon and Madagascar), and envelope and spike protein-encoding genes (in Brazil). The total community-DNA was extracted and used for bacterial community analysis based on the 16S rRNA gene. To unravel likely interaction between pharmaceutical compounds and/or SARS-CoV-2 with the water bacterial community, multivariate statistics were performed. Chlorhexidine was found in hospital wastewater effluent from Brazil with a maximum concentration value of 89.28 µg/L. Additionally, antibiotic residues such as azithromycin and levofloxacin were also present at concentrations between 0.32-7.37 µg/L and 0.11-118.91 µg/L, respectively. In Cameroon, azithromycin was the most found antibiotic present at concentrations from 1.14 to 1.21 µg/L. In Madagascar instead, ceftriaxone (0.68-11.53 µg/L) and levofloxacin (0.15-0.30 µg/L) were commonly found. The bacterial phyla statistically significant different (P < 0,05) among participating countries were Proteobacteria, Patescibacteria and Dependentiae which were mainly abundant in waters sampled in Africa and, other phyla such as Firmicutes, Campylobacterota and Fusobacteriota were more abundant in Brazil. The phylum Caldisericota was only found in raw hospital wastewater samples from Madagascar. The canonical correspondence analysis results suggest significant correlation of azithromycin, meropenem and levofloxacin with bacteria families such as Enterococcaceae, Flavobacteriaceae, Deinococcaceae, Thermacetogeniaceae and Desulfomonilaceae, Spirochaetaceae, Methanosaetaceae, Synergistaceae, respectively. Water samples were also positive for SARS-CoV-2 with the lowest number of hospitalized COVID-19 patients in Madagascar (n = 7) and Brazil (n = 30). Our work provides new data about the bacterial community profile and the presence of pharmaceutical compounds in the hospital effluents from Brazil, Cameroon, and Madagascar, whose limited information is available. These compounds can exacerbate the spreading of antibiotic resistance and therefore pose a risk to public health.

Alterations in cell arrangements of group B streptococcus due to virulence factor expression can bias estimates of bacterial populations based on colony count measures.

Group B streptococcus (GBS) is a chain-forming commensal bacterium and opportunistic pathogen that resides in the gastrointestinal and genitourinary tract of healthy adults. GBS can cause various infections and related complications in pregnant and nonpregnant women, adults, and newborns. Investigations of the mechanisms by which GBS causes disease pathogenesis often utilize colony count assays to estimate bacterial population size in experimental models. In other streptococci, such as group A streptococcus and pneumococcus, variation in the chain length of the bacteria that can occur naturally or due to mutation can affect facets of pathogenesis, such as adherence to or colonization of a host. No studies have reported a relationship between GBS chain length and pathogenicity. Here, we used GBS strain 874391 and several derivative strains displaying longer chain-forming phenotypes (874391pgapC, 874391ΔcovR, 874391Δstp1) to assess the impact of chain length on bacterial population estimates based on the colony-forming unit (c.f.u.) assay. Disruption of GBS chains via bead beating or sonication in conjunction with fluorescence microscopy was used to compare chaining phenotypes pre- and post-disruption to detect long- and short-chain forms, respectively. We used a murine model of GBS colonization of the female reproductive tract to assess whether chaining may affect bacterial colonization dynamics in the host during chronic infection in vivo. Overall, we found that GBS exhibiting long-chain form can significantly affect population size estimates based on the colony count assay. Additionally, we found that the length of chaining of GBS can affect virulence in the reproductive tract colonization model. Collectively, these findings have implications for studies of GBS that utilize colony count assays to measure GBS populations and establish that chain length can affect infection dynamics and disease pathogenesis for this important opportunistic pathogen.

Antimicrobial Residue Accumulation Contributes to Higher Levels of Rhodococcus equi Carrying Resistance Genes in the Environment of Horse-Breeding Farms.

Antimicrobial residues excreted in the environment following antimicrobial treatment enhance resistant microbial communities in the environment and have long-term effects on the selection and maintenance of antimicrobial resistance genes (AMRGs). In this study, we focused on understanding the impact of antimicrobial use on antimicrobial residue pollution and antimicrobial resistance (AMR) in the environment of horse-breeding farms. Rhodococcus equi is an ideal microbe to study these associations because it lives naturally in the soil, exchanges AMRGs with other bacteria in the environment, and can cause disease in animals and humans. The environment is the main source of R. equi infections in foals; therefore, higher levels of multidrug-resistant (MDR) R. equi in the environment contribute to clinical infections with MDR R. equi. We found that macrolide residues in the environment of horse-breeding farms and the use of thoracic ultrasonographic screening (TUS) for early detection of subclinically affected foals with R. equi infections were strongly associated with the presence of R. equi carrying AMRGs in the soil. Our findings indicate that the use of TUS contributed to historically higher antimicrobial use in foals, leading to the accumulation of antimicrobial residues in the environment and enhancing MDR R. equi.

Droplet-based methodology for investigating bacterial population dynamics in response to phage exposure.

An alarming rise in antimicrobial resistance worldwide has spurred efforts into the search for alternatives to antibiotic treatments. The use of bacteriophages, bacterial viruses harmless to humans, represents a promising approach with potential to treat bacterial infections (phage therapy). Recent advances in microscopy-based single-cell techniques have allowed researchers to develop new quantitative methodologies for assessing the interactions between bacteria and phages, especially the ability of phages to eradicate bacterial pathogen populations and to modulate growth of both commensal and pathogen populations. Here we combine droplet microfluidics with fluorescence time-lapse microscopy to characterize the growth and lysis dynamics of the bacterium Escherichia coli confined in droplets when challenged with phage. We investigated phages that promote lysis of infected E. coli cells, specifically, a phage species with DNA genome, T7 (Escherichia virus T7) and two phage species with RNA genomes, MS2 (Emesvirus zinderi) and Qß (Qubevirus durum). Our microfluidic trapping device generated and immobilized picoliter-sized droplets, enabling stable imaging of bacterial growth and lysis in a temperature-controlled setup. Temporal information on bacterial population size was recorded for up to 25 h, allowing us to determine growth rates of bacterial populations and helping us uncover the extent and speed of phage infection. In the long-term, the development of novel microfluidic single-cell and population-level approaches will expedite research towards fundamental understanding of the genetic and molecular basis of rapid phage-induced lysis and eco-evolutionary aspects of bacteria-phage dynamics, and ultimately help identify key factors influencing the success of phage therapy.

Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight.

This work uses Compositional Data Analysis (CoDA) to examine the typical human faecal bacterial diversity in 39 healthy volunteers from the Andalusian region (Spain). Stool samples were subjected to high-throughput sequencing of the V3 and V4 regions of the 16S ribosomal RNA gene using Illumina MiSeq. The numbers of sequences per sample and their genus-level assignment were carried out using the Phyloseq R package. The alpha diversity indices of the faecal bacterial population were not influenced by the volunteer's sex (male or female), age (19-46 years), and weight (48.6-99.0 kg). To study the relationship between these variables and the faecal bacterial population, the ALDEx2 and coda4microbiome CoDA packages were used. Applying ALDEx2, a trend suggesting a connection between sex and the genera Senegalimassilia and Negatibacillus (slightly more abundant in females) and Desulfovibrio (more abundant in males) was found. Moreover, age was tentatively associated with Streptococcus, Tizzerella, and Ruminococaceae_UCG-003, while weight was linked to Senegalimassilia. The exploratory tool of the coda4microbiome package revealed numerous bacterial log-ratios strongly related to sex and, to a lesser extent, age and weight. Moreover, the cross-sectional analysis identified bacterial signature balances able to assign sex to samples regardless of controlling for volunteers' age or weight. Desulfovibrio, Faecalitalea, and Romboutsia were relevant in the numerator, while Coprococcus, Streptococcus, and Negatibacillus were prominent in the denominator; the greater presence of these could characterise the female sex. Predictions for age included Caproiciproducens, Coprobacter, and Ruminoclostridium in the numerator and Odoribacter, Ezakiella, and Tyzzerella in the denominator. The predictions depend on the relationship between both groups, but the abundance of the first group and scarcity of the second could be related to older individuals. However, the association of the faecal bacterial population with weight did not yield a satisfactory model, indicating scarce influence. These results demonstrate the usefulness of the CoDA methodology for studying metagenomics data and, specifically, human microbiota.

A high-throughput cytotoxicity screening platform reveals agr-independent mutations in bacteraemia-associated Staphylococcus aureus that promote intracellular persistence.

Staphylococcus aureus infections are associated with high mortality rates. Often considered an extracellular pathogen, S. aureus can persist and replicate within host cells, evading immune responses, and causing host cell death. Classical methods for assessing S. aureus cytotoxicity are limited by testing culture supernatants and endpoint measurements that do not capture the phenotypic diversity of intracellular bacteria. Using a well-established epithelial cell line model, we have developed a platform called InToxSa (intracellular toxicity of S. aureus) to quantify intracellular cytotoxic S. aureus phenotypes. Studying a panel of 387 S. aureus bacteraemia isolates, and combined with comparative, statistical, and functional genomics, our platform identified mutations in S. aureus clinical isolates that reduced bacterial cytotoxicity and promoted intracellular persistence. In addition to numerous convergent mutations in the Agr quorum sensing system, our approach detected mutations in other loci that also impacted cytotoxicity and intracellular persistence. We discovered that clinical mutations in ausA, encoding the aureusimine non-ribosomal peptide synthetase, reduced S. aureus cytotoxicity, and increased intracellular persistence. InToxSa is a versatile, high-throughput cell-based phenomics platform and we showcase its utility by identifying clinically relevant S. aureus pathoadaptive mutations that promote intracellular residency.

Comparison the effects of probiotic and prebiotic as antibiotic alternatives on Salmonella colonization, performance, and egg quality in laying hens challenged with Salmonella enterica serotype Enteritidis.

Background: Consumption of contaminated eggs with Salmonella enterica serotype Enteritidis (SE) cause gastroenteritis in human. Aims: The present study examined the effect of probiotic and prebiotic compared to antibiotic on the colonization of SE in the ceca, and the quantity and quality of produced eggs in the laying hens challenged with SE. Methods: One hundred Hy-Line W-36 laying hens with 44-week-olds were studied for 13 weeks in a randomized complete block design containing five treatments and four replicates with five birds in each replicate. Treatments included: negative control, positive control, and antibiotic: diets containing antibiotic (Oxytetracycline 0.15 g/kg diet), probiotic (Bactocell® 0.1 g/kg diet), and prebiotic (Diamond V Original XPCTM 1.25 g/kg diet). All experimental groups except negative control were challenged with 1 ml of suspension solution containing 1 × 107 CFU/ml SE by oral gavage at the start of the ninth week of the experiment. Laying performance traits and cecal bacterial population were measured at the end of each week. Results: Probiotic and prebiotic showed a greater effect in the reduction of yolk cholesterol and blood cholesterol level before and after challenge with SE, respectively (P<0.05). In pre-challenge period, treatments had no effect on the cecal bacterial population; but after the challenge, three dietary supplements decreased the colonization of SE in the ceca of laying hens, and prebiotic showed more preventive effect (P<0.05). Conclusion: The result of this study showed that the prebiotic can be effective in reducing and preventing SE colonization in laying hens and act as an alternative to antibiotics.

Effect of Dietary Supplementation of Hydrolyzed Yeast on Growth Performance, Digestibility, Rumen Fermentation, and Hematology in Growing Beef Cattle.

This experiment was conducted to assess the effect of hydrolyzed yeast (HY) on growth performance, nutrient digestibility, rumen fermentation, and hematology in growing crossbred Bos indicus cattle. Twenty crossbred beef cattle with an initial body weight (BW) of 142 ± 12 kg were randomly assigned to one of four treatments for 90 d in a randomized complete block design (RCBD) having five blocks based on a homogenous subpopulation of sex and BW. Cattle were fed with a total mixed ration (TMR) and supplemented with HY at 0, 1, 2, and 3 g/kg dry matter (DM), respectively. Supplementation with the HY did not change average daily gain (ADG), dry matter intake (DMI), and gain to feed ratio (G:F) (p ≥ 0.06). The addition of HY did not adversely affect nutrient intake (p ≥ 0.48), while the digestibility of crude protein (CP) increased quadratically (p= 0.03) in the cattle receiving HY. The addition of HY did not affect rumen pH, but NH3-N concentration increased linearly (p = 0.02) in the cattle. The total volatile fatty acid (total VFA) increased quadratically (p= 0.03) when cattle were fed with HY supplementation. The proportion of acetate decreased cubically (p= 0.03) while propionate increased cubically (p= 0.01), resulting in a decrease in the acetate to propionate ratio (p= 0.01) when cattle were fed with HY supplementation. In addition, acetate was the lowest, but total VFA and propionate were the highest in cattle fed the HY at 2 g/kg DM. Butyrate increased cubically (p = 0.02) with the addition of HY. The protozoal and fungal populations were similar among treatments (p ≥ 0.11), but the bacterial population increased linearly (p < 0.01) with the addition of HY. Supplementation of HY did not influence blood urea nitrogen (BUN), red blood cells (RBC), hemoglobin, hematocrit, white blood cells (WBC), lymphocytes, or eosinophils (p≥ 0.10). However, monocytes and neutrophils increased linearly (p = 0.04 and p = 0.01, respectively) by HY supplementation. In conclusion, supplementation of HY at 2 g/kg DM promotes CP digestibility, rumen fermentation efficiency, and hematology but does not affect the growth performance of growing beef cattle.

Evaluation of plant elicitation with methyl-jasmonate, salicylic acid and benzo (1,2,3)-thiadiazole-7-carbothioic acid-S-methyl ester for the sustainable management of the pine wilt disease.

Treatment with plant elicitors can be a promising method to induce Pinus pinaster tolerance against the pinewood nematode (PWN), Bursaphelenchus xylophilus, by promoting plant antioxidant system, micronutrient accumulation and by modulating plant-associated bacterial populations. To test this hypothesis, plants were sprayed with methyl jasmonate (MeJA), salicylic acid (SA) or benzo (1,2,3)-thiadiazole-7-carbothioic acid-S-methyl ester (BTH), and evaluated until 35 days after-inoculation (dai) for: i) extent of foliar symptoms; ii) nematode density inside stem tissues; iii) proxies for oxidative damage and antioxidant activity, iv) micronutrient concentration and v) bacterial diversity. Compared with non-elicited plants, plant elicitation, particularly with BTH, significantly decreased nematodes density inside stem tissues (by 0.63-fold). Concordantly, without elicitation plant mortality reached 12.5% while no mortality was observed in elicited plants. BTH-elicited plants had significantly higher concentrations of anthocyanins and carotenoids at the end of the assay than SA-elicited and MeJA-elicited plants, which possibly contributed to the lower PWN colonization and degree of foliar symptoms observed. Accordingly, MeJA and SA led to increased lipid peroxidation at 28 dai (by 2.64- and 2.52-fold, respectively) in comparison with BTH (by 1.10-fold), corroborating its higher potential in increasing plant antioxidative response during infection. Moreover, carotenoids showed a negative correlation with nematode migration, whereas polyphenols showed a positive correlation. Elicitors also induced changes in the bacterial community of infected P. pinaster plants, increasing the diversity of specific populations. Finally, elicitors induced significant changes in micronutrients accumulation in plant tissues, namely a decrease in the concentration of B, Mn and Ni in plants treated with BTH compared to those treated with the other elicitors. Altogether, results suggest that elicitation with MeJA, SA and, particularly, BTH, increases tolerance against B. xylophilus by promoting plant antioxidant system, changing the accumulation of essential micronutrients and modulating plant-associated bacterial diversity.

Possibilities of transmission electron microscopy in assessing the quality of bacterial cells and microbial population.

Determination of changes in the morphostructure of microorganisms under the influence of antibiotics, disinfectants, biocins, physical and chemical agents is carried out using the method of visualization of ultrathin sections in a transmission electron microscope. The aim is to develop methodological techniques for express preparation and visualization of the ultrastructure of bacteria in a transmission electron microscope to detect structural damage to cells and assess the quality of the microbial population. A technique of accelerated sample preparation for visualization of the fine structure of bacteria and diagnosis of structural damage to cells in a transmission electron microscope has been developed. The use of this method will make it possible to more effectively investigate the mechanisms of inactivation of microorganisms at different stages of contact with antibiotics, disinfectants, biocines, including various stressful, damaging and lethal physical and chemical effects.

Optimization and Fabrication of Multi-Level Microchannels for Long-Term Imaging of Bacterial Growth and Expansion.

Bacteria are unicellular organisms whose length is usually around a few micrometers. Advances in microfabrication techniques have enabled the design and implementation of microdevices to confine and observe bacterial colony growth. Microstructures hosting the bacteria and microchannels for nutrient perfusion usually require separate microfabrication procedures due to different feature size requirements. This fact increases the complexity of device integration and assembly process. Furthermore, long-term imaging of bacterial dynamics over tens of hours requires stability in the microscope focusing mechanism to ensure less than one-micron drift in the focal axis. In this work, we design and fabricate an integrated multi-level, hydrodynamically-optimized microfluidic chip to study long-term Escherichia coli population dynamics in confined microchannels. Reliable long-term microscopy imaging and analysis has been limited by focus drifting and ghost effect, probably caused by the shear viscosity changes of aging microscopy immersion oil. By selecting a microscopy immersion oil with the most stable viscosity, we demonstrate successful captures of focally stable time-lapse bacterial images for ≥72 h. Our fabrication and imaging methodology should be applicable to other single-cell studies requiring long-term imaging.

Effect of phenyllactic acid on silage fermentation and bacterial community of reed canary grass on the Qinghai Tibetan Plateau.

BACKGROUND: This study aimed to investigate the effect of phenyllactic acid as an additive on silage fermentation and bacterial community of reed canary grass (RCG, Phalaris arundinacea L.) on the Qinghai Tibetan Plateau. At the heading stage, RCG was harvested, chopped and ensiled in small bag silos. The silage was treated without (control, 1.0 g/mL sterile water, on a fresh matter basis (FM)) or with phenyllactic acid (PLA, 3 mg/mL, FM), antimicrobial additive (PSB, a mixture of potassium sorbate and sodium benzoate, 2%, FM), lactic acid bacteria inoculant (LABi, L. plantarum + L. curvatus, 1 × 106 cfu/g, FM) and PLA + LABi, and then stored in a dark room at the ambient temperature (5 ~ 15 °C) for 60 days. RESULTS: Compared with control, PLA decreased lactic acid, acetic acid and ammonia-N contents, and subsequently increased CP content of RCG silage. PLA enhanced the growth of lactic acid bacteria and reduced the count of yeasts (P < 0.05) in RCG silage, with reduced bacterial richness index (Chao1), observed operational taxonomic units and diversity index (Simpson). In relative to control, moreover, PLA and PLA + LABi increased the relative abundance of Lactococcus in RCG silage by 27.73 and 16.93%, respectively. CONCLUSIONS: Therefore, phenyllactic acid at ensiling improved nutritional quality of RCG silage by advancing the disappearance of yeasts and the dominance of Lactococcus.

Large-scale comparative genomics to refine the organization of the global Salmonella enterica population structure.

The White-Kauffmann-Le Minor (WKL) scheme is the most widely used Salmonella typing scheme for reporting the disease prevalence of the enteric pathogen. With the advent of whole-genome sequencing (WGS), in silico methods have increasingly replaced traditional serotyping due to reproducibility, speed and coverage. However, despite integrating genomic-based typing by in silico serotyping tools such as SISTR, in silico serotyping in certain contexts remains ambiguous and insufficiently informative. Specifically, in silico serotyping does not attempt to resolve polyphyly. Furthermore, in spite of the widespread acknowledgement of polyphyly from genomic studies, the prevalence of polyphyletic serovars is not well characterized. Here, we applied a genomics approach to acquire the necessary resolution to classify genetically discordant serovars and propose an alternative typing scheme that consistently reflect natural Salmonella populations. By accessing the unprecedented volume of bacterial genomic data publicly available in GenomeTrakr and PubMLST databases (>180 000 genomes representing 723 serovars), we characterized the global Salmonella population structure and systematically identified putative non-monophyletic serovars. The proportion of putative non-monophyletic serovars was estimated higher than previous reports, reinforcing the inability of antigenic determinants to depict the complexity of Salmonella evolutionary history. We explored the extent of genetic diversity masked by serotyping labels and found significant intra-serovar molecular differences across many clinically important serovars. To avoid false discovery due to incorrect in silico serotyping calls, we cross-referenced reported serovar labels and concluded a low error rate in in silico serotyping. The combined application of clustering statistics and genome-wide association methods demonstrated effective characterization of stable bacterial populations and explained functional differences. The collective methods adopted in our study have practical values in establishing genomic-based typing nomenclatures for an entire microbial species or closely related subpopulations. Ultimately, we foresee an improved typing scheme to be a hybrid that integrates both genomic and antigenic information such that the resolution from WGS is leveraged to improve the precision of subpopulation classification while preserving the common names defined by the WKL scheme.

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.

Effects of Atrazine on Chernozem Microbial Communities Evaluated by Traditional Detection and Modern Sequencing Technology.

Atrazine is a long residual herbicide commonly used in maize fields. Although atrazine can effectively control weeds and improve crop yield, long-term application leads to continuous pollution in the agricultural ecological environment, especially in the soil ecosystem, and its impact on soil microorganisms is still not clear. Four methods were used in the experiment to clarify the effect of atrazine on the bacterial populations of cultivated soil layers of chernozem in a cold region in different periods: high-performance liquid chromatography (HPLC), colorimetry, microplate, and high-throughput sequencing. The level of residual atrazine in cold chernozem decreased from 4.645 to 0.077 mg/kg soil over time, and the residue gradually leached into deep soil and then decreased after accumulating to a maximum value. Atrazine significantly affected the activities of urease and polyphenol oxidase activity in the soil layers at different periods but had no significant effect on sucrase and phosphatase activity. Atrazine significantly reduced the diversity of microbial carbon source utilization and total activity in soil layers of 0-10 and 20-30 cm but only reduced the diversity of microbial carbon source utilization in the 10-20 cm layer. Atrazine had no significant effect on bacterial populations (10-12 phyla, 29-34 genera), but had a slight effect on the relative abundance of various groups. Atrazine significantly reduced the diversity of bacterial populations in cultivated soil layers of chernozem in a cold region, and the diversity of bacterial populations decreased with decreased residue. This lays a foundation for guiding the safe use of herbicides on farmland in Northeast China.

Segregational Drift Constrains the Evolutionary Rate of Prokaryotic Plasmids.

Plasmids are extrachromosomal genetic elements in prokaryotes that have been recognized as important drivers of microbial ecology and evolution. Plasmids are found in multiple copies inside their host cell where independent emergence of mutations may lead to intracellular genetic heterogeneity. The intracellular plasmid diversity is thus subject to changes upon cell division. However, the effect of plasmid segregation on plasmid evolution remains understudied. Here, we show that genetic drift during cell division-segregational drift-leads to the rapid extinction of novel plasmid alleles. We established a novel experimental approach to control plasmid allele frequency at the levels of a single cell and the whole population. Following the dynamics of plasmid alleles in an evolution experiment, we find that the mode of plasmid inheritance-random or clustered-is an important determinant of plasmid allele dynamics. Phylogenetic reconstruction of our model plasmid in clinical isolates furthermore reveals a slow evolutionary rate of plasmid-encoded genes in comparison to chromosomal genes. Our study provides empirical evidence that genetic drift in plasmid evolution occurs at multiple levels: the host cell and the population of hosts. Segregational drift has implications for the evolutionary rate heterogeneity of extrachromosomal genetic elements.

Dietary Tributyrin Administration Improves Intestinal Morphology and Selected Bacterial and Short-Chain Fatty Acid Profiles in Broilers Under an Isocaloric Feeding Regime.

The current study was conducted to investigate the effect of dietary tributyrin (TB) administration on the intestinal and growth performances in Arbor Acres (AA) broilers under an isocaloric feeding regime. A total of 540 day-old healthy AA broilers were randomly assigned to five treatments with 12 replicates (pens) per treatment and nine birds per pen for 42 days. The dietary treatments were basal diet (control) and basal diet with TB at doses of 0.23 g/kg (TB1), 0.46 g/kg (TB2), 0.92 g/kg (TB3), and 1.84 g/kg (TB4). Particularly, to achieve the isocaloric and cost-saving experimental diets, soybean oil was replaced by the TB product (Eucalorie®) with equivalent metabolic energy contents, and the formulas were rebalanced with zeolite to get the sum of all the feed ingredients to 100%. On days 21 and 42, after weighing, the birds (one bird per replicate) whose body weight was close to the replicate average were euthanized to investigate the effect of dietary TB on intestinal morphology, intestinal bacterial population, and short-chain fatty acid contents. The results revealed that dietary TB administration increased the average daily gain, gain/feed ratio, and European broiler index (P < 0.05) and improved the intestinal morphology (P < 0.05) as indicated by higher villus height and the ratios of villus height/crypt depth in broilers. The incremental levels of TB increased the ileal Lactobacillus content (P = 0.05) and cecal Bacillus content (P = 0.02), respectively. Moreover, dietary TB administration also increased the contents of most of the selected short-chain fatty acids in ileal and cecal digesta (P < 0.05). Collectively, dietary TB administration quadratically improved the growth performance, intestinal morphology, beneficial bacterial population, and short-chain fatty acid levels under the isocaloric feeding regime, indicating better profit return potential in practical poultry operation.

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. III: Relation with solid passage rate and pH on prokaryotic fatty acid profile and community in continuous culture.

Our objectives were to evaluate potential interactions in culture conditions that influence how exogenously dosed branched-chain VFA (BCVFA) would be recovered as elongated fatty acids (FA) or would affect bacterial populations. A 2 × 2 × 2 factorial arrangement of treatments evaluated 3 factors: (1) without versus with BCVFA (0 vs. 2 mmol/d each of isobutyrate, isovalerate, and 2-methylbutyrate; each dose was partially substituted with 13C-enriched tracers before and during the collection period); (2) high versus low pH (ranging diurnally from 6.3 to 6.8 vs. 5.7 to 6.2); and (3) low versus high particulate-phase passage rate (kp; 2.5 vs. 5.0%/h) in continuous cultures administered a 50:50 forage:concentrate diet twice daily. Samples of effluent were collected and composited before harvesting bacteria from which FA and DNA were extracted. Profiles and enrichments of FA in bacteria were evaluated by gas chromatography and isotope-ratio mass spectrometry. The 13C enrichment in bacterial FA was calculated as percentage recovery of dosed 13C-labeled BCVFA. Dosing BCVFA increased the even-chain iso-FA, preventing the reduced concentration at higher kp and potentially as a physiological response to decreased pH. However, decreasing pH decreased recovery of 13C in these even-chain FA, suggesting greater reliance on isobutyrate produced from degradation of dietary valine. The iso-FA were decreased, whereas anteiso-FA and 16:0 increased with decreasing pH. Thus, 2-methylbutyrate still appeared to be important as a precursor for anteiso-FA to counter the increased rigidity of bacterial membranes that had more saturated straight-chain FA when pH decreased. Provision of BCVFA stimulated the relative sequence abundance of Fibrobacter and Treponema, both of which require isobutyrate and 2-methylbutyrate. Numerous bacterial community members were shifted by low pH, including increased Prevotella and genera within the phylum Proteobacteria, at the expense of members within phylum Firmicutes. Because of relatively few interactions with pH and kp, supplementation of BCVFA can stimulate neutral detergent fiber degradability via key fibrolytic bacteria across a range of conditions. Decreasing pH shifted bacterial populations and their FA composition, suggesting that further research is needed to distinguish pH from dietary changes.