Abundant Operational Taxonomic Units Research Articles

211 Analysis of microbial communities from a commercial-size swine manure pit and their association with production of volatile organic compounds

Abstract Global pollution and emission concerns have been linked to concentrated animal feeding operations (CAFOs). Indeed, the U.S Environmental Protection Agency (US EPA) warns that there is a significant danger to human health, soil, and water quality from CAFOs. Volatile organic compounds (VOCs), which are amongst air contaminants that pose a serious risk, are abundantly produced in swine manure pits. While VOC emissions from swine manure have been well studied, the microbial species responsible for their production remain mostly uncharacterized. Thus, a deeper comprehension of the microorganisms responsible for VOC production in swine manure pits may help in the development of management approaches that target the microbiome in these environments. In this context, this study aimed to identify the major bacterial species populating the manure pit of a commercial-size swine wean-to-finish research facility. Manure collected from two sampling locations at different time points were analyzed using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from microbial genomic DNA, followed by Illumina MiSeq 2X300 sequencing. An analysis of the most highly represented microorganisms identified 24 bacterial Operational Taxonomic Units (OTUs), with only four showing a species-level nucleotide sequence identity to currently known or valid species. As these results indicated that the majority of bacterial species from this manure pit were unknown, a metagenomics approach was used to assemble partial to full length genomes from the two most abundant OTUs: Pit_9-00239 [5.09% - 19.44%; Clostridium saccharoperbutylacetonicum (96.60%)] and Pit_ 7-00035 [5.58% - 17.30%; Bacteroides eggerthii (87.66%)]. From genome assembly analysis, 979 contigs were generated for a combined length of 12,367,510 bp, which together included 21,776 coding sequences. Predicted metabolic functions from these contig sets included pathways involved in carbohydrate utilization (glycolysis), vitamin synthesis (riboflavin), and butyrate production (volatile fatty acids). Notably, an enzyme responsible for the production of indole, a common VOC produced from swine manure pits, was also identified. Together, the results from this analysis provide insights on metabolic capabilities of abundant bacterial species from manure pits. These can in turn be used for the future development of management strategies or products that can reduce VOC emissions that result from swine CAFO manure storage.

227 Comparative analysis of rumen bacterial communities from bison heifers fed two forage-based diets of different quality

Abstract Bison have a demonstrated ability to thrive on low-quality forage, an attribute that distinguishes them from their domestic ruminant counterparts. This could be attributed to the capability of their rumen symbiotic microorganisms in extracting more nutrients out of plant biomass. To gain further insight into the role of the bison microbiome in this beneficial adaptation, the primary objective of this study was to determine the diversity and composition of ruminal bacteria in bison fed poor versus good quality forage-based diets. Ruminal content was collected by stomach tubing from 25 bison heifers fed good quality forage (GQG) during the summer (last week of June 2023) at the McGinley Ranch (Gordon, Nebraska, USA). The same individuals were then transitioned to low quality hay (PQG) in pen confinement for approximately 4 to 5 wk before resampling. Data generated from Illumina MiSeq (2×300) sequencing of PCR amplicons targeting the V1-V3 region of the 16S rRNA gene were analyzed using a combination of custom Perl scripts, and publicly available software (Mothur v.1.40, RDP classifier and NCBI Blast). Principal Coordinate Analysis (PCoA) showed a clear distinction in bacterial composition between the two types of forages (Figure 1). Further analysis of species-level operational taxonomic units (OTUs) was performed, and a total of 78,808 OTUs were identified across all samples. From the 20 most highly represented OTUs, the respective abundance of twelve OTUs showed significant differences between the two forage types (Kruskal-Wallis’s sum-rank test; P < 0.05). For example, OTUs SD_Bb-00014 (µGQG = 1.06% vs µPQG = 0.19%), and SD_Bb-00049 (µGQG = 0.98% vs µPQG = 0.08%) showed significant decreases in abundance when animals switched to PQG. Conversely, OTUs SD_Bb-00071 (µGQG = 0.2% vs µPQG = 2.71%), SD_Bb-00049 (µGQG = 0.68% vs µPQG = 1.67%) and OTUs SD_Bb-00148 (µGQG = 0.19% vs µPQG = 1.40%) exhibited a significant increase in abundance in response to the forage transition. Notably, only one of the assessed OTUs, SD_Bb-00071, showed high sequence identity to its closest valid relative, Fibrobacter succinogenes (98.41%). In contrast, most of the other highly represented OTUs were found to be very dissimilar to known species, suggesting that they might represent novel or currently uncharacterized bacterial species (Table 1). Together, these results demonstrate the significant impact of variations in nutritional value and forage quality on the composition of rumen bacterial communities in the North American bison. Poor forage quality appeared to favor bacterial species such as Fibrobacter succinogenes, known for its cellulolytic capabilities, presumably because of its greater efficiency in breaking down more resistant plant cell walls. Its ability and that of other abundant OTUs to efficiently convert plant fibers into assimilable nutrients is likely critical in allowing bison to perform better on poor-quality forage compared with domesticated ruminants.

Selection of the Dominant Endophytes Based on Illumina Sequencing Analysis for Controlling Bacterial Wilt of Patchouli Caused by Ralstonia solanacearum.

Bacterial wilt caused by Ralstonia solanacearum (RS) is one of the most devastating diseases in patchouli (Pogostemon cablin [Blanco] Benth.), which results in low yield and quality of patchouli. However, no stable and effective control methods have been developed yet. To evaluate the potential of dominant bacterial endophytes in biocontrol, the endophytic bacterial diversity of patchouli was investigated based on Illumina sequencing analysis, and the ability of isolates belonging to the dominant bacterial genera to control RS wilt of patchouli was explored in pot experiments. A total of 245 bacterial genera were detected in patchouli plants, with the highest relative abundance of operational taxonomic units belonging to the genus Pseudomonas detected in roots, leaves, and stems. The Pseudomonas isolates S02, S09, and S26 showed antagonistic activity against RS in vitro and displayed many plant growth-promoting characteristics, including production of indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylic acid deaminase and phosphate- and potassium-solubilizing capability. Inoculation of patchouli plants with the isolates S02, S09, and S26 significantly improved shoot growth and decreased the incidence of bacterial wilt caused by RS. The results suggest that screening of dominant bacterial endophytes for effective biocontrol agents based on Illumina sequencing analysis is more efficient than random isolation and screening procedures.

Comparison of Daily versus Admission and Discharge Surveillance Cultures for Multidrug-Resistant Organism Detection in an Intensive Care Unit.

Admission and discharge screening of patients for asymptomatic gut colonization with multidrug-resistant organisms (MDROs) is a traditional approach to active surveillance, but its sensitivity for detecting colonization is uncertain. Daily rectal or fecal swab samples and clinical data were collected over 12 months from patients in one 25-bed intensive care unit (ICU) in Chicago, IL USA and tested for the following multidrug-resistant organisms (MDROs): vancomycin-resistant enterococci (VRE); third-generation cephalosporin-resistant Enterobacterales, including extended-spectrum β-lactamase-producing Enterobacterales (ESBL); and carbapenem-resistant Enterobacterales (CRE). MDRO detection by (1) admission/discharge surveillance cultures or (2) clinical cultures were compared to daily surveillance cultures. Samples underwent 16S rRNA gene sequencing to measure the relative abundance of operational taxonomic units (OTUs) corresponding to each MDRO. Compared with daily surveillance cultures, admission/discharge cultures detected 91% of prevalent MDRO colonization and 63% of incident MDRO colonization among medical ICU patients. Only a minority (7%) of MDRO carriers were identified by clinical cultures. Higher relative abundance of MDRO-associated OTUs and specific antibiotic exposures were independently associated with higher probability of MDRO detection by culture. Admission and discharge surveillance cultures underestimated MDRO acquisitions in an ICU. These limitations should be considered when designing sampling strategies for epidemiologic studies that use culture-based surveillance.

The faecal microbiome of the Pacific banana slug, Ariolimax columbianus, displays seasonal variation

ABSTRACT The Pacific banana slug, Ariolimax columbianus, is the largest land mollusc in North America and occurs in forests ranging from northwestern California to Alaska. We explored the microbial community found within the faeces of 24 slugs from the Oregon Coast Range. Twenty-four slugs were collected in 2019, 12 in the spring and 12 in the fall. These two time points were selected to investigate the composition of microbial populations in wild-caught slugs, also in response to seasonal changes in available plants as food sources. Results from 16S rRNA gene amplicon sequencing indicate that the most prevalent phyla detected from A. columbianus were Proteobacteria (66%) and Bacteriodetes (16%), similar to previous observations from six other species/genera of terrestrial gastropods (Stylommatophora). The most abundant operational taxonomic units across all specimens were Enterobacter sp., Pseudomonas sp. and Flavobacterium sp. Significant seasonal variation was observed for several species of Flavobacteriales, Firmicutes and Proteobacteria, with the majority showing higher abundance in fall. In contrast to Cornu aspersum (previously Helix aspersa, parapatric with A. columbianus) and Geomaculus maculosus, A. columbianus harbours very low levels of Buttiauxella (0.35%). These findings raise questions about the origin, specificity and selection of specific bacteria as components of the intestinal microbiome of terrestrial gastropods.

Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach.

Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg-1) like Cu (0.009-0.01), Ni (0.005-0.002), Mn (0.078-0.056), Cr (0.015-0.009), Pb (0.008-0.006), Zn (0.225-0.086), Fe (2.124-0.764), Al (3.477-22.277), and Ti (99.792-45.012) along with high content of chlorophenol, and lignin. The comparative analysis of organic pollutants in sediment samples using gas chromatography-mass spectrometry (GC-MS) revealed the presence of major highly refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc in sediment samples which are reported as a potential toxic compounds. Simultaneously, high-throughput sequencing targeting the V3-V4 hypervariable region of the 16S rRNA genes, resulted in the identification of 1,249 and 1,345 operational taxonomic units (OTUs) derived from a total of 115,665 and 119,386 sequences read, in PPS-1 and PPS-2, respectively. Analysis of rarefaction curves indicated a diversity in OTU abundance between PPS-1 (1,249 OTUs) and PPS-2 (1,345 OTUs). Furthermore, taxonomic assignment of metagenomics sequence data showed that Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), and Planctomycetes (5.40%; 4.70%) were the most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), and Gammaproteobacteria were the most recorded classes in PPS-1 and PPS-2, respectively. At the genus level, Thiobacillus (7.60%; 4.50%) was the most abundant genera grown in sediment samples. The results indicate significant differences in both the diversity and relative abundance of taxa in the bacterial communities associated with PPS-2 when compared to PPS-1. This study unveils key insights into contaminant characteristics and shifts in bacterial communities within contaminated environments. It highlights the potential for developing efficient bioremediation techniques to restore ecological balance in pulp-paper mill waste-polluted areas, stressing the importance of identifying a significant percentage of unclassified genera and species to explore novel genes.

Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum

BackgroundBacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial community directly associated with the pathogen make up the pathobiome. While the overall soil bacterial community associated with Fusarium wilt diseases has been widely examined, the specific bacterial populations that directly interact with the Fusarium wilt pathogens are yet to be discovered. In this study, we define the bacterial community associated with the hyphae of Fusarium oxysporum f. sp. niveum race 2 (FON2). Using the 16S rRNA gene metabarcoding, we describe the hyphosphere pathobiome of three isolates of FON2.ResultsOur results show a core microbiome that is shared among the three tested hyphospheres. The core hyphosphere community was made up of 15 OTUs (Operational Taxonomic Units) that were associated with all three FON2 isolates. This core consisted of bacterial members of the families, Oxalobacteraceae, Propionibacteriaceae, Burkholderiaceae, Micrococcaceae, Bacillaceae, Comamonadaceae, Pseudomonadaceae and unclassified bacteria. The hyphosphere of FON2 was dominated by order Burkholderiales. While all three isolate hyphospheres were dominated by these taxa, the specific OTU differed. We also note that while the dominant OTU of one hyphosphere might not be the largest OTU for other hyphospheres, they were still present across all the three isolate hyphospheres. Additionally, in the correlation and co-occurrence analysis the most abundant OTU was negatively correlated with most of the other OTU populations within the hyphosphere.ConclusionsThe study indicates a core microbiota associated with FON2. These results provide insights into the microbe-microbe dynamic of the pathogen's success and its ability to recruit a core pathobiome. Our research promotes the concept of pathogens not being lone invaders but recruits from the established host microbiome to form a pathobiome.

Identification of keystone taxa in root canals and periapical lesions of post-treatment endodontic infections: Next generation microbiome research.

The aim of this study was to analyse and compare the microbiome present in root canals and periapical lesions of teeth with post-treatment infections, and to identify the presence of keystone taxa in both habitats using next-generation sequencing analysis. Apices and periapical lesions of patients with post-treatment apical periodontitis were surgically extracted. Specimens were cryo-pulverized, bacterial DNA was extracted, and the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced using the Illumina Miseq platform. Bioinformatic analysis was carried out with Mothur software, whilst diversity indices were obtained using operational taxonomic units (OTUs). The diversity indices were compared with the Kruskal-Wallis test, and community composition differences were explored with Permutational Multivariate Analysis of Variance (PERMANOVA). A bacterial functional study was performed with the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Co-occurrence network analyses were performed using the Sparse Correlations for Compositional data (SparCC). Eigencentrality, clr-based abundance and ubiquitousness were applied to infer keystone taxa. P values <.05 were considered statistically significant. Thirty-two apices and thirty-nine periapical lesions were sequenced and analysed. A similar alpha-diversity (p < .05) and community composition (p = .91) was observed for apices and lesion samples. The most abundant OTUs identified amongst all samples included Fusobacterium nucleatum, Prevotella loescheii, Streptococcus intermedius, Porphyromonas gingivalis, Parvimonas micra, Synergistetes bacterium, Tannerella forsythia and Peptostreptococcus stomatis. The metabolic pathways with >0.81% abundances included membrane transport, genetic information processing and metabolic pathways. F. nucleatum was identified as a keystone taxon as it showed ubiquitousness, an eigenvector centrality value of 0.83 and a clr-based abundance >4. The microbiome in apices and periapical lesions of post-treatment endodontic infections showed a similar diversity and taxonomic composition. Co-occurrence network analyses at OTU level identified F. nucleatum as a keystone taxon candidate in these infections.

Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms.

Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.

Community structure and association network of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

The Bering-Chukchi shelf is one of the world's most productive areas and characterized by high benthic biomass. Sedimentary microbial communities play a crucial role in the remineralization of organic matter and associated biogeochemical cycles, reflecting both short-term changes in the environment and more consistent long-term environmental characteristics in a given habitat. In order to get a better understanding of the community structure of sediment-associated prokaryotes, surface sediments were collected from 26 stations in the Bering-Chukchi shelf and adjacent northern deep seas in this study. Prokaryote community structures were analyzed by metabarcoding of the 16S rRNA gene, and potential interactions among prokaryotic groups were analyzed by co-occurrence networks. Relationships between the prokaryote community and environmental factors were assessed. Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the dominant bacterial classes, contributing 35.0, 18.9, and 17.3% of the bacterial reads, respectively. The phototrophic cyanobacteria accounted for 2.7% of the DNA reads and occurred more abundantly in the Bering-Chukchi shelf. Prokaryotic community assemblages were different in the northern deep seas compared to the Bering-Chukchi shelf, represented by the lowered diversity and the increased abundant operational Taxonomic Units (OTU), suggesting that the abundant taxa may play more important roles in the northern deep seas. Correlation analysis showed that latitude, water depth, and nutrients were important factors affecting the prokaryote community structure. Abundant OTUs were distributed widely in the study area. The complex association networks indicated a stable microbial community structure in the study area. The high positive interactions (81.8-97.7%) in this study suggested that symbiotic and/or cooperative relationships accounted for a dominant proportion of the microbial networks. However, the dominant taxa were generally located at the edge of the co-occurrence networks rather than in the major modules. Most of the keystone OTUs were intermediately abundant OTUs with relative reads between 0.01 and 1%, suggesting that taxa with moderate biomass might have considerable impacts on the structure and function of the microbial community. This study enriched the understanding of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity.

A more detailed understanding of the mechanisms underlying the formation of microbial communities is essential for the efficient management of microbial ecosystems. The stable states of microbial communities are commonly perceived as static and, thus, have not been extensively examined. The present study investigated stabilizing mechanisms, minority functions, and the reliability of quantitative ana-lyses, emphasizing a metabolic network perspective. A bacterial community, formed by batch transferred cultures supplied with phenol as the sole carbon and energy source and paddy soil as the inoculum, was analyzed using a principal coordinate ana-lysis (PCoA), mathematical models, and quantitative parameters defined as growth activity, community-changing activity, community-forming activity, vulnerable force, and resilience force depending on changes in the abundance of operational taxonomic units (OTUs) using 16S rRNA gene amplicon sequences. PCoA showed succession states until the 3rd transferred cultures and stable states from the 5th to 10th transferred cultures. Quantitative parameters indicated that the bacterial community was dynamic irrespective of the succession and stable states. Three activities fluctuated under stable states. Vulnerable and resilience forces were detected under the succession and stable states, respectively. Mathematical models indicated the construction of metabolic networks, suggesting the stabilizing mechanism of the community structure. Thirteen OTUs coexisted during stable states, and were recognized as core OTUs consisting of majorities, middle-class, and minorities. The abundance of the middle-class changed, whereas that of the others did not, which indicated that core OTUs maintained metabolic networks. Some extremely low abundance OTUs were consistently exchanged, suggesting a role for scavengers. These results indicate that stable states were formed by dynamic metabolic networks with members functioning to achieve robustness and plasticity.

Composition and diversity of culturable cyanobacteria in sediment samples from the upper layers of two tropical reservoirs

Benthic cyanobacteria research in high mountain reservoirs remains limited, mainly due to their complexity and knowledge gaps that persist in relation to their ecology in tropical regions. This study aimed to explore the composition, diversity, and toxic potential of cyanobacterial in the upper sediment of two Colombian reservoirs. Our investigation involved multiple methodologies, such as germination experiments, that allowed us to assess the presence and viability of cyanobacteria in upper sediment samples, while the competitive ELISA assay allowed for the quantification of toxins within the cultures. The molecular analysis of Operational Taxonomic Units (OTUs) from subsamples of sediment cultures focused on evaluating cyanobacterial diversity and richness among prokaryotic phyla, and the Phylogenetic analysis of culturable cyanobacteria. Chlorophyll-a measurements confirmed the presence of viable populations in sediment cultures, while microscopic identification demonstrated the growth capacity of cyanobacteria from the orders Nostocales, Chroococcales, Oscillatoriales, and Synechococcales under controlled laboratory conditions. Despite low microcystin levels in culture, the prior detection of mcy genes in direct sediment samples suggests a possible toxic potential of cyanobacterial inhabiting the upper sediments. Community analysis, based on the OTUs abundance, revealed a notably diverse microbial community in both reservoir sediments, with a higher relative abundance of cyanobacteria compared to other prokaryotic phyla. These findings support the hypothesis that surface sediments play a fundamental role as a repository for cyanobacteria that may pose inherent risks to ecosystem health. In conclusion, this research underscores the necessity of further studies to achieve a holistic comprehension of benthic cyanobacteria dynamics in high-mountain tropical reservoirs.

Wound healing of experimental equine skin wounds and concurrent microbiota in wound dressings following topical propylene glycol gel treatment.

Topical wound treatments rely on carrier formulations with little to no biological impact. The potential for a common vehicle, a propylene glycol (PG) gel, to affect wound healing measures including microbiota is not known. Microbiome characterization, based on next generation sequencing methods is typically performed on tissue or directly obtained wound fluid samples. The utility for primary wound dressings to characterize equine wound microbiota in the context of topical treatments is currently unknown. This investigation reports the topical effect of an 80% PG based gel on wound healing and microbiota in wound dressings. Experiments were performed in six mature horses utilizing a surgical, distal limb wound model, histology of sequential wound biopsies, photographic wound measurements and microbiota profiling via 16s rRNA sequencing of wound dressing samples. Experimental wounds were surveyed for 42 days and either treated (Day 7, 14, 21 and 28; at 0.03 ml/cm2) or unexposed to the PG gel. Wound surface area, relative and absolute microbial abundances, diversity indices and histologic parameters were analyzed in the context of the experimental group (treatment; control) using qualitative or quantitative methods depending on data characteristics. Compared to controls, treatment slowed the wound healing rate (17.17 ± 4.27 vs. 18.56 ± 6.3 mm2/day), delayed the temporal decline of polymorphonucleated cells in wound beds and operational taxonomic units (OTU) in wound dressings and lowered alpha-diversity indices for microbiota in primary wound dressing. Relative abundances of OTUs were in line with those previously reported for equine wounds. Clinical outcomes 42 days post wounding were considered similar irrespective of PG gel exposure. Results highlight the potential for vehicle exposure to alter relevant wound outcome measures, imposing the need for stringent experimental control measures. Primary wound dressings may represent an alternate sample source for characterization of the wound microbiome alleviating the need for additional interventions. Further studies are warranted to contrast the microbiome in wound dressings against that present on wound surfaces to conclude on the validity of this approach.

Effects of nanocarbon and nano‐calcium carbonate on soil enzyme activities and soil microbial community in wheat (Triticum aestivum L.) rhizosphere soil

AbstractBackgroundNanofertilisers can enhance the efficiency of nutrient utilization in crop production. Nevertheless, it is unclear how soil microbial and enzyme activities are affected by the application of nanofertilisers to wheat inter‐root soil.AimsThe study aims to investigate the influences of nanocarbon (NC) and nano‐calcium carbonate (NCC) on soil enzyme activities and microbial community in the open field setting.MethodsThe effects of nanofertilisers on soil wheat rhizosphere soil were studied through the evaluation of soil microbial quantity, enzyme activity, and microbial diversity.ResultsThe findings revealed that the combined utilization of nanofertilizers and compound fertilizers (CF) led to an augmentation in the diversity of the soil microbial community. When comparing the effects of 100% composite nanofertilizers (100% CF + 50% NC + 50% NCC) with the control (CK) (100% CF), it was observed that the activities of urease (EC 3.5.1.5), catalase (EC 1.11.1.6), alkaline phosphatase (EC 3.1.3.1), sucrase (EC.3.2.1.26), as well as the number of fungi, actinomycetes, and bacteria, increased by 22.4%, 7.7%, 17.8%, 9.3%, 35.9%, 27.7%, and 26.0%, respectively. Similarly, the employment of 70% composite nanofertilizers (70% CF + 35% NC + 35% NCC) also resulted in an enhancement of these aforementioned indicators. The magnitude of increase over the 100% CF was 19.0%, 6.6%, 13.6%, 6.2%, 26.8%, 21.3%, and 23.5%, respectively. Notably, there was no significant difference observed between 100% CF + 50% NC + 50 % NCC and 70% CF + 35% NC + 35% NCC within the 0–35 d after anthesis. Furthermore, both 100% CF + 50% NC + 50% NCC and 70% CF + 35% NC + 35% NCC contributed to an improvement in the species uniformity and operational taxonomic unit abundance of wheat rhizosphere microorganisms, while also increasing the abundance of Proteobacteria and Actinobacteria compared to the CK. The relative abundance of Bacteroidetes and Actinobacteria was found to be elevated in the nanomaterials‐treated groups, both at 0–7 d and 14–21 d after anthesis, and positively correlated with soil enzyme activities and soil microbial populations.ConclusionsThese results indicate that the application of composite nanofertilizers can enhance the soil microenvironment in wheat fields, particularly under reduced fertilization conditions.

Reorganizing heterogeneous information from host–microbe interaction reveals innate associations among samples

AbstractThe information on host–microbe interactions contained in the operational taxonomic unit (OTU) abundance table can serve as a clue to understanding the biological traits of OTUs and samples. Some studies have inferred the taxonomies or functions of OTUs by constructing co‐occurrence networks, but co‐occurrence networks can only encompass a small fraction of all OTUs due to the high sparsity of the OTU table. There is a lack of studies that intensively explore and use the information on sample‐OTU interactions. This study constructed a sample‐OTU heterogeneous information network and represented the nodes in the network through the heterogeneous graph embedding method to form the OTU space and sample space. Taking advantage of the represented OTU and sample vectors combined with the original OTU abundance information, an Integrated Model of Embedded Taxonomies and Abundance (IMETA) was proposed for predicting sample attributes, such as phenotypes and individual diet habits. Both the OTU space and sample space contain reasonable biological or medical semantic information, and the IMETA using embedded OTU and sample vectors can have stable and good performance in the sample classification tasks. This suggests that the embedding representation based on the sample‐OTU heterogeneous information network can provide more useful information for understanding microbiome samples. This study conducted quantified representations of the biological characteristics within the OTUs and samples, which is a good attempt to increase the utilization rate of information in the OTU abundance table, and it promotes a deeper understanding of the underlying knowledge of human microbiome.

Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries

BackgroundOral microbiome sequencing has revealed key links between microbiome dysfunction and dental caries. However, these efforts have largely focused on Western populations, with few studies on the Middle Eastern communities. The current study aimed to identify the composition and abundance of the oral microbiota in saliva samples of children with different caries levels using machine learning approaches.MethodsOral microbiota composition and abundance were identified in 250 Saudi participants with high dental caries and 150 with low dental caries using 16 S rRNA sequencing on a NextSeq 2000 SP flow cell (Illumina, CA) using 250 bp paired-end reads, and attempted to build a classifier using random forest models to assist in the early detection of caries.ResultsThe ADONIS test results indicate that there was no significant association between sex and Bray-Curtis dissimilarity (p ~ 0.93), but there was a significant association with dental caries status (p ~ 0.001). Using an alpha level of 0.05, five differentially abundant operational taxonomic units (OTUs) were identified between males and females as the main effect along with four differentially abundant OTUs between high and low dental caries. The mean metrics for the optimal hyperparameter combination using the model with only differentially abundant OTUs were: Accuracy (0.701); Matthew’s correlation coefficient (0.0509); AUC (0.517) and F1 score (0.821) while the mean metrics for random forest model using all OTUs were:0.675; 0.054; 0.611 and 0.796 respectively.ConclusionThe assessment of oral microbiota samples in a representative Saudi Arabian population for high and low metrics of dental caries yields signatures of abundances and diversity.

Marine Bacterial Community Structures of Selected Coastal Seawater and Sediment Sites in Qatar.

Severe environmental conditions can have a diverse impact on marine microorganisms, including bacteria. This can have an inevitable impact on the biofouling of membrane-based desalination plants. In this work, we have utilized indicator bacteria such as total coliform, fecal coliform, and Pseudomonas aeruginosa, as well as 16S rRNA sequencing, to investigate the impact of environmental conditions and spatial variations on the diversity of bacterial communities in the coastal waters and sediments from selected sites in Qatar. The concentration levels of indicator bacteria were affected by increasing temperatures and pH, and by decreasing salinity of seawater samples. Diversity indices and the molecular phylogeny demonstrated that Proteobacteria, Bacteroidetes, and Cyanobacteria were the dominant phyla in all locations. The most abundant operational taxonomic units (OTUs) at the family level were from Flavobacteriaceae (27.07%, 4.31%) and Rhodobacteraceae (22.51%, 9.86%) in seawater and sediment, respectively. Alphaproteobacteria (33.87%, 16.82%), Flavobacteria (30.68%, 5.84%), and Gammaproteobacteria (20.35%, 12.45%) were abundant at the species level in both seawater and sediment, while Clostridia (13.72%) was abundant in sediment only. The results suggest that sediment can act as a reservoir for indicator bacteria, with higher diversity and lower abundance compared to seawater.

Influence of Soil Type, Land Use, and Rootstock Genotype on Root-Associated Arbuscular Mycorrhizal Fungi Communities and Their Impact on Grapevine Growth and Nutrition

Soil characteristics, land management practices, and plant genotypes influence arbuscular mycorrhizal fungi (AMF) communities, leading to the proliferation of AMF taxa with different growth and nutritional outcomes in their hosts. However, the specific patterns driving these relationships are still not well understood. This study aimed to (1) evaluate the influence of soil characteristics, land use, and rootstock on AMF diversity and community structure and (2) assess the effect of those AMF communities on grapevine growth and nutrition. Soil samples were collected from vineyard and non-agricultural areas in Lisbon and Pegões, Portugal, and trap cultures established using Richter 110 and 1103 Paulsen rootstocks. After 3.5 months growth under greenhouse conditions, root-associated AMF communities were assessed by amplicon metagenomic sequencing using AMF-specific primers. Alpha diversity was only influenced by the soil type, while in β-diversity, an interaction was found between the soil type and land use. Both diversity measures were positively correlated with foliar K and negatively with leaf Mn and Mg. Notably, the concentrations of these nutrients were highly correlated with the relative abundance of operational taxonomic units (OTUs) within the genera Glomus, Rhizophagus, and Claroideoglomus. These results are valuable for supporting AMF selection for improved plant nutrition based on varying soil types and land uses.

Predicting foodborne pathogens and probiotics taxa within poultry-related microbiomes using a machine learning approach

BackgroundMicrobiomes that can serve as an indicator of gut, intestinal, and general health of humans and animals are largely influenced by food consumed and contaminant bioagents. Microbiome studies usually focus on estimating the alpha (within sample) and beta (similarity/dissimilarity among samples) diversities. This study took a combinatorial approach and applied machine learning to microbiome data to predict the presence of disease-causing pathogens and their association with known/potential probiotic taxa. Probiotics are beneficial living microorganisms capable of improving the host organism’s digestive system, immune function and ultimately overall health. Here, 16 S rRNA gene high-throughput Illumina sequencing of temporal pre-harvest (feces, soil) samples of 42 pastured poultry flocks (poultry in this entire work solely refers to chickens) from southeastern U.S. farms was used to generate the relative abundance of operational taxonomic units (OTUs) as machine learning input. Unique genera from the OTUs were used as predictors of the prevalence of foodborne pathogens (Salmonella, Campylobacter and Listeria) at different stages of poultry growth (START (2–4 weeks old), MID (5–7 weeks old), END (8–11 weeks old)), association with farm management practices and physicochemical properties.ResultWhile we did not see any significant associations between known probiotics and Salmonella or Listeria, we observed significant negative correlations between known probiotics (Bacillus and Clostridium) and Campylobacter at the mid-time point of sample collection. Our data indicates a negative correlation between potential probiotics and Campylobacter at both early and end-time points of sample collection. Furthermore, our model prediction shows that changes in farm operations such as how often the houses are moved on the pasture, age at which chickens are introduced to the pasture, diet composition and presence of other animals on the farm could favorably increase the abundance and activity of probiotics that could reduce Campylobacter prevalence.ConclusionIntegration of microbiome data with farm management practices using machine learning provided insights on how to reduce Campylobacter prevalence and transmission along the farm-to-fork continuum. Altering management practices to support proliferation of beneficial probiotics to reduce pathogen prevalence identified here could constitute a complementary method to the existing but ineffective interventions such as vaccination and bacteriophage cocktails usage. Study findings also corroborate the presence of bacterial genera such as Caloramator, DA101, Parabacteroides and Faecalibacterium as potential probiotics.

260 Identification of Candidate Gut Bacterial Species from Atlantic Salmon (Salmo salar) That Can Metabolize Ingredients Derived from Bioprocessed Soybean Meal

Abstract In the aquaculture industry, plant-based protein sources have emerged as an economically and environmentally sustainable replacement for traditional animal protein sources. Yet, due to decreased digestibility, the presence of anti-nutritional factors, and an increased risk of inflammation of the digestive system, the inclusions of plant-based protein ingredients must be limited in the diets of carnivorous fishes. To gain further insight on the adaptation of the fish digestive tract to plant-based protein ingredients, slurry from cultured Atlantic Salmon (Salmo salar) was used as a proxy in an in vitro model system to identify candidate gut bacterial species from fish that can metabolize bioprocessed soybean meal. Triplicate slurry cultures were supplemented with one of each of the following ingredients: fishmeal (FM – control#1), soybean meal (SBM-control#2), MEPro (bioprocessed soybean meal product), as well as three ingredients derived from bioprocessed soybean meal (SPC1 - soy protein isolate #1; SPC2 - soy protein isolate #2; SPC3 - soy protein isolate #3). Data were generated by Illumina MiSeq 2X300 sequencing of PCR-generated amplicons targeting the V1-V3 regions of the 16S rRNA gene. A comparative analysis of the most highly represented Operational Taxonomic Units (OTU) using the non-parametric Kruskal-Wallis sum-rank test and Wilcoxon pairwise test identified candidate bacterial species that were enriched in cultures supplemented with specific bioprocessed soybean meal-derived ingredients compared with non-supplemented cultures (negative control). These results indicate that certain species may utilize these ingredients. Notably, OTUs Ss_1-37437 and Ss_1-13316 were found in the greatest abundance in cultures supplemented with SPC1 (31.4 - 49.7%) and SPC2 (7.2 - 17.4%), respectively. Interestingly, both OTUs were likely to represent novel bacterial species, based on their limited nucleotide sequence identity to their corresponding valid relative: Ss_1-37437: Prevotella paludivivens (96.58%); Ss_1-13316: Acetoanaerobium sticklandii (86.51%). In contrast, the most abundant OTUs enriched in SBM- and MePro-supplemented cultures were likely strains of known bacterial species. Indeed, OTU Ss_1-00386 was most abundant in SBM-supplemented cultures (16.4 - 32.5%), and it was found to be closely related to Leuconostoc mesenteroides (98.69%), a bacterial species with reported probiotic properties, while OTU SS_1-10030, a close relative of Bacteroides graminisolvens (99.24%), was most highly represented in MePro-supplemented cultures (21.9 - 32.7%). Together, these results suggest that ingredients derived from bioprocessed soybean meal have the potential to be developed as prebiotics to modulate the gut microbiome of aquaculture fish species.