Abundant Phyla Research Articles

The Rumen Microbiome Composition of Raramuri Criollo and European Cattle in an Extensive System

Understanding the relationship between Raramuri Criollo cattle (RC) and their microbial ruminal ecosystem will help identify advantageous characteristics of adapted cattle as alternatives to achieve sustainable beef production systems. Our objective was to characterize the rumen microbiome of RC in comparison to Angus and Hereford breeds (European, E) and the cross between them (E × RC). Ruminal fluid was collected from 63 cows in their second productive cycle after grazing in the same paddock for 45 d, in the dry (n = 28) and rain (n = 35) seasons. DNA from ruminal fluid was isolated for 16s rRNA gene next-generation sequencing. The data were analyzed with QIIME2 and compared against the SILVA 16s rRNA database. Beta diversity was different (p < 0.05) between RC and E in both seasons. A microbial core was represented by the most abundant phyla. Planctomycetes and Spirochaetes represented above 1% in the rain season and below 1% in the dry one, whereas Euryarchaeota was below 1% and around 3%, respectively. LEfSe analysis identified differentiated (p < 0.05) key microbial groups that explain the differences between lineages at different taxonomic levels, reflecting the ability of the rumen ecosystem of RC cattle to adapt to hostile environmental conditions by having microbial groups specialized in the degradation of highly fibrous content.

The effect of environmental and anthropogenic factors on the microbiome of the sponge, Halichondria panicea, at three coastal sites with different bathing water quality in North east England

The breadcrumb sponge, Halichondria panicea, is a cosmopolitan marine species. Life functions, such as feeding, metabolism and defence, are maintained through microbial symbiosis. As such, perturbations to the symbiotic balance can be expected to affect the health and survival of the sponge. Although generally tolerant of environmental variables, such as temperature, pH and salinity, responses to anthropogenic factors are poorly understood. In this study, the microbial community of the H. panicea was examined over the course of 1 year. Sponge and seawater samples were collected in January, April, July and October 2022, from three locations with different levels of bathing water quality, according to the UK’s Environment Agency. Samples were sequenced using the 16S ribosomal RNA (rRNA) gene, and amplicon sequence variants (ASVs) were inferred from the generated data. Differences in bacterial diversity and abundance among sponge samples from the three locations were examined. A correlation test was used to study the effect of physical and chemical environmental factors along with faecal indicator bacteria on the abundance of the top ten most abundant bacterial phyla. Environmental factors (determined from seawater physicochemical properties) and pollution (determined from trace metals, nutrients and faecal bacteria levels) were found to play an important role in shaping the microbial community of this sponge. The sponge microbiome showed a noticeable seasonal shift, with some species flourishing in January and others emerging in April, notably the faecal and coliform bacteria. Sponge microbiomes from sites with poor-quality bathing water were generally less diverse and had lower microbial abundance, resulting in a greater range of intra-species dispersion than those of sponges living in excellent–good quality waters.

Impact of Triclosan on Bacterial Biodiversity and Sediment Enzymes - A Microcosm Study.

Triclosan (TCS), a widely used antimicrobial biocide, has raised serious concern among the scientific community in recent years owing to its ubiquitous presence around the globe and toxicity to aquatic organisms. The current study investigated the alterations in bacterial diversity, nutrients, and sediment enzyme activity in TCS-exposed sediment. TCS concentrations of 3mg/L (T1) and 6mg/L (T2) were applied in a microcosm setup for 28 days to sediment collected from Versova Creek, Mumbai. Among sediment enzymes, dehydrogenase activity exhibited the greatest degree of variability in 3mg/L exposed sediment. Nitrite, total nitrogen and urease exhibited higher concentrations in 6mg/L TCS exposed sediment. The concentration of ammonia was observed to be decreasing in treatments exposed to 6mg/L TCS. Total heterotrophic bacteria exhibited an increase in count in T1 and a decrease in T2. Metagenomics data showed a higher relative abundance of bacteria in T1 compared to T2 on the 28th day of sampling. Proteobacteria was found to be the most abundant phylum in all samples, and their relative abundance was reduced by 0.14% in T1 and 5.48% in T2. The results confirm the alterations in the composition of sediment bacterial communities and their enzymatic activities due to TCS exposure.

New insights into the spatial variability of microbial diversity and density in peatlands exposed to various electron acceptors with an emphasis on methanogenesis and CO2 fluxes.

Peatlands are vital in the global carbon cycle, acting as significant sinks for carbon and releasing methane (CH4) and carbon dioxide (CO2) into the atmosphere. However, the complex interactions between environmental factors and the microbial communities responsible for these greenhouse gas emissions remain insufficiently understood. To address this knowledge gap, a pilot-scale mesocosm study was conducted to assess the impact of different terminal electron acceptors (TEAs), including sulfate (SO4 2-), humic acid (HA), and goethite, on CH4 and CO2 emissions and microbial community structures in peatlands. Our results revealed that the addition of TEAs significantly altered the CH4 and CO2 emissions. Specifically, the addition of SO4 2- nearly doubled CO2 production while substantially inhibiting CH4 emissions. The combined addition of SO4 2- and HA, as well as HA alone, followed a similar pattern, albeit with less pronounced effects on CH4. Goethite addition resulted in the highest inhibition of CH4 among all treatments but did not significantly increase CO2 production. Community composition and network analysis indicated that TEAs primarily determined the structure of microbial communities, with each treatment exhibiting distinct taxa networks. Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes were the most abundant phyla across all mesocosms. The presence of methanotrophs, including Methylomirabilales and Methylococcales, was linked to the inhibition of CH4 emissions in these mesocosms. This study provides novel insights into the spatial variability of microbial diversity and density in peatlands under various TEAs, emphasizing the role of methanogenesis and CO2 fluxes in carbon cycling. Our findings enhance the understanding of carbon cycling in microbe-rich environments exposed to TEAs and highlight the potential for future studies to investigate the long-term effects of TEAs on microbial communities, enzymes, and carbon storage.

Effects of Intercropping of Sisal and Three Different Leguminous Plants on Soil Bacterial Diversity

Intercropping is widely utilised in agricultural production to enhance land use efficiency because of its benefits, such as heightened crop productivity and optimised resource utilisation. We investigated the effects of Pinto peanut/sisal (HST), Stylo/sisal (strT) and Grona styracifolia/sisal (JqT) intercropping systems on soil bacterial communities compared with sisal continuous cropping (CK) by using Illumina MiSeq high-throughput sequencing technology. The intercropping system significantly increased the total nitrogen (TN), soil pH and soil moisture levels and decreased the levels of available phosphorus (AP) and available potassium (AK). Minimal variations were observed in Shannon’s and Simpson’s diversity indices between the monoculture and intercropping systems as well as among different intercropping systems. The most abundant phyla observed within the four groups were Proteobacteria, Acidobacteria, Cyanobacteria and Bacteroidetes. At the phylum level, the relative abundances of Proteobacteria, Acidobacteria, Cyanobacteria and Bacteroidetes were 37.37–54.35%, 10.54–21.21%, 3.46–20.43% and 2.15–5.67%, respectively. Compared with ZCK, StrT, JqT and HST treatments led to higher abundance of Cyanobacteria (from 3.46% to 20.43%, 11.37% and 16.58%, respectively) and Bacteroidetes (from 2.15% to 5.67%, 5.21% and 5.10%, respectively). The results of the linear discriminant analysis of effect sizes demonstrated notable variations in the relative abundance of bacterial taxa among various intercropping systems. The dominant categories of the genus in strT and JqT groups were Blastocatellia and Blastocatellaceae-Subgroup4, while Firmicutes was the dominant category of the genus in the HST group. The structure of bacterial communities did not vary between intercropping and monoculture systems. The findings indicated that the impact of the intercropping system on the bacterial community structure was not contingent on the specific intercropping patterns employed.

Biotechnological potential in agriculture of soil Antarctic microorganisms revealed by omics approach.

The biotechnological potential for agricultural applications in the soil in the thawing process on Whalers Bay, Deception Island, Antarctica was evaluated using a metagenomic approach through high-throughput sequencing. Approximately 22.70% of the sequences were affiliated to the phyla of the Bacteria dominion, followed by 0.26% to the Eukarya. Proteobacteria (Bacteria) and Ascomycota (Fungi) were the most abundant phyla. Thirty-two and thirty-six bacterial and fungal genera associated with agricultural biotechnological applications were observed. Streptomyces and Pythium were the most abundant genera related to the Bacteria and Oomycota, respectively. The main agricultural application associated with bacteria was nitrogen affixation; in contrast for fungi, was associated with phytopathogenic capabilities. The present study showed the need to use metagenomic technology to understand the dynamics and possible metabolic pathways associated with the microbial communities present in the soil sample in the process of thawing recovered from the Antarctic continent, which presented potential application in processes of agro-industrial interest.

ASSOCIATIONS BETWEEN PRE- AND POST-NATAL EXPOSURE TO PHTHALATE AND DINCH METABOLITES AND GUT MICROBIOTA IN ONE-YEAR OLD CHILDREN

The gut microbiota is a collection of symbiotic microorganisms in the gastrointestinal tract. Its sensitivity to chemicals with widespread exposure, such as phthalates, is little known. We aimed to investigate the impact of perinatal exposure to phthalates on the infant gut microbiota at 12 months of age. Within SEPAGES cohort (Suivi de l’Exposition à la Pollution Atmosphérique durant la Grossesse et Effet sur la Santé), we assessed 13 phthalate metabolites and 2 di(isononyl) cyclohexane-1,2-dicarboxylate (DINCH) metabolites in repeated urine samples collected in pregnant women and their offspring. We obtained stool samples from 356 children at 12 months of age and sequenced the V3-V4 region of the 16S rRNA gene, allowing gut bacterial profiling. We used single-chemical (linear regressions) and mixture (BKMR, Bayesian Kernel Machine Regression) models to examine associations of phthalates and DINCH metabolites, with gut microbiota indices of α-diversity (specific richness and Shannon diversity) and the relative abundances of the most abundant microbiota phyla and genera. After correction for multiple testing, di(2-ethylhexyl) phthalate (ΣDEHP), diethyl phthalate (DEP) and bis(2-propylheptyl) phthalate (DPHP) metabolites 12-month urinary concentrations were associated with higher Shannon α-diversity of the child gut microbiota in single-chemical models. The multiple-chemical model (BKMR) suggested higher α-diversity with exposure to the phthalate mixture at 12 months, driven by the same phthalates. There were no associations between phthalate and DINCH exposure biomarkers at other time points and α-diversity after correction for multiple testing. ΣDEHP metabolites concentration at 12 months was associated with higher Coprococcus genus. Finally, ΣDEHP exposure at 12 months tended to be associated with higher phylum Firmicutes, an association not maintained after correction for multiple testing. Infancy exposure to phthalate might disrupt children’s gut microbiota. The observed associations were cross-sectional, so that reverse causality cannot be excluded.

Characterization of the oral mycobiome of Portuguese with allergic rhinitis and asthma

Allergic rhinitis and asthma are two prevailing chronic airway diseases and serious public health concerns. Previous research has already described the role of the airway bacteriome in these two diseases, but almost no study so far has explored the mycobiome and its possible association to airway inflammation. Here we sequenced the internal transcribed spacers (ITS) 1 and 2 to characterize the oral mycobiome of 349 Portuguese children and young adults with allergic rhinitis alone (AR) or with asthma (ARAS), asthmatics (AS) and healthy controls (HC). Our genomic analyses showed that the two most abundant fungal phyla (Ascomycota and Basidiomycota) and 3-5 of the 14 most abundant fungal genera (Cladosporium, Aspergillus, Aleurina, Candida and Rhodotorula) in the mouth differed significantly (P≤0.04) between both rhinitic groups and HC. However, none of the same taxa varied significantly between the three respiratory disease groups (AR, ARAS and AS). The oral mycobiomes of respiratory ill patients showed the highest intra-group diversity (microbial richness and evenness), while HC showed the lowest, with all alpha-diversity indices varying significantly (P≤0.0424) between them. Similarly, all disease groups showed significant differences (P≤ 0.0052) in microbial structure (i.e., beta-diversity indices) when compared to HC samples. Thirty metabolic pathways (PICRUSt2) were differentially abundant (Wald's test) between AR or ARAS and HC patients, but only one of them (D-galactose degradation I) was over abundant (log2 Fold Change >0.75) in the ARAS group. Spiec-Easi fungal networks varied greatly among groups, which suggests chronic respiratory allergic diseases may alter fungal connectivity in the mouth. This study increases our comprehension of the role of the oral mycobiome in allergy-related conditions. It shows for the first time that the oral mycobiota changes during health and allergic rhinitis (with and without asthma comorbidity) and highlights specific taxa, metabolic pathways and fungal interactions that may relate to chronic airway disease.

Metagenome sequencing and 982 microbial genomes from Kermadec and Diamantina Trenches sediments

Deep-sea trenches representing an intriguing ecosystem for exploring the survival and evolutionary strategies of microbial communities in the highly specialized deep-sea environments. Here, 29 metagenomes were obtained from sediment samples collected from Kermadec and Diamantina trenches. Notably, those samples covered a varying sampling depths (from 5321 m to 9415 m) and distinct layers within the sediment itself (from 0~40 cm in Kermadec trench and 0~24 cm in Diamantina trench). Through metagenomic binning process, we reconstructed 982 metagenome assembled genomes (MAGs) with completeness >60% and contamination <5%. Within them, completeness of 351 MAGs were >90%, while an additional 331 were >80%. Phylogenomic analysis for the MAGs revealed nearly all of them were distantly related to known cultivated isolates. The abundant bacterial MAGs affiliated to phyla of Proteobacteria, Planctomycetota, Nitrospirota, Acidobacteriota, Actinobacteriota, and Chlorofexota, while the abundant archaeal phyla affiliated with Nanoarchaeota and Thermoproteota. These results provide a dataset available for further interrogation of diversity, distribution and ecological function of deep-sea microbes existed in the trenches.

The genetic composition of Anopheles mosquitoes and the diverse population of gut-microbiota within the Anopheles subpictus and Anopheles vagus mosquitoes in Tamil Nadu, India.

In recent days, in tropical and subtropical regions, secondary vectors of Anopheles mosquitoes are becoming more important in transmitting diseases to humans as primary vectors. Various molecular techniques have separated closely related Anopheles subpictus and Anopheles vagus mosquitoes based on their diversity with other mosquito species. Despite their widespread distribution, the An. subpictus and An. vagus mosquitoes, which carry Plasmodium in their salivary glands, were not considered primary malaria vectors in India. An. vagus mosquitoes are zoophilic and physically similar to An. subpictus. We intend to identify An. subpictus and An. vagus mosquito's sister species based on their Interspaced Transcribed Region-2 (ITS2). We isolated the midgut gDNA from each mosquito and used ITS2-PCR and Sanger sequencing to characterize the mosquito species. BioEdit software aligned the sequences, and MEGA7 built a phylogenetic tree from them. According to this study, the information gathered from these mosquito samples fits the An. subpictus species A form and the An. vagus Indian form. Furthermore, gut microbiome plays an important role in providing nutrients, immunity, and food processing, whereas mosquitoes' midgut microbiota changes their hosts and spreads illnesses. So, we used the Illumina sequencer to look at the gut microbiome diversity of An. subpictus and An. vagus mosquitoes using 16S rRNA-based metagenomic sequencing. Both mosquito species had an abundant phylum of Pseudomonadota (Proteobacteria), Bacillota, Bacteroidota, and Actinomycetota in their gut microbiomes. Notably, both mosquito species had the genus Serratia in their gut. In the subpictus midgut, the genus of Haematosprillum bacteria was dominant, whereas in the vagus mosquito, the genus of Salmonella was dominant. Notably, current research has observed the Sodalis spp. Bacterial genus for the first time.

The Marine-Origin Exopolysaccharide-Producing Bacteria Micrococcus Antarcticus HZ Inhibits Pb Uptake in Pakchoi (Brassica chinensis L.) and Affects Rhizosphere Microbial Communities.

Exopolysaccharides (EPSs) produced by microorganisms play an important role in biotolerance and reducing heavy metal (HM) contamination by limiting the migration of HMs into plants. However, research on the application of EPS-producing marine bacteria for soil heavy metal remediation remains limited, particularly regarding their mechanisms of HM immobilization in soil and impact on plant growth. In this study, the EPS-producing marine bacterium Micrococcus antarcticus HZ was investigated for its ability to immobilize Pb and produce EPSs in soil filtrate. The effects on the growth quality and biomass of pakchoi (Brassica chinensis L.), as well as bacterial communities in inter-root soil contaminated with Pb, were also investigated. The results indicated that HZ could reduce the Pb concentration in the soil filtrate, achieving a removal rate of 43.25-63.5%. The EPS content and pH levels increased in the presence of Pb. Pot experiments showed that adding HZ significantly increased the biomass of pakchoi (9.45-14.69%), vitamin C (Vc) (9.69-12.92%), and soluble protein content (22.58-49.7%). HZ reduced the Pb content in the roots (17.52-47.48%) and leaves (edible tissues) (43.82-52.83%) of pakchoi. HZ increased soil enzyme activities (alkaline phosphatase, dehydrogenase, and urease), and the contents of ammonium nitrogen and nitrate nitrogen. Additionally, HZ also increased the relative abundance of beneficial bacteria (e.g., Proteobacteria, Cyanobacteria, and Chlorobacteria) in the inter-root soil, which have prophylactic and heavy-metal fixation functions. In summary, HZ reduces effective Pb content in edible tissues, roots, and inter-root soil by regulating inter-root soil microbial community structure, increasing soil pH, nitrogen content, and soil enzyme activity, and altering dominant phylum abundance.

Tetracycline and quinolone contamination mediate microbial and antibiotic resistant gene composition in epiphytic biofilms of mesocosmic wetlands

The fate and ecological impact of antibiotics on aquatic ecosystems have not been properly elucidated in mesocosm wetlands scale. This study explored how tetracyclines (TCs, including tetracycline TC and oxytetracycline) and fluoroquinolones (QNs, including ciprofloxacin CIP and levofloxacin) affect mesocosm wetlands vegetated by V. spiralis, focusing on their impact on epiphytic biofilm microbial communities and antibiotic resistance genes (ARGs). Results showed that submerged plants absorbed more antibiotics than sediment. Both TCs and QNs disrupted microbial communities in different ways and increased eukaryotic community diversity in a concentration-dependent manner (2-4 mg/L for CIP, 4-8 mg/L for TC). TCs mainly inhibited epiphytic bacteria, while CIP increased bacterial phyla abundance. TC reduced Cyanobacteriota, Acidobacteriota, and Patescibacteria but increased Bacillota, Bacteroidota, and Armatimonadota. In contrast, CIP reduced Bacteroidota, Cyanobacteriota, and Gemmatimonadota but increased Bacillota, Planctomycetota, and Acidobacteriota. Significant differences in ARG profiles were observed between QNs and TCs, with TCs having a more substantial effect on ARGs due to their stronger impact on bacterial communities. Both antibiotics raised ARG levels with higher concentrations, particularly for multidrug resistance, tetracyclines, trimethoprim, sulfonamides, aminoglycosides, and fosfomycin, emphasizing their role in antimicrobial resistance. The study suggests that antibiotics can either stimulate or inhibit ARGs depending on their effects on bacterial communities. This study provides key evidence on the ecological mechanisms underlying the impact of TCs and QNs on epiphytic microbes of mesocosm wetlands.

Analysis of the gut microbiota and fecal metabolites in people living with HIV.

The gut microbiome has a pivotal function in human immunodeficiency virus (HIV). However, the associated alterations in the gut microbiome-host interaction are unknown. Herein, we aimed to investigate the gut microbiota and fecal metabolites in people living with HIV (PLWH). We collected stool samples from 70 PLWH and 34 healthy controls (HCs) and carried out 16S rRNA gene sequencing and analyzed the metabolites using liquid chromatography-mass spectrometry. Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota were the most abundant phyla in both groups. Among genera, the level of Escherichia-Shigella was upregulated significantly in the PLWH group, whereas in the HC group, Bacteroides spp. were upregulated. Prediction of microbial function indicated significant reductions in alanine, aspartate, glutamate, and histidine metabolism. Furthermore, a comparison of the fecal metabolites between the HC and PLWH groups identified 38 differentially abundant metabolites in four differentially enriched human metabolic pathways. According to Spearman correlation analysis, there are close relationships between four differentially abundant microbiota members and five differentially abundant fecal metabolites, which might influence particular human metabolic pathways. Our findings provide a basis for further experimental investigation of the contribution of the gut microbiota and its associated metabolites to HIV/AIDS, providing a novel perspective for the further study of HIV/AIDS.IMPORTANCEGrowing evidence demonstrates that the gut microbiota is associated with HIV. This study investigated changes in the gut microbiota and fecal metabolites in PLWH. We identified 38 differentially abundant metabolites in four differentially enriched human metabolic pathways. Moreover, close relationships were noted between the four differentially abundant microbiota members and five differentially abundant fecal metabolites, which might influence particular human metabolic pathways. Thus, to benefit PLWH, potential pathobionts could be reduced (e.g., g_Enterococcus); probiotics could be increased (e.g., g_Faecalibacterium and g_Agathobacter); or certain metabolites (e.g., N-acetyl-L-phenylalanine and trehalose) could be reduced by changes in diet or the use of nutritional supplements. Our results provide insights into the interaction between the gut microbiota and the host, identifying possible targets that might be beneficial for PLWH.

Impact of a Potent Strain of Plant Growth-Promoting Bacteria (PGPB), Bacillus subtilis S1 on Bacterial Community Composition, Enzymatic Activity, and Nitrogen Content in Cucumber Rhizosphere Soils.

Antagonistic bacterial strains from Bacillus spp. have been widely studied and utilized in the biocontrol of phytopathogens and the promotion of plant growth, but their impacts on the rhizosphere microecology when applied to crop plants are unclear. Herein, the effects of applying the antagonistic bacterium Bacillus subtilis S1 as a biofertilizer on the rhizosphere microecology of cucumbers were investigated. In a pot experiment on cucumber seedlings inoculated with S1, 3124 bacterial operational taxonomic units (OTUs) were obtained from the rhizosphere soils using high-throughput sequencing of 16S rRNA gene amplicons, and the most abundant phylum was Proteobacteria that accounted for 49.48% in the bacterial community. S1 treatment significantly reduced the abundances of soil bacterial taxa during a period of approximately 30days but did not affect bacterial diversity in the rhizosphere soils of cucumbers. The enzymatic activities of soil nitrite reductase (S-Nir) and dehydrogenase (S-DHA) were significantly increased after S1 fertilization. However, the activities of soil urease (S-UE), cellulase (S-CL), and sucrase (S-SC) were significantly reduced compared to the control group. Additionally, the ammonium- and nitrate-nitrogen contents of S1-treated soil samples were significantly lower than those of the control group. S1 fertilization reshaped the rhizosphere soil bacterial community of cucumber plants. The S-CL activity and nitrate-nitrogen content in rhizosphere soil affected by S1 inoculation play important roles in altering the abundance of rhizosphere soil microbiota.

Characteristics of Semiconducting Minerals Affects Microbial Communities in Purple Soils

Purple soil is rich in semiconducting minerals, but the impact of these minerals on soil properties and associated microbiome assemblages has received little attention. To better understand the influence of semiconducting minerals in soils, samples were collected from 4 soil classifications, including purple soil, siltstone, farmland, and new formed soil. Goethite was the main semiconducting mineral in purple soil followed by rutile and birnessite, while for siltstone, rutile was the major semiconducting mineral. Proteobacteria (77.77–98.56%) was the most prevalent phylum among all samples, with the second most abundant phylum being Cyanobacteria (purple soil and farmland) and Firmicutes (siltstone and new formed soil). According to the average path length in network analysis, purple soil showed higher species segregation, which suggested purple soil was potentially more susceptible to external interference than the other types. The relationship between microbes may be synergistic due to the positive links between microbial phyla. Rutile affected microbial composition to the greatest extent, accounting for 13.66% of the total variation in microbial assembly, while goethite (r= –0.0947) and birnessite (r = 0.0215) content were also associated with changes in microbial composition. These results demonstrated that semiconducting minerals affected the structure and potential energy utilization of soil microbial communities.

PSX-14 Effect of starch supplementation on rumen bacterial abundance in Bos taurus taurus steers consuming low-quality forage

Abstract Low-quality forage provides a limited supply of ruminally available nitrogen and is generally resistant to digestion, inhibiting microbial growth in the rumen and ultimately decreasing forage utilization. Supplementation with protein is well documented to increase forage utilization by promoting microbial growth. Even when protein requirements are met, additional energy, often provided as starch, may be required to meet performance expectations. The objective of this study was to evaluate the effect of increasing starch supplementation on rumen bacterial populations in Bos taurus taurus steers supplemented protein and consuming low-quality forage. Ruminal samples were collected from ruminally-cannulated Angus steers [n = 5; body weight (BW) = 375 ± 45 kg] used in a 4 × 4 Latin square fed a basal diet of King Ranch Bluestem Hay (3.5% CP, 73% NDF) ad libitum, and supplemented with one of four isonitrogenous (130 mg N/kg BW) supplements with increasing starch (2% starch = 100% soybean meal; 20% starch = 73% soybean meal, 26.2% corn, 0.8% urea; 38% starch = 47% soybean meal, 51.6% corn, 1.4% urea; 56% starch = 19% soybean meal, 78.6% corn, 2.4% urea). Rumen content samples were collected via rumen cannula 4 h after supplementation and immediately frozen. Microbial DNA was extracted; full length 16S rRNA amplicon libraries were prepared using Kinnex kits and sequenced on the PacBio Revio platform. Reads were analyzed using DADA2 and QIIME2. Statistical analysis was performed with the GLIMMIX procedure of SAS 9.4 (SAS Inst. Inc., Cary, NC). Firmicutes and Bacteriodata were the most abundant phyla in all treatments (82% and 11%, respectively), and were not affected by starch supplementation (P ≥ 0.45). Actinobacteriota and Euryarchaeota abundance responded quadratically (P &amp;lt; 0.01) to increasing starch provision. Christensenellaceae R-7 group, Rikenellaceae RC9 gut group, Lachnospiraceae XPB1014 group, Butyrvibrio, Lachnospiraceae NK3A20 group, and Prevotella represented the most abundant genera for all treatments. Increasing supplemental starch resulted in a quadratic response (P &amp;lt; 0.01) for abundance of Christensenellaceae R-7 and Lachnospiraceae XPB1014 groups. Relative abundance of Butyrvibrio was 4.05% for steers fed 2% starch supplement and increased to 18.24 and 11.85% for 20 and 38% starch, respectively and then decreased to 4.34% for steers fed 56% starch supplement (quadratic, P &amp;lt; 0.01) Abundance of Pseudobutyrvibrio followed a similar but less dramatic pattern (quadratic, P &amp;lt; 0.01). In contrast, abundance of Streptococcus and Methanobrevibacter decreased with the first two levels of starch and then increased with 56% (quadratic; P &amp;lt; 0.01). In conclusion, responses to the first two increments of starch supplementation suggest increased fibrolytic and decreased methanogenic activity. These results are supported by the previously reported increase in TDOMI for 20 and 38% starch 49.0 and 48.2 g/kg MBW, respectively versus 45.7 and 44.3 g/kg MBW for 2 and 56%, respectively.

PSX-15 Effect of starch supplementation on rumen bacterial abundance in Bos taurus indicus steers consuming low-quality forage

Abstract Deficient ruminally available nitrogen caused by a basal diet of low-quality forage can limit microbial growth in the rumen and decrease forage utilization. Protein supplementation is well-documented to improve forage digestibility and performance. Additionally, starch has been evaluated to increase energy supply to grazing cattle when the forage cannot support adequate levels of production. However, most research in this area has been conducted in Bos taurus taurus, especially the response of the rumen microbiome to supplementation. Accordingly, the objective of this study was to evaluate the effects of increasing starch supplementation on rumen bacterial populations in Bos taurus indicus steers supplemented protein and consuming low-quality forage. Ruminal samples were collected from five ruminally-cannulated Brahman steers (BW 420 ± 55 kg) used in a 4×4 Latin square fed a basal diet of King Ranch Bluestem Hay (3.5% CP and 73% NDF) provided ad libitum, and one of four isonitrogenous (130 mg N/kg BW) supplements with increasing levels of starch (2% starch= 100% soybean meal; 20% starch= 73% soybean meal, 26.2% corn, 0.8% urea; 38% starch = 47% soybean meal, 51.6% corn, 1.4% urea; 56% starch= 19% soybean meal, 78.6% corn, 2.4% urea). Rumen content samples were collected via rumen cannula at 4h post-feeding. Microbial DNA was extracted; full length 16S rRNA amplicon libraries were prepared using Kinnex kits and then sequenced on the PacBio Revio platform. Reads were analyzed using DADA2 and QIIME2. Statistical analysis was performed with the GLIMMIX procedure of SAS 9.4 (SAS Inst. Inc., Cary, NC). Firmicutes, Bacteroidata, Actinobacteriota, Verrucomicrobiota, and Euryarchaeota were the most abundant phyla in all treatments (83, 10, 3, 0.4, and 1%, respectively), and were not affected by treatment (P ≥ 0.10). Christensenellaceae R-7 group, Rikenellaceae RC9 gut group, Lachnospiraceae-XPB1014-group, Butyrvibrio, Lachnospiraceae-NK3A20-group, and Prevotella represented the most abundant genera for all treatments (7, 5, 11, 9, 7, and 3%, respectively). Lachnospiraceae-XPB1014-group and Lachnospiraceae-NK3A20-group responded quadratically (P ≤ 0.02) to increasing starch with decreased abundance for the 20% and 38% starch supplement. Comparatively, relative abundance of Butyrvibrio responded quadratically (P &amp;lt; 0.01) with increased abundance in the 20% and 38% starch supplement. Pseudobutyrvibrio increased with supplementation of 20% starch and then decreased as starch supplementation increased (quadratic, P = 0.04). In conclusion, supplementation of starch elicited changes in microbial relative abundance at the genus level with the response in Butyrivibrio suggesting greater fibrolytic activity. Forage and total digestible NDF intake in these steers decreased with increased starch supplementation; however, TDOMI was not affected by starch provision.

PSVI-5 Bacteriophage biocontrol of avian pathogenic Escherichia coli in laying hens does not produce collateral effects on the cecal microbiota

Abstract Bacteriophages have shown promise as an alternative to antibiotics for managing or preventing avian pathogenic Escherichia coli (APEC) in the egg industry. In a previous study, a phage cocktail comprising 3 virulent phages was shown to prevent APEC infections in laying hens. The aim of this study was to investigate whether orally and intramuscularly administered phages affect the intestinal barrier function of chickens, with a focus on cecal microbiome. In a 4-d trial, a total of 35 laying hens were randomly assigned to one of four treatment groups: 1) Medium control group (bacterial broth + phage buffer), 2) APEC only control (APEC + buffer); 3) IM group (Phage +APEC), or 4) DW group (phage in drinking water (4 d prior to APEC + APEC). Cecum samples were subjected to 16S rRNA gene sequencing targeting the V4 region to assess the effects of phages on cecal bacterial diversity. A 1-way ANOVA was used to evaluate alpha diversity with respect to treatment and time. Microbial community structure was analyzed using β-dispersion and permutational multivariate analysis of variance (PERMANOVA) to determine the effect of each treatment. Significant (P &amp;lt; 0.05) differentially abundant genera were identified with DESeq2 by fitting a negative binomial model to each treatment vs treatment comparison (“~Treatment”). Across the treatment and control groups, 13 phyla were identified. Firmicutes (53.81%), Bacteroidota (23.83%), Actinobacteriota (1.84%), and Proteobacteria (1.02%) were the most abundant phyla among the amplicon sequence variants (ASVs), with 18.39% being unclassified. Neither richness (P = 0.448) nor Shannon diversity (P = 0.687) exhibited significance in α- diversity metric between treatment and control groups. β-dispersion analysis showed no significant difference (P = 0.239) between treatment and control groups, indicating similar bacterial variability among groups. Moreover, the β-diversity representing microbiota structure was not affected by any phage treatment (P = 0.083). In each treatment group, 76 unique genera were identified, with Megamonas (15.80 %), Lactobacillus (8.76%), Faecalibacterium (7.70 %), Megasphaera (1.58%), Alloprevotella (1.54%), [Ruminococcus] torques group (1.29%), Prevotellaceae UCG-001 (1.14%), Bifidobacterium (1.04%), and Olsenella (0.48%) being the most abundant. Notably, Lactobacillus was more abundant (~ 10 to 20%) in medium control group compared with phage treated and APEC only treatment groups. Furthermore, gene expression profiles of various genera (pairwise) were analyzed using log2 fold change (log2FC), revealing differences (P &amp;lt; 0.05) between control and treatment groups for a total of 58 genera. It was concluded that bacteriophage selectively killed APEC population without comprising the population and structure of cecal microbiome in laying hens.

PSLBI-13 Characterizing the seminal microbiota in mature rams managed on divergent planes of nutrition, and in their male offspring

Abstract Increasing evidence suggests that the bovine semen harbors commensal microbiota, and it may be important in male fertility. However, much is unknown regarding the seminal microbiota, its evolution and factors shaping this community in sheep. The objective of this study was to evaluate whether managing the rams on divergent planes of nutrition can influence the seminal microbiota in mature rams and their male offspring. For this, Rambouillet rams (n = 24; 1.5 to 4 yr old) were randomly assigned to one of three groups: 1) a positive plane of nutrition [target 12% gain in their initial body weight (BW; POS, n = 8); 2) a maintenance [maintain the initial BW (MNT, n = 8)]; and 3) a negative [target a 12% reduction in BW (NEG; n = 8)] plane of nutrition over 84 d. The rams were individually housed and fed a common diet, and feed allocations were adjusted weekly. Following the 84-d feeding period, these rams were used to breed 240 mature Rambouillet ewes (1:10 ram:ewe ratio) over 28 d of breeding. After lambing, the male lambs were maintained on a similar diet for 124 d. Semen samples from the mature rams (F0 generation) were collected on d 28, 56, and 84, and semen samples from offspring rams (F1 generation) were collected at 330 d of age via electroejaculation. Genomic DNA was extracted from semen samples and the seminal microbiota characterized using 16S rRNA gene (V3-V4) sequencing. Several environmental and negative extraction controls were also sequenced to assess potential contaminants in these samples. Overall community structure of the seminal microbiota in F0 rams was not affected by the divergent planes of nutrition (PERMANOVA: P ≥ 0.05) or by sampling time (P &amp;gt; 0.05). Microbial richness (observed ASVs) was also not different (P &amp;gt; 0.05) between the three groups of F0 rams at any of the sampling time points; however, microbial diversity (P &amp;lt; 0.05) in the F0 rams was influenced by sire dietary treatment. Microbial community structure, richness and diversity did not differ among the POS, MNT and NEG F1 generation rams (P &amp;gt; 0.05). Actinobacteriota, Firmicutes, Bacteroidota, Proteobacteria and Fusobacteriota were the most abundant phyla. Only Bacteroidota abundance was significantly (P &amp;lt; 0.05) different between three F0 groups, with POS rams had greater (18.6%) of this phylum on d 28 as compared with MNT (2.1%) and NEG (5.1%). The predominant genera identified included Fastidiosipila, Corynebacterium, Trueperella, Arthrobacter, Dietzia, Bifidobacterium, Streptobacillus, Ornithinimicrobium, and Porphyromonas, and their relative abundance was not affected (P &amp;gt; 0.05) by the dietary treatment in F0 rams. Overall, rams managed on positive and negative planes of nutrition harbored similar seminal microbiota to control rams, and divergent nutrition also had no effect on the offspring ram seminal microbiota.

PSIX-2 Skin microbial compositions differ among dog body sites and are affected by dietary probiotics

Abstract The study aimed to characterize the skin microbiota across four distinct body sites and investigate the impact of dietary probiotics on the skin microbiota of healthy adult dogs. Healthy adult dogs [n = 60; mean age = 6.2 ± 2.8 yr; mean body weight (BW) = 13.1 ± 4.0 kg] were randomly assigned into three treatment groups and fed for 60 d: a control kibble diet (CON; n = 20; 29.0% crude protein, 10.1% crude fat, 9.9% crude fiber, 7.1% ash, as-fed), CON supplemented with Bifidobacterium longum 548 (CON-B; n = 20), or CON supplemented with Bifidobacterium longum 548 and Lactobacillus rhamnosus 451 (CON-B-L; n = 20). All dogs were individually housed in a temperature- and humidity-controlled research facility. Protocols were approved by the facility’s Institutional Animal Care and Use Committee before the study. On d 60, skin swab samples were collected from the dorsal lumbar area, right axilla, right groin, and right ear concave pinnae of each dog using sterile swabs. These samples were placed into bead tubes and stored at -20°C until analysis. DNA extraction from skin swab samples was followed by sequencing the V4 region of 16S rRNA using Illumina sequencing on a MiSiq. Sequence data were processed through QIIME 2.0, and statistical analysis was performed using R 4.3.1. to test differences between body sites and diets, with a significance threshold set at P &amp;lt; 0.05. The predominant bacterial phyla observed across all body sites were Actinobacteria (40 ± 21.7%), Firmicutes (31.2 ± 17.9 %), Proteobacteria (17.9 ± 13.3%), and Bacteroidetes (6.6 ± 6.1%). Additionally, Acidobacteria, Gemmatimonadetes, and Verrucomicrobia were exclusive to the groin region. Considering data from all body sites, diets affected relative abundances of phyla and genera in dogs. At phylum level, dogs fed the CON-B diet displayed greater (P &amp;lt; 0.05) relative abundance of Actinobacteria compared with those on the CON diet. The CON-B diet also resulted in a greater (P &amp;lt; 0.05) relative abundance of Firmicutes than dogs on either the CON or CON-B-L diets. At genus level, dogs on the CON-B diet showed significantly greater (P &amp;lt; 0.05) relative abundance of Clostridium, Clostridiaceae unclassified, and Lachnospiraceae unclassified compared with the other diet groups. Dogs on the CON diet displayed a greater (P &amp;lt; 0.05) relative abundance of Dietzia compared with those on probiotic-supplemented diets. These findings underscore the variation in skin microbial composition across distinct body sites, contributing valuable data to limited information available on the skin microbiota of dogs. Moreover, consumption of probiotic influenced the skin microbial compositions in dogs, which warrant further studies to elucidate the relationship between probiotics, skin microbiota, and skin health in dogs.