Abundant Phyla Research Articles

Detection and comparison of tumor cell-associated microbiota from different compartments of colorectal cancer.

Intratumoral microbes play an important role in the development of colorectal cancer (CRC). However, studying intratumoral microbes in CRC faces technical challenges, as tumor microbe communities are often contaminated by fecal microbes due to the structure of the gut folds and villi. The present study aimed to develop a new method for isolating tumor cell-associated microbiota and comparing microbial populations from different compartments. The distribution of intestinal bacteria was detected using immunohistochemistry combined with 5R-16s rRNA gene sequencing to explore the effects of the sampling site and number of washes on the detection of microbiota. The 5R-16s rRNA gene sequencing was performed using 44 samples from 11 patients with CRC, including CRC tumor tissues (TT), normal tissues adjacent to CRC (NT), tumor cells (TC), and normal cells (NC). TC and NC were obtained from the TT and NT using an enzymatic digestion method. The microbiota and their potential functions in the four groups were analyzed and compared to determine the differential microbiota related to CRC. Bacteria were mainly distributed in the feces covering intestinal tissues and in the epithelial cells and macrophages within the tissues. Different sampling sites and number of washes led to detection of different microbiota distributions. Although the cleaning method could be controlled, sampling sites varied and led to different microbiota distributions. The phyla of Firmicutes and Bacteroidetes were highly abundant in the conventionally used tissue samples, whereas Proteobacteria was the most abundant phyla in the cell samples isolated with the new method (i.e., after cell enzymatic hydrolysis). Detection of CRC cell-associated microbiota using a cell enzymatic digestion method showed that some bacteria, such as Fusobacterium, Eikenella, Shewanella, and Listeria, were more abundant in TT than NT, whereas the abundance of Akkermansia was lower in TT than NT. The tumor/normal ratios of some bacteria, such as Gemella, Escherichia, Shigella, and Blautia, were different between the cell and tissue samples. The cell enzymatic digestion method reduced fecal bacterial contamination, enabling low biomass intratumoral microbiota to be detected and allowing prediction of bacterial distributions.

Supplementing flaxseed meal with sucrose, flaxseed oil, or both: Effects on milk enterolactone, ruminal microbiota profile, production performance, and nutrient utilization in dairy cows

Flaxseed is the richest source of secoisolariciresinol diglucoside, which is converted by ruminal microorganisms primarily to the mammalian lignan enterolactone. Our objective was to investigate the effect of diets containing soybean meal or flaxseed meal (FM) supplemented with sucrose, flaxseed oil, or both, on milk enterolactone concentration yield, diversity, and relative abundance of ruminal bacterial taxa, ruminal fermentation profile, production performance, milk fatty acids (FA) yield, and nutrient utilization in dairy cows. Sixteen Holstein cows (8 multiparous [4 ruminally cannulated] and 8 primiparous) averaging (mean ± SD) 134 ± 54.1 DIM and 679 ± 78.9 kg of BW in the beginning of the study were assigned to treatment sequences in a replicated 4 × 4 Latin square design. Each experimental period lasted 25 d, with 18 d for diet adaptation and 7 d for data and sample collection. Diets were formulated to contain a 60:40 forage:concentrate ratio and included the following (DM basis): (1) 8% soybean meal and 23% ground corn (SBM); (2) 15% FM, 10.7% ground corn, and 5% sucrose (FLX+S); (3) 15% FM, 15.4% ground corn, and 3% flaxseed oil (FLX+O); and (4) 15% FM, 10.2% ground corn, 5% sucrose, and 3% flaxseed oil (FLX+SO). Compared with SBM, the concentration and yield of milk enterolactone increased in cows fed the FM diets but did not differ among FLX+S, FLX+O, and FLX+SO. The relative abundances of the phyla Firmicutes, Verrucomicrobiota, and Actinobacteriota, and those of the bacterial genera Lachnospiraceae NK3A20 group, Eubacterium coprostanoligenes group, Anaeromusa-Anaeroarcus, WCHB1-41, and p-251-o5 decreased, whereas Prevotella and NK4A214 group increased when comparing SBM against at least 1 diet containing FM. Furthermore, the relative abundances of Firmicutes and Actinobacteriota and those of Prevotella, Lachnospiraceae NK3A20 group, Eubacterium coprostanoligenes group, Acetitomaculum, Lachnospiraceae unclassified, NK4A214 group, and Anaeromusa-Anaeroarcus changed (increased or decreased) across the FLX+S, FLX+O, and FLX+SO diets. However, all these changes in the relative abundance of the ruminal bacterial taxa were not conclusively associated with the effect of diets on milk enterolactone. Diets did not affect ruminal pH and concentrations of NH3-N and total VFA. Dry matter intake and yields of milk, milk fat, and milk true protein all decreased in cows fed FLX+O or FLX+SO. Yields of milk total odd-chain FA, branched-chain FA, total <16C FA, and total 16C FA decreased with feeding FLX+O and FLX+SO. The apparent total-tract digestibilities of DM and OM were lowest in the FLX+S and FLX+O diets, with CP and ADF digestibilities lowest in cows receiving FLX+S or FLX+O, respectively. Urinary excretion of total N was lowest with feeding SBM. Contrarily, diets did not affect the urinary excretion of total purine derivatives. In brief, despite the effect of diets on the relative abundance of several ruminal microbiota phyla and genera, we were unable to conclusively associate these changes with increased milk enterolactone in FM-containing diets versus SBM.

Spatiotemporal structure and composition of the microbial communities in hypersaline Lake Magadi, Kenya

Background Soda lakes are habitats characterized by haloalkaline conditions also known to host unique microbial communities. The water chemistry changes with seasons due to evaporative concentration or floods from the surrounding grounds. However, it is not yet clear if the change in physiochemical changes influences the spatiotemporal diversity and structure of microbial communities in these ecosystems. Methods Using 16S rRNA gene amplicon sequencing, we investigated the diversity and structure of microbial communities in water and brine samples taken from Lake Magadi between June and September 2018. Additionally, physicochemical parameters were also analyzed for every sampling site. Additionally, physicochemical parameters were also analyzed for every sampling site. Results The abundant bacterial phyla were Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Verrumicrobia, Deinococcus-Thermus, Spirochaetes, and Chloroflexi. The Archaeal diversity was represented by phyla Euryachaeota, Crenarchaeota, Euryarchaeota, and Thaumarchaeota. The dominant bacterial species were: Euhalothece sp. (10.3%), Rhodobaca sp. (9.6%), Idiomarina sp. (5.8%), Rhodothermus sp. (3.0%), Roseinatronobacter sp. (2.4%), Nocardioides sp. (2.3%), Gracilimonas sp. (2.2%), and Halomonas sp. (2%). The dominant archaeal species included Halorubrum sp. (18.3%), Salinarchaeum sp. (5.3%), and Haloterrigena sp. (1.3%). The composition of bacteria was higher than that of archaea, while their richness and diversity varied widely across the sampling seasons. The α-diversity indices showed that high diversity was recorded in August, followed by September, June, and July in that order. The findings demonstrated that temperature, pH, P+, K+, NO3 -, and total dissolved solids (TDS) contributed majorly to the diversity observed in the microbial community. Multivariate analysis revealed significant spatial and temporal effects on β-diversity and salinity and alkalinity were the major drivers of microbial composition in Lake Magadi. Conclusions We provide insights into the relationships between microbial structure and geochemistry across various sampling sites in Lake Magadi.

Association among polydisperse aerodynamic size of bioaerosols, biodiversity and urbanization in kindergartens

The aerodynamic sizes of bioaerosols may significantly affect their behaviors, respiratory deposition and biodiversity. The respirable bacterial size, biodiversity, and human-associated bacteria (HAB) related bioaerosols were evaluated at three kindergartens in Taiwan. Kindergartens A, B, and C were in urban, semi-urban, and rural areas, respectively. A six-stage viable Andersen cascade impactor was used to collect bioaerosols and to determine their size distributions. The geometric mean diameter (GMD), geometric standard deviation (GSD), heat maps, and uniformity were used to evaluate the association of bacteria characteristics. A BD Phoenix-100 automated interpretation system was used to identify the airborne bacteria species.The results revealed that 1425 colonies of the sampled airborne bacteria contained 63 species in 29 genera, and overall, 63.0% were HABs. The most abundant phylum was Actinobacteria (56.6 ± 22.2%) and Firmicutes (31.6 ± 22.3%), and from the taxonomic analysis, both airborne Micrococcus and the Staphylococcus aureus are the dominant genus. All the bacteria aerodynamic particle size distributions were polydisperse distributions. The heat map and uniformity analysis had revealed most of the sampled bioaerosols distributed between 1.1–3.3 μm, and most of the polydisperse airborne Streptococcus spp. had a size in the respirable range, due to urbanization, they have potentially contributed to respiratory risk in the kindergartens. The Shannon diversity index (H) and inverse Simpson diversity index (D) of the bioaerosols in urban kindergarten were negatively correlated with GMD and GSD. The Pearson correlations revealed that the kindergarten in the rural area, with a higher temperature, a lower relative humidity, and a lower CO2 concentration than the others, tended to have the largest H and D values (P < 0.05). Multiple and stepwise regression revealed that bioaerosol aerodynamic size was statistically significantly correlated with H (P = 0.001) and D values (P = 0.002). This study sheds light on the characteristics of bioaerosols and their associations with microbiome.

Integrated multiple-omics reveals the regulatory mechanism underlying the effects of homologous Bacillus tequilensis (GCB-3) on growth performance of grass carp (Ctenopharyngodon idellus)

The purpose of this study was to investigate the regulatory mechanism of Bacillus tequilensis (GCB-3) in improving the growth performance of grass carp by microbiome and targeted metabolomics analysis. Fish were fed with different amounts of GCB-3 including B0 (0 CFU/g), B6 (1×106 CFU/g), B7 (1×107 CFU/g), B8 (1×108 CFU/g), and B9 (1×109 CFU/g) for 8 weeks. The results indicate that with the increase of dietary GCB-3 concentration, grass carp showed a significant linear trend in growth performance, and appetite factors showed a significant linear and quadratic trend, the growth performance and appetite-promoting factors in the B8 group reach their maximum value in the B8 group. Microbiome analysis found that Proteobacteria and Actinobacteria were the most abundant phylum in the gut microbiota of grass carp. The functional potential predicted that GCB-3 affected the synthesis and degradation of carbohydrates, amino acids, fatty acids and lipids. It found that GCB-3 also affected the tricarboxylic acid (TCA) cycle VII (acetate-producers) pathway. The results of targeted metabolomics showed a significant linear and quadratic increase in intestinal acetate with GCB-3 concentration and a maximum in the B8 group. The results of the correlation analysis showed a significant positive correlation between Actinobacteria abundance and acetic acid content, and also between TCA cycle VII (acetate-producers) pathway abundance and Actinobacteria abundance and acetic acid content. In B8 group, grass carp showed a faster regulation speed of blood glucose levels after glucose injection, and the GLP-1 content remained stable. The activities of glycolytic enzymes, lipolytic enzymes, protein metabolism enzymes, and their related mRNA expression levels in grass carp showed a linear or quadratic increasing trend. However, the expression levels of gluconeogenic enzymes and fatty acid synthesis enzyme related mRNA showed an opposite trend. In summary, the addition of 1×108 CFU/g GCB-3 in grass carp feed can improve the abundance of dominant bacterial phyla in the intestine, especially Actinobacteria, increase the concentration of intestinal acetate, provide substrate for the TCA cycle VII (acetate-producers) pathway, thereby regulating the nutrient metabolism of grass carp and ultimately promoting growth.

Metagenomic comparison of gut communities between wild and captive Himalayan griffons.

Himalayan griffons (Gyps himalayensis), known as the scavenger of nature, are large scavenging raptors widely distributed on the Qinghai-Tibetan Plateau and play an important role in maintaining the balance of the plateau ecosystem. The gut microbiome is essential for host health, helping to maintain homeostasis, improving digestive efficiency, and promoting the development of the immune system. Changes in environment and diet can affect the composition and function of gut microbiota, ultimately impacting the host health and adaptation. Captive rearing is considered to be a way to protect Himalayan griffons and increase their population size. However, the effects of captivity on the structure and function of the gut microbial communities of Himalayan griffons are poorly understood. Still, availability of sequenced metagenomes and functional information for most griffons gut microbes remains limited. In this study, metagenome sequencing was used to analyze the composition and functional structures of the gut microbiota of Himalayan griffons under wild and captive conditions. Our results showed no significant differences in the alpha diversity between the two groups, but significant differences in beta diversity. Taxonomic classification revealed that the most abundant phyla in the gut of Himalayan griffons were Fusobacteriota, Proteobacteria, Firmicutes_A, Bacteroidota, Firmicutes, Actinobacteriota, and Campylobacterota. At the functional level, a series of Kyoto Encyclopedia of Genes and Genome (KEGG) functional pathways, carbohydrate-active enzymes (CAZymes) categories, virulence factor genes (VFGs), and pathogen-host interactions (PHI) were annotated and compared between the two groups. In addition, we recovered nearly 130 metagenome-assembled genomes (MAGs). In summary, the present study provided a first inventory of the microbial genes and metagenome-assembled genomes related to the Himalayan griffons, marking a crucial first step toward a wider investigation of the scavengers microbiomes with the ultimate goal to contribute to the conservation and management strategies for this near threatened bird.

203 The relationship between potentiated zinc oxide and monovalent copper in a dietary administration for weanling piglets

Abstract The aim of this study was to evaluate different dietary level of Zinc (Zn) and Copper (Cu) supplementation according to European and non-European levels on the health and performance of pigs 14 d after weaning. A total of 120 piglets [initial body weight = 7.14 ± 0.92 kg] were divided into 4 experimental treatments: positive control (PC, 2,500 ppm of Zn, ZnO) and 3 treatments in which Zn and Cu were added through potentiated ZnO and Cu2O according to different European and non-European levels of inclusion: EU (120 ppm of Zn; 140 ppm of Cu), non-EU+ (300 ppm of Zn; 200 ppm of Cu) and non-EU- (300 ppm of Zn; 140 ppm of Cu). Growth performance, serum Zn and Cu concentrations, fecal score, blood biomarkers of intestinal integrity, and fecal microbial composition were examined and analyzed using GLM and MIXED procedures of SAS. Fecal samples at 14 d were collected and the V3–V4 hypervariable regions of the bacterial 16S gene were sequenced in one Illumina MiSeq run. Body weight (BW), average daily gain (ADG), average daily feed intake (ADFI), feed conversion ratio (FCR) and (feed efficiency (FE) were not affected by the experimental treatments. The fecal score suggests that during the first 14d, the consistency of the feces tended (P &amp;lt; 0.10) to be less in the three treatment groups while in PC, the greatest concentration of Zn favored a better fecal consistency. The initial serum Zn and Cu concentrations were similar for all dietary treatment groups. After 14 d, serum Zn concentration was significantly greater in PC (15.71 ± 6.25 µg/L, P &amp;lt; 0.05). No differences were highlighted in serum Zn concentration among the other 3 treatment groups. Serum Cu concentrations revealed statistically significant results (P &amp;lt; 0.05) on 14 d after weaning in EU, non-EU+ and non-EU- groups, showing greater concentrations of Cu (17.65 ± 5.49 µmol/L, 17.73± 3.46 µmol/L 18.33 ± 4.13 µmol/L, respectively) compared with PC (11.87 ± 3.60 µmol/L). These results suggested that the EU level of inclusion of both potentiated Zn and monovalent Cu is enough to reach the same Cu and Zn plasma concentrations of non-EU treatments. Plasma DAO was negatively (P &amp;lt; 0.05) affected in non-EU-. Firmicutes and Bacteroidetes were the most abundant phyla in fecal microbiome. Non-EU- contributed to a significant decrease in biodiversity in fecal microbiota as depicted with Shannon for diversity and Simpson for evenness indexes (P &amp;lt; 0.05). In fecal samples, the presence of genera linked to a greater disruption of the gut barrier (Escherichia-Shigella) was depicted in non-EU- group, indicating significant modifications of the microbial community. These results suggest the need for a balanced supplementation of Cu and Zn through more bioavailable sources. The use of potentiated ZnO and Cu2O according to European levels could represent a valid strategy to enhance weanling piglets gut health and to reduce the environmental impact.

Fungi associated with fine roots of Fraxinus excelsior affected by ash dieback detected by next-generation sequencing

AbstractThe decline of European ash by dieback caused by Hymenoscyphus fraxineus together with stem collar necroses and rots caused by various fungi has been investigated intensively during the last years. Nevertheless, hitherto nearly nothing is known about the species diversity of the fungal rhizobiome of ash trees. Here we investigated the fine roots of affected ash trees on 15 sampling sites in 6 federal countries of Germany. Fine-root samples have been treated in three different sample regimes each as root-adhering soil, unsterilized fine roots and sterilized fine roots. The samples of trees in sampling sites were pooled to get an overview of the species-richness in the area. The next-generation sequencing platform Oxford Nanopore MinION was used to sequence the entire ITS of pooled probes. Most abundant phyla in all samples were the Basidiomycota and Ascomycota. Species richness in sterilized roots was significantly different from unsterilized roots and root-adhering soil. Surprisingly most abundant genera in sterilized roots were the genera Mycena, Mycenella and Delicatula, all of them agaricoids with saprophytic lifestyle. Eleven genera of Glomeromycota have been detected in various abundances, whereas the detection of H. fraxineus was neglectable.

PSVI-14 Changes in zinc oxide concentration in feed and effects of probiotic addition to weaning to finishing pig diet by microbiome analysis

Abstract To analyze the implications of dietary zinc oxide (ZnO) with probiotic administration on productivity, fecal index, meat quality characteristics, odorous substances, and microbiome analysis in weaning-finishing pigs, 200 weaned piglets (3 barrows and 2 gilts) were radomly assigned (average body weight = 6.65 ± 0.66 kg) into four treatments with ten repetitions per treatment. The treatments consisted of varying ZnO content (2,500 ppm or 75 ppm) and probiotic percentages (0.1% or 0.3%), as follows: TRT1 (75 ppm ZnO), TRT2 (75 ppm ZnO with 0.3% or 0.1% probiotic), TRT3 (2,500 ppm or 75 ppm ZnO), and TRT4 (2,500 ppm or 75 ppm ZnO with 0.3% or 0.1% probiotic). In comparison with the TRT1 treatment group, the TRT2 and TRT4 treatment groups had greater (P &amp;lt; 0.05) body weight at wk 12, 18, and 22 of the trial and greater (P &amp;lt; 0.05) average daily gain at wk 12, 18, 22, and the overall period (P &amp;lt; 0.05). Additionally, pigs fed ZnO with the probiotic included a diet that reduced (P &amp;lt; 0.05) NH3 and H2S at wk 18 and 22, and CO2 at wk 22, in the TRT2 and TRT4 groups compared with the TRT1 group. However, the fecal score and meat quality exhibited no substantial change (P &amp;gt; 0.05). By incorporating probiotics into the pig diet along with ZnO supplementation, a significant (P &amp;lt; 0.05) increase in alpha diversity and beta diversity, as well as a higher relative abundance of phyla and genera of Firmicutes was found. Furthermore, based on taxonomic analysis, the dietary treatment group (TRT 4) showed a significant (P &amp;lt; 0.05) increase in beneficial bacteria (Prevotella, Lactobacillus) while simultaneously reducing (P &amp;lt; 0.05) pathogenic bacteria (Clostridium_sunsu_strico_1, Campylobacteria, Olsenella) compared with the TRT1 treatment group. An improvement in diversity and expansion of the identified taxonomic groups has been associated with healthier gut health. The results indicated that the effects of ZnO with probiotics on the improvement of performance and reduced gas emissions in pigs may be associated with the modulatory effect on the gut microbiome. In conclusion, the current study provides insights into using decreased ZnO with probiotic inclusion as a novel feeding strategy to improve pig gut health and overall performance.

Blood bacterial microbiota of the Texas tortoise, Gopherus berlandieri, in Tamaulipas, Mexico

The blood bacterial microbiota of the Texas tortoise (Gopherus berlandieri) in Tamaulipas, Mexico, was characterized by next-generation sequencing. In 2019, blood was collected from 6 free-living tortoises. DNA was extracted, the V3-V4 region of the 16S rRNA gene was amplified, and Illumina sequencing was performed. The results showed 9 phyla, 20 classes, 42 orders, 81 families, 176 genera and 299 bacterial species. Firmicutes was the most abundant phylum in the blood of G. berlandieri; this taxon has been recorded as predominant in the intestine, excrement, nasal exudates and saliva of other species of the genus Gopherus. The dominant bacterial genera were Caldalkalibacillus, Anaerobacillus, Nesterenkonia and Bacillus. These taxa have been recorded in alkaline and halophilic soils, such as those found in G. berlandieri burrows. All of these bacterial taxa can enter the bloodstream of G. berlandieri via intestinal, oral and nasal translocation. Likewise, 3 bacterial taxa (Coxiella sp., Ehrlichia sp. and Anaplasma phagocytophilum) that are transmitted by arthropod vectors, as well as the potentially pathogenic Salmonella enterica were recorded. This information is the first bacteriological reference for the blood of G. berlandieri, and is expected to be useful for health and conservation programs.

Sponge-associated microbes in the twilight zone of Curaçao

Mesophotic reefs, located in the "Twilight Zone" of the ocean, are coral reefs that exist in relatively deep waters ranging from approximately 30 to 150 m below the surface. These reefs are situated just beyond the reach of conventional SCUBA diving and are typically explored using advanced diving techniques or with the aid of submersibles. In the present study, we used a state-of-the-art submersible to sample 26 sponge specimens belonging to 11 species. High (HMA) or low (LMA) microbial abundance status was assigned to species based on TEM imagery. Prokaryotic communities associated with these sponges were, furthermore, assessed using high-throughput sequencing. Proteobacteria, Chloroflexi, Actinobacteriota, and Acidobacteriota were the most abundant phyla overall. HMA/LMA status proved to be a highly significant predictor of prokaryotic composition. HMA sponges also tended to be more diverse in terms of richness and evenness than LMA sponges. 14 predictor-classes were identified using an exploratory technique based on machine learning including classes within the phyla Chloroflexi (e.g., Dehalococcoidia and JG30-KF-CM66) and Acidobacteriota (Thermoanaerobaculia and Subgroups 11 and 21). Previous studies have demonstrated the prevalence of the HMA/LMA dichotomy in shallow waters and, recently, the deep sea. Our results demonstrate its prevalence in the mesophotic realm.

Biological Sex Differences in Heat Acclimation and Gut Microbiome Responses

Purpose: Our broad aim was to elucidate the relationship between gut microbiome (gMB) and heat tolerance/acclimation. In this study, we hypothesized that the gMB is affected by acute exercise-heat stress/acclimation and is biologically sex-specific. Methods: Physically active men (M: n=10, 21±2yo, VO2max 51.8±6.6mL−1·kg−1·min−1) and women (W: n=6, 26±5yo, VO2max 45.5±8.0mL−1·kg−1·min−1) completed a modified heat tolerance test (HTT; 65% vVO2max, 2% grade treadmill run, 40°C, 40% relative humidity) until rectal temperature reached 39.5°C (TT39.5) or failure before (preHA) and after (postHA) a 5-day heat acclimation (HA). DNA from stool samples was sequenced via 16S rRNA (V4). a-diversity (Shannon Index) and rarified abundances of phyla, family, and genus were calculated by subsampling to 10,000 reads per sample. Blood inflammation markers were measured with commercially available kits. Significant differences (p≤0.05) were determined by nonparametric analyses for gMB indices and parametric analyses for all other variables were reported as mean ± standard deviation and Z scores for compared groups. Results: All subjects acclimated, but W were more resilient to HTT pre and postHA (preHA TT39.5: 29.14±7.14min (M), 35.02±3.67min (W), p=0.042; postHA TT39.5: 31.11±5.61min (M), 38.13±3.14min (W), p&lt;0.01). gMB changes were observed among all subjects with reductions in Peptostreptococcaceae and Proteobacteria at postHA (vs. preHA, p&lt;0.05). Comparison of W and M revealed marked differences. M had lower (vs. W) Christensenella (Z=-2.119, p=0.034), Erysipelotrichaceae (Z=-2.495, p=0.013) and higher Lactococcus (Z=-2.254, p=0.024), Peptostreptococcaceae (Z=-2.386, p=0.017), Pasteurellaceae(Z=-2.210, p=0.027), and Haemophilus (Z=-2.210, p=0.027) preHA. PostHA, M had lower (v. W) Eggerthella (Z=-2.022, p=0.043), Family XIII (Z=-2.025, p=0.043), Erysipelotrichaceae (Z=-2.061, p=0.039), Oxalobacteraceae (Z=-2.445, p=0.014), and higher Peptostreptococcaceae (Z=-2.173, p=0.030) with no differences in Shannon Index. Biomarkers IL-1β and IFN-γ were increased postHA (v. preHA, p&lt;0.05), but W had distinct I-FABP (decreased v. M, p&lt;0.05) and IFN-γ (increased v. M, p&lt;0.05) responses. Conclusion: gMB changes during heat acclimation include bacteria associated with heat stress responses in previous literature. W and M differ in gMB, acute heat tolerance, and acclimation responses with concomitant sex differences in inflammatory and metabolite markers potentially related to gMB. Ongoing research investigates associations of targets such as Proteobacteria with previous findings related to heat tolerance and acclimation and metabolite patterns in systemic circulation associated with bacterial species significantly affected by HA. DoD BA200299. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Metagenomic Study of Bacteria Diversity and Functional Profile in Bulk and Rhizosphere Soils of Fusarium-Wilt Infected Plantain (Musa paradisiaca)

Soil contains a great diversity of microorganisms, including bacteria which are known to be drivers of soil ecosystem functions. This study was aimed at investigating the bacterial communities in bulk and rhizosphere soil of Fusarium wilt-infected plantain (Musa paradisiaca). Physicochemical analysis revealed that electrical conductivity (312 µS/cm), cation exchange capacity (15.62 meq/100g), phosphate (0.16 mg/kg), nitrogen (1.53 mg/kg), moisture (19.45 mg/kg), potassium (1.39 mg/kg), magnesium (0.61 mg/kg), clay (60 %), and silt (35%) were higher in bulk soil than rhizosphere soil. The 16S rRNA metagenomic sequences quantified a total of 89341 bacterial taxonomic units from bulk soil which consist of 10 phyla, 13 classes, 16 orders, 18 families, 21 genera, and 19 species. A total of 88034 bacterial taxonomic units which comprised of 9 phyla, 13 classes, 23 orders, 22 families, 26 genera, and 25 species, were found in rhizosphere soil. The most abundant phyla in bulk soil are Actinobacteria (31%), Proteobacteria (26%), and Gemmatimonadetes (17%) Acidobacteria (17%) and Planctomycetes (3%) while the prominent phyla in rhizosphere soil are Actinobacteria (63%) Proteobacteria (24%), Acidobacteria (7%) and Planctomycetes (3%). The major functional profiles of bacterial communities in both bulk and rhizosphere soils are metabolism of amino acids, carbohydrates, terpenoids, polyketides, cofactors, and xenobiotic degradation. Alpha diversities among the bacterial community were higher in Simpson’s reciprocal index for both bulk and rhizosphere soils. This study opens up new frontiers in expanding metagenomics studies on environmental samples which would capture and contribute to the identification of soil bacteria useful to ecosystem functions.

Characteristics and health impacts of bioaerosols in animal barns: A comprehensive study

Bioaerosols produced during animal production have potential adverse effects on the health of workers and animals. Our objective was to investigate characteristics, antibiotic-resistance genes (ARGs), and health risks of bioaerosols in various animal barns. Poultry and swine barns had high concentrations of airborne bacteria (11156 and 10917 CFU/m3, respectively). Acinetobacter, Clostridium sensu stricto, Corynebacterium, Pseudomonas, Psychrobacter, Streptococcus, and Staphylococcus were dominant pathogenic bacteria in animal barns, with Firmicutes being the most abundant bacterial phylum. Based on linear discriminant analysis effect size (LEfSe), there were more discriminative biomarkers in cattle barns than in poultry or swine barns, although the latter had the highest abundance of bacterial pathogens and high abundances of ARGs (including tetM, tetO, tetQ, tetW sul1, sul2, ermA, ermB) and intI1). Based on network analyses, there were higher co-occurrence patterns between bacteria and ARGs in bioaerosol from swine barns. Furthermore, in these barns, relative abundance of bacteria in bioaerosol samples was greatly affected by environmental factors, mainly temperature, relative humidity, and concentrations of CO2, NH3, and PM2.5. This study provided novel data regarding airborne bio-contaminants in animal enclosures and an impetus to improve management to reduce potential health impacts on humans and animals.

Gender Impacted Gut Microbiota and Growth Performance in the Blotched Snakehead (Channa maculata).

The blotched snakehead Channa maculata is an important economical freshwater species in East Asia. However, there has been relatively little research conducted on the correlation between gender and gut microbes. In this study, 36 of 1000 blotched snakeheads were randomly selected for growth performance measurement and gut microbiota high-throughput sequencing. Results showed that microbial diversity, composition, and metabolic functions were altered by gender and growth performance except the microbial network. In our study, Proteobacteria were the most abundant phylum, with Fusobacteria showing enrichment in males and Bacteroidetes in females. Notably, phylum Deinococcus-Thermus was identified as a significant biomarker. The Cetobacterium was the most abundant genus-level taxon. Furthermore, gut microbes specializing in the production of gut-healthy substances, such as coenzymes and vitamins, were identified as biomarkers in the fast-growing group. Our investigation highlighted the impact of gender on the composition and abundance of gut microbial biomarkers in both males and females, thereby influencing differential growth performance through the modulation of specific metabolic functions.

Diversity of fungal communities on Cabernet and Aglianico grapes from vineyards located in Southern Italy.

Grape-associated microbial community is influenced by a combination of viticultural, climatic, pedological and anthropological factors, collectively known as terroir. Therefore, grapes of the same cultivar grown in different areas can be appreciated for their distinctive biogeographic characteristics. In our previous study, we showed that the phenotypic response of Aglianico and Cabernet grapevines from Molise and Sicily regions is significantly influenced by the prevailing pedoclimatic conditions, particularly soil physical properties. However, the scale at which microbial communities differ could be important in clarifying the concept of terroir, including whether it is linked to the grape variety present in a particular vineyard. To explore this further, in the research presented here, a comparative study on the fungal communities inhabiting the berry surfaces of Cabernet and Aglianico cultivars was conducted on different vineyards located in Southern Italy (Molise, Sicily and Campania regions, the first two of which had been involved in our previous study) by using high-throughput sequencing (HTS) and multivariate data analysis. The descriptive approach through relative abundance analysis showed the most abundant phyla (Ascomycota, Basidiomycota, and Chytridiomycota), families (Cladosporiaceae, Saccotheciaceae, Pleosporaceae, Saccharomycodaceae, Sporidiobolaceae, Didymellaceae, Filobasidiaceae, Bulleribasidiaceae, and Saccharomycetaceae) and genera (Cladosporium, Aureobasidium, Alternaria, Stemphylium and Filobasidium) detected on grape berries. The multivariate data analysis performed by using different packages (phyloseq, Vegan, mixOmics, microbiomeMarker and ggplot2) highlighted that the variable "vineyard location" significantly affect the fungal community, while the variable "grape variety" has no significant effect. Thus, some taxa are found to be part of specific vineyard ecosystems rather than specific grape varieties, giving additional information on the microbial contribution to wine quality, thanks to the presence of fermentative yeasts or, conversely, to the involvement in negative or detrimental roles, due to the presence of grape-deriving fungi implied in the spoilage of wine or in grapevine pathogenesis. In this connection, the main functions of core taxa fungi, whose role in the vineyard environment is still poorly understood, are also described.

Identification of microbial communities and multi-species biofilms contamination in seafood processing environments with different hygiene conditions

Biofilms formed by spoilage and pathogenic bacteria increase microbial persistence, causing an adverse influence on the quality of seafood. The mono-species biofilms are widely reported, however, the contamination of multi-species biofilms and their matrix in food environments are still not fully understood. Here, we assessed the contamination of multi-species biofilms in three seafood processing environments with different hygiene levels by detecting bacterial number and three biofilm matrix components (carbohydrates, extracellular DNA (eDNA), and proteins). Samples comprising seven food matrix surfaces and eight food processing equipment surfaces were collected from two seafood processing plants (XY and XC) and one seafood market (CC). The results showed that the bacterial counts ranged from 1.89 to 4.91 CFU/cm2 and 5.68 to 9.15 BCE/cm2 in these surfaces by cultivation and real-time PCR, respectively. Six biofilm hotspots were identified, including four in CC and two in XY. Among the three processing environments, the amplicon sequence variants (ASVs) of Proteobacteria, Bacteroidetes, and Actinobacteria decreased with improved processing hygiene, while Firmicutes showed a decrease in the four most abundant phyla. The most prevalent bacteria belonged to genera Psychrobacter, Acinetobacter, and Pseudomonas, demonstrating the significant differences and alteration in bacterial community composition during different environments. From the biofilm hotspots, 15 isolates with strong biofilm forming ability were identified, including 7 Pseudomonas, 7 Acinetobacter, and 1 Psychrobacter. The Pseudomonas isolates exhibited the highest production of EPS components and three strong motilities, whose characteristics were positively correlated. Thus, this study verified the presence of multi-species biofilms in seafood processing environments, offering preliminary insights into the diversity of microbial communities during processing. It highlights potential contamination sources and emphasizes the importance of understanding biofilms composition to control biofilms formation in seafood processing environments.

Gut microbiota and its relationship with early vascular ageing in a Spanish population (MIVAS study).

Gut microbiota and its by-products are increasingly recognized as having a decisive role in cardiovascular diseases. The aim is to study the relationship between gut microbiota and early vascular ageing (EVA). A cross-sectional study was developed in Salamanca (Spain) in which 180 subjects aged 45-74 years were recruited. EVA was defined by the presence of at least one of the following: carotid-femoral pulse wave velocity (cf-PWV), cardio-ankle vascular index (CAVI) or brachial-ankle pulse wave velocity (ba-PWV) above the 90th percentile of the reference population. All other cases were considered normal vascular ageing (NVA). cf-PWV was measured by SphygmoCor® System; CAVI and ba-PWV were determined by Vasera 2000® device. Gut microbiome composition in faecal samples was determined by 16S rRNA Illumina sequencing. Mean age was 64.4 ± 6.9 in EVA group and 60.4 ± 7.6 years in NVA (p < .01). Women in EVA group were 41% and 53% in NVA. There were no differences in the overall composition of gut microbiota between the two groups when evaluating Firmicutes/Bacteriodetes ratio, alfa diversity (Shannon Index) and beta diversity (Bray-Curtis). Bilophila, Faecalibacterium sp.UBA1819 and Phocea, are increased in EVA group. While Cedecea, Lactococcus, Pseudomonas, Succiniclasticum and Dielma exist in lower abundance. In logistic regression analysis, Bilophila (OR: 1.71, 95% CI: 1.12-2.6, p = .013) remained significant. In the studied Spanish population, early vascular ageing is positively associated with gut microbiota abundance of the genus Bilophila. No relationship was found between phyla abundance and measures of diversity.

Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand.

Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.

A Baseline Study of Bacterial Pathogens in Greywater Samples in Jordan Using Ribotyping

As Jordan advances in an attempt to promote greywater reuse, it is important to investigate the composition of bacteria in these new sources. To evaluate the presence of enteric pathogens in greywater, a pilot study investigating enteric pathogens in household washing machines and kitchen sink effluents from residential premises was conducted. In the culture-dependent method, bacteria were identified after using Sanger sequencing of 16S rRNA. Bacteria in the phylum Proteobacteria have been found to be the most abundant phyla, which may indicate that they play an important environmental role and might be representative of adaptation to different environments. Klebsiella sp. and Pseudomonas sp. were the two major genera found in this study and accounted for 78.57% of the total isolates. This is the first investigation of enteric pathogens in household washing machines and kitchen sink effluents in Jordan. To my knowledge, no study has identified the microbial hazards associated with greywater reuse in Jordan yet. Additional research with more adequate methodology is needed to assist our findings.