Individual Operational Taxonomic Units Research Articles

Changes in the Gut Microbiota Composition during Implantation of Composite Scaffolds Based on Poly(3-hydroxybutyrate) and Alginate on the Large-Intestine Wall.

The development of biopolymer scaffolds for intestine regeneration is one of the most actively developing areas in tissue engineering. However, intestinal regenerative processes after scaffold implantation depend on the activity of the intestinal microbial community that is in close symbiosis with intestinal epithelial cells. In this work, we study the impact of different scaffolds based on biocompatible poly(3-hydroxybutyrate) (PHB) and alginate (ALG) as well as PHB/ALG scaffolds seeded with probiotic bacteria on the composition of gut microbiota of Wistar rats. Implantation of PHB/ALG scaffolds on the large-intestine wall to close its injury showed that alpha diversity of the gut microbiota was not reduced in rats implanted with different PHB/ALG scaffolds except for the PHB/ALG scaffolds with the inclusion of Lactobacillus spheres (PHB/ALG-L). The composition of the gut microbiota of rats implanted with PHB/ALG scaffolds with probiotic bacteria or in simultaneous use of an antimicrobial agent (PHB/ALG-AB) differed significantly from other experimental groups. All rats with implanted scaffolds demonstrated shifts in the composition of the gut microbiota by individual operational taxonomic units. The PHB/ALG-AB construct led to increased abundance of butyrate-producing bacteria: Ileibacterium sp. dominated in rats with implanted PHB/ALG-L and Lactobacillus sp. and Bifidobacterium sp. dominated in the control group. In addition, the PHB/ALG scaffolds had a favourable effect on the growth of commensal bacteria. Thus, the effect of implantation of the PHB/ALG scaffold compared to other scaffolds on the composition of the gut microbiota was closest to the control variant, which may demonstrate the biocompatibility of this device with the microbiota.

Macrophage-related gingival transcriptomic patterns and microbiome alterations in experimental periodontitis in nonhuman primates.

This study examined the microbiome features specifically related to host macrophage polarization in health, initiation and progression of periodontitis, and in resolution samples using a nonhuman primate model of ligature-induced periodontitis. The oral microbiome is a complex of bacterial phyla, genera, and species acquired early in life into the individual autochthonous oral ecology. The microbiome changes overtime in response to both intrinsic and extrinsic stressors, and transitions to a dysbiotic ecology at sites of periodontal lesions. Comparisons were made between the microbial and host features in young (≤7 years) and adult (≥12 years) cohorts of animals. Footprints of macrophage-related genes in the gingival tissues were evaluated using expression profiles including M0, M1, and M2 related genes. Within the gingival tissues, similar macrophage-related gene patterns were observed with significant increases with disease initiation and continued elevation throughout disease in both age groups. Approximately, 70% of the taxa were similar in relative abundance between the two groups; however, the adults showed a large number of OTUs that were significantly altered compared with the younger animals. Developing a correlation map identified three major node levels of interactions that comprised approximately ⅓ of the Operational Taxonomic Units (OTUs) that dominated the microbiomes across the samples. Also noted was a much greater frequency of significant correlations of individual OTUs with the macrophage phenotype markers, compared with disease and resolution samples in both age groups, with a greater frequency in the younger group. Moreover, these correlations were assigned to differentially expressed genes representing M0, M1, and M2-related phenotypes. A cluster analyses across the macrophage-related transcriptome and the OTUs demonstrated multiple somewhat distinct bacterial consortia, incorporating both commensal and putative pathogens, linked to the gene responses that differed in health, disease, and resolution samples. Finally, there were minimal alterations in the OTUs in individual clusters with specific macrophage-related responses in the younger group, while in the adult samples substantial variations were noted with genes from all macrophage phenotypes. The results confirmed important features that could reflect macrophage polarization in periodontal lesions, and provided some initial data supporting specific members of the oral microbiome feature prominently related to specific gene response patterns consistent with macrophages in the gingival tissues.

Exploring the bacterial genetic diversity and community structure of crude oil contaminated soils using microbiomics

The impact of environmental pollution in air and water is reflected mainly in the soil ecosystem as it impairs soil functions. Also, since the soil is the habitat for billions of organisms, the biodiversity is in turn altered. Microbes are precise sensors of ecological contamination, and bacteria have a key and important function in terms of bioremediation of the contaminated soil. Hence in the current work, we aimed at assessing the unidentified bacterial population through Illumina MiSeq sequencing technology and their community structural changes in different levels of petroleum-contaminated soil and sludge samples (aged, sludge, and leakage soil) to identify unique bacteria for their potential application in remediation. The studies showed that major bacterial consortiums namely, Proteobacteria (57%), Alphaproteobacteria (31%), and Moraxellaceae (23%) were present in aged soil, whereas Proteobacteria (52%), Alphaproteobacteria (33%), and Rhodobacteraceae (28%) were dominantly found in sludge soil. In leakage soil, Proteobacteria (59%), Alphaproteobacteria (33%), and Rhodobacteraceae (29%) were abundantly present. The Venn diagrams are used to analyze the distribution of abundances in individual operational taxonomic units (OTUs) within three soil samples. After data filtering, they were grouped into OTU clusters and 329 OTUs were identified from the three soil samples. Among the 329, 160 OTUs were common in the three soil samples. The bacterial diversity is estimated using alpha diversity indices and Shanon index and was found to be 4.490, 4.073 and 4.631 in aged soil, sludge soil and leakage soil, respectively and similarly richness was found to be 618, 417 and 418. The heat map was generated by QIIME software and from the top 50 enriched genera few microbes such as Pseudomonas, Bacillus, Mycobacterium, Sphingomonas and Paracoccus, were shown across all the samples. In addition, we also analyzed various physicochemical properties of soil including pH, temperature, salinity, electrical conductivity, alkalinity, total carbon, total organic matter, nitrogen, phosphorus and potassium to calculate the soil quality index (SQI). The SQI of aged, sludge and leakage soil samples were 0.73, 0.64, and 0.89, respectively. These findings show the presence of unexplored bacterial species which could be applied for hydrocarbon remediation and further they can be exploited for the same.

Occurrence of Styxosaurus (Sauropterygia: Plesiosauria) in the Cenomanian: implications for relationships of elasmosaurids of the Western Interior Seaway

The systematics of the elasmosaurid plesiosaurs from the Late Cretaceous of the Western Interior Seaway have been contentious, with studies supporting an endemic Elasmosaurinae clade. In this study four elasmosaurids from the Western Interior Seaway are examined in detail, and others discussed, to clarify the validity and ingroup relationships of the clade Elasmosaurinae. Two of the taxa examined here are Campanian in age: the holotype of Styxosaurus snowii, and an indeterminate species of Styxosaurus (‘Alzadasaurus pembertoni’). The other two specimens are Cenomanian: the holotype of Thalassomedon haningtoni, and an elasmosaurid specimen from Nebraska previously referred to Thalassomedon haningtoni. We find that the Nebraska specimen is referable to Styxosaurus. We therefore refer the Nebraska material to the new species Styxosaurus rezaci, distinguished by an extremely large caniniform tooth in the second maxillary tooth position, circular external nares, and the frontal forming the entire posterior margin of the external naris. We examined a matrix of 134 operational taxonomic units (OTUs) and 283 morphological characters with a parsimony analysis in TNT. We scored each of these elasmosaurs listed above as an individual OTU; also listed as OTUs were Styxosaurus browni and AMNH 1495 (Elasmosauridae indet.). We find that Thalassomedon and the species of Styxosaurus do form an endemic clade. However, the long-necked taxa Terminonatator and Albertonectes are not recovered as members of this clade, due to missing data for both taxa. We recovered Styxosaurus as a monophyletic clade diagnosed by features of the squamosal, the exclusion of the frontal from the orbit margin, and 60–63 cervical vertebrae. We refer the headless skeleton, AMNH 1495, to Elasmosauridae (indet.). We conclude that the genus Styxosaurus was a long-lived clade that inhabited the Western Interior Seaway for at least 12 million years. http://zoobank.org/urn:lsid:zoobank.org:pub:7E81A26D-9E19-42FE-9CAD-D58908EDCF7A

Abstract C078: The association between the oral microbiome and body mass index among Black women

Abstract Background. The prevalence of obesity (defined as ≥30 kg/m2) has increased by 40% over the past two decades. Black women have the highest prevalence of obesity of any US population group, with 57% of Black women classified as obese. The adverse health consequences of obesity include increased risk for type 2 diabetes, cardiovascular disease, cancer, and premature mortality. Evidence has mounted from animal and human studies that the gut microbiota, in particular bacteria, is associated with obesity. Few studies have examined the association between the oral microbiota and obesity. Methods. In the current study, we included Black Women’s Health Study participants who donated a saliva sample using an oral wash kit and whose oral microbiome was sequenced in prior nested case-control studies of pancreatic and lung cancer. Participants were cancer-free at the time of oral wash collection. A total of 624 participants with whole metagenome shotgun sequencing data were available for this research. Body mass index (BMI, kg/m2) was calculated and classified according to the World Health Organization: normal weight (18.5–24.9 kg/m2, n=132), overweight (25.0–29.9 kg/m2, n=228), and obesity (≥30.0 kg/m2, n=264). Raw sequencing reads were processed using PathoScope (v 2.0). Data were filtered based on total read counts for individual operational taxonomic units (OTUs) and average relative genus abundance. Thus, 3,629 OTUs representing 103 genera were retained. We corrected for batch effects using ComBat-Seq. We conducted differential abundance analyses, adjusting for age, smoking, alcohol, diabetes, and tooth loss. For detecting differentially abundant microbes, we used DESeq2, Limma, and ANCOM-BC, both separately and in combination, at the genus and species levels. Results. Fifty-two genera were differentially abundant by BMI category in at least one of our analyses. Of these, three genera—Corynebacterium, Haemophilus, and Solobacterium—were commonly differentially abundant across all analyses. Notably, Solobacterium was more abundant in individuals with obesity, compared to individuals with normal or overweight, whereas Corynebacterium and Haemophilus were less abundant in individuals with overweight but not normal weight or obesity. On the species level, 98 species were differentially abundant by BMI category in at least one of our analyses. Three species were differentially abundant across all analyses: Cardiobacterium valvarum, Neisseria bacilliformis, and S. moorei (the only known species of Solobacterium). Conclusions. Our findings demonstrate that multiple oral microbial taxa are significantly differentially abundant by BMI category in Black women, who have a higher prevalence of obesity than any other race-gender group and suffer greatly from the adverse health effects of obesity. In particular, women with obesity had a higher abundance of S. moorei. This bacterium was also recently identified as more abundant in the gut microbiome of Chinese men and women with obesity and the abundance decreased with a weight loss intervention. Citation Format: Jessica L. Petrick, Howard J. Fan, Lynn Rosenberg, Julie R. Palmer, W. Evan Johnson. The association between the oral microbiome and body mass index among Black women [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C078.

Mapping Microbial Abundance and Prevalence to Changing Oxygen Concentration in Deep-Sea Sediments Using Machine Learning and Differential Abundance.

Oxygen constitutes one of the strongest factors explaining microbial taxonomic variability in deep-sea sediments. However, deep-sea microbiome studies often lack the spatial resolution to study the oxygen gradient and transition zone beyond the oxic-anoxic dichotomy, thus leaving important questions regarding the microbial response to changing conditions unanswered. Here, we use machine learning and differential abundance analysis on 184 samples from 11 sediment cores retrieved along the Arctic Mid-Ocean Ridge to study how changing oxygen concentrations (1) are predicted by the relative abundance of higher taxa and (2) influence the distribution of individual Operational Taxonomic Units. We find that some of the most abundant classes of microorganisms can be used to classify samples according to oxygen concentration. At the level of Operational Taxonomic Units, however, representatives of common classes are not differentially abundant from high-oxic to low-oxic conditions. This weakened response to changing oxygen concentration suggests that the abundance and prevalence of highly abundant OTUs may be better explained by other variables than oxygen. Our results suggest that a relatively homogeneous microbiome is recruited to the benthos, and that the microbiome then becomes more heterogeneous as oxygen drops below 25 μM. Our analytical approach takes into account the oft-ignored compositional nature of relative abundance data, and provides a framework for extracting biologically meaningful associations from datasets spanning multiple sedimentary cores.

181 Evaluation of the Fecal Microbiota in Commercial Sows with Variable Risk for Pelvic Organ Prolapse During Late Gestation

Abstract Sow mortality has increased during the last decade with a large portion due to pelvic organ prolapse (POP) manifesting during late gestation and early lactation. Approximately 21% of sow mortality is attributed to POP, creating a significant economic and animal welfare concern. The study objective was to identify differences in sow fecal microbiota associated with POP risk and to determine if fecal and vaginal microbial communities are correlated. Using an established perineal scoring (PS) system, 2,864 sows were assigned PS1 (low), PS2 (moderate), or PS3 (high) based on phenotypic observations and presumed POP risk during gestation week 15. Of those sows scored, 1.0%, 2.7%, and 23.4% of PS1, PS2, and PS3 assigned sows, respectively, subsequently experienced POP. At the time of scoring, fecal swabs were collected from sows (n = 213) and DNA was extracted for 16S rRNA gene Illumina MiSeq sequencing, and analyzed using mothur, phyloseq and SAS. Additionally, co-occurrence networks were constructed between fecal and vaginal microbial communities using CoNet (V1.1.1), to identify correlations in taxa abundance. Differences in fecal community composition (PERMANOVA; P < 0.05), structure (alpha diversity measurements; P < 0.05), and 13 individual operational taxonomic units (OTU; Q < 0.05) were detected between PS1 and PS3 sows. The abundance of several taxa were correlated across sample collection sites, suggesting the fecal and vaginal microbial communities may influence one another. Collectively, fewer differences exist in fecal microbiota in sows differing risk for POP than previously observed in vaginal microbiota, suggesting the vaginal microbial communities may be a better indicator of POP risk. Understanding correlations between the fecal and vaginal microbial communities may provide strategies or targets for combatting POP. This project was supported by the National Pork Board and the Foundation for Food and Agriculture Research.

Microbiome Analysis via OTU and ASV-Based Pipelines—A Comparative Interpretation of Ecological Data in WWTP Systems

Linking community composition and ecosystem function via the cultivation-independent analysis of marker genes, e.g., the 16S rRNA gene, is a staple of microbial ecology and dependent disciplines. The certainty of results, independent of the bioinformatic handling, is imperative for any advances made within the field. In this work, thermophilic anaerobic co-digestion experimental data, together with primary and waste-activated sludge prokaryotic community data, were analyzed with two pipelines that apply different principles when dealing with technical, sequencing, and PCR biases. One pipeline (VSEARCH) employs clustering methods, generating individual operational taxonomic units (OTUs), while the other (DADA2) is based on sequencing error correction algorithms and generates exact amplicon sequence variants (ASVs). The outcomes of both pipelines were compared within the framework of ecological-driven data analysis. Both pipelines provided comparable results that would generally allow for the same interpretations. Yet, the two approaches also delivered community compositions that differed between 6.75% and 10.81% between pipelines. Inconsistencies were also observed linked to biologically driven variability in the samples, which affected the two pipelines differently. These pipeline-dependent differences in taxonomic assignment could lead to different conclusions and interfere with any downstream analysis made for such mis- or not-identified species, e.g., network analysis or predictions of their respective ecosystem service.

The Evolution of Ecological Diversity in Acidobacteria.

Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success.

Characterization of two microalgae consortia grown in industrial wastewater for biomass valorization

The use of microalgae-bacteria consortium coupled with biomass valorization is promising for environmentally friendly and economical wastewater treatment. However, a significant challenge associated with microalgae consortia grown in wastewater is predicting how different species will grow together and how this will affect both, the composition and the productivity of different batches. Therefore, this study aimed to examine microbiome associated with a green alga consortium versus a cyanobacteria consortium, both evolved from the same initial consortium, to compare their wastewater treatment efficiency as well as the metabolites of interest produced. Cultures of both consortia were conducted in a semi-continuous mode in 2 L photobioreactors for 51 days with standard culture medium with or without wastewater. Analysis of individual OTUs (operational taxonomic units) from the microbial community revealed that 1) Trebouxiophyceae and Gomphosphaeriaceae are the most abundant organisms in the green algae and cyanobacteria consortia respectively; and 2) both consortia shared 28% and 15% of identified prokaryotes and eukaryotes OTUs, respectively. Although the cultures enriched with wastewater did not achieve the yields obtained with a standard medium, growth was observed with a nutrient removal efficiency up to 91% and 63% for total nitrogen and total carbon respectively. The algal biomass as well as the supernatants from the two consortia were analyzed by UPLC-QTOF-MS and GC–MS. Results showed valuable bioactive compounds such as lecanoric acid (antimicrobial, antioxidant and anticancer) and high added-value lipids. Also, polyunsaturated fatty acids were the most abundant fatty acids in our samples (51% to 66%). Results suggest that even though an initial native consortium evolved into two different consortia, both can grow in presence of wastewater. Moreover, both were able to remove a high part of nitrogen and carbon while producing interesting compounds, which paves the way for a potential economically viable wastewater treatment process.

Fecal microbiota in inflammatory bowel disease: Studies of lactobacillus and bifidobacteria diversity

<br><b>Background:</b> Diversity of microbial species is a hallmark of dysbiosis in inflammatory bowel disease (IBD). This study was undertaken to determine whether the diversity of lactobacilli and bifidobacteria, two regulatory microbial genera, is altered in patients with IBD. <b>Methods:</b> DNA from fecal samples of 20 healthy volunteers, 20 patients with ulcerative colitis (UC), and 25 patients with Crohn's disease (CD) was amplified by the polymerase chain reaction (PCR) for 16S ribosomal RNA gene sequences specific to genus Lactobacillus and Bifidobacterium. Real-time PCR was done to quantitate bacterial abundance. Amplified DNA was also bar coded and sequenced on the Roche 454 platform. Individual operational taxonomic units (OTUs) were taken as sequences with at least 97% similarity. <b>Results:</b> Abundance of Lactobacillus was significantly increased in UC compared to controls; no other difference in Lactobacillus or Bifidobacterium abundance was found between the three groups. Median reads for genus Lactobacillus was similar between control (940), UC (994), and CD (960) groups. The median number of OTUs per sample was not significantly different between controls (6), UC (5.5) and CD (7). The Shannon index of community diversity was similar between controls (median 1.12), UC (median 1.13) and CD (median 1.11). The Simpson D index was also similar between controls (median 0.393), UC (median 0.439) and CD (median 0.409). Median reads for genus Bifidobacterium was similar between control (846), UC (1052), and CD (964) groups. The median number of Bifidobacteria OTUs per sample was similar for controls (6), UC (7) and CD (8.5). The Shannon index of community diversity was similar between controls (median 0.75), UC (median 1.0) and CD (median 1.14). The Simpson D index was also similar between controls (median 0.570), UC (median 0.422) and CD (median 0.409). <b>Conclusion:</b> The abundance of Lactobacillus was increased in UC. Diversity of genus Lactobacillus and Bifidobacterium was not altered in either UC or CD.<br>

Infant gut bacterial community composition and food-related manifestation of atopy in early childhood.

Background:Immunoglobulin E–mediated food allergy (IgE-FA) has emerged as a global public health concern. Immune dysregulation is an underlying mechanism for IgE-FA, caused by “dysbiosis” of the early intestinal microbiota. We investigated the association between infant gut bacterial composition and food-related atopy at age 3–5 years using a well-characterized birth cohort.Methods:The study definition of IgE-FA to egg, milk, or peanut was based on physician panel retrospective review of clinical and questionnaire data collected from birth through age 3–5 years. Using 16S rRNA sequencing, we profiled the bacterial gut microbiota present in stool specimens collected at 1 and 6 months of age.Results:Of 447 infants with data for analysis, 44 (9.8%) met physician panel review criteria for IgE-FA to ≥1 of the three allergens. Among children classified as IgE-FA at 3–5 years, infant stool samples showed significantly less diversity of the gut microbiota compared with the samples of children classified as no IgE-FA at age 3–5 years, especially for milk and peanut (all covariate-adjusted p’s for alpha metrics <.007). Testing of individual operational taxonomic units (OTUs) revealed 6-month deficiencies in 31 OTUs for IgE-FA compared with no IgE-FA, mostly in the orders Lactobacillales, Bacteroidales, and Clostridiales.Conclusions:Variations in gut microbial composition in infant stool were associated with a study definition of IgE-FA at 3–5 years of age. This included evidence of a lack of bacterial diversity, deficiencies in specific OTUs, and delayed microbial maturation. Results support dysbiosis in IgE-FA pathogenesis.

Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal.

Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.

The Effect of Biochar-Based Organic Amendments on the Structure of Soil Bacterial Community and Yield of Maize (Zea mays L.)

The taxonomic and functional diversity of bacteria in seven different experimental variants applied to soil under a maize plantation was determined by means of next-generation sequencing and biochemical methods. The aim of the study was to discover differences in the structure of bacteria and the level of soil enzymatic activity (BIF—biochemical index of fertility) after the application of a biofertiliser made of lignocellulosic substrate and biochar containing various microorganisms (algae, mycorrhizal fungi of the Glomus genus or the consortium of Bacillus sp. bacteria). The chemical composition and yield of crops was a measurable indicator of the effectiveness of the fertilisers. The biofertilisers influenced both the structure and the percentage share of individual bacterial operational taxonomic units (OTU). The cultivation of maize also modified qualitative and quantitative changes in the soil bacterial microbiome. A canonical variate analysis (CVA) showed that the soil pH exhibited a minimal positive correlation with the soil enzymatic activity and selected plant parameters, with the exception of the biofertiliser variant with arbuscular mycorrhiza (AM). Moreover, the AM biofertiliser significantly increased the BIF value, the yield of maize seeds and the starch content in the plants. The comprehensive nature of the research allowed for a deepening and systematization of the existing knowledge on the influence of biochar with the addition of selected microorganisms on the biochemical parameters of the soil and the bacterial biodiversity of the soil environment. Additionally, the inclusion of the chemical, sanitary composition and yield of maize in the research brought a measurable view of the changes taking place in the soil and plant environment under the influence of the discussed factor. Apart from the agronomic aspect (integrated crop cultivation—Directive 2009/128/EC) of our study, it was also closely related to environmental protection, as it proved that biochar-based biofertilisers could be an alternative to mineral fertilisation.

Seasonal Distribution of Cyanobacteria in Three Urban Eutrophic Lakes Results from an Epidemic-like Response to Environmental Conditions.

Cyanobacterial communities of three co-located eutrophic sandpit lakes were surveyed during 2016 and 2017 over season and depth using high-throughput DNA sequencing of the 16S rRNA gene. All three lakes were stratified except during April 2017 when the lakes were recovering from a strong mixing event. 16S rRNA gene V4 sequences were parsed into operational taxonomic units (OTUs) at 99% sequence identity. After rarefaction of 139 samples to 25,000 sequences per sample, a combined total of 921,529 partial 16S rRNA gene sequences were identified as cyanobacteria. They were binned into 19,588 unique cyanobacterial OTUs. Of these OTUs, 11,303 were Cyanobium. Filamentous Planktothrix contributed 1537 and colonial Microcystis contributed 265. The remaining 6482 OTUs were considered unclassified. For Planktothrix and Microcystis one OTU accounted for greater than 95% of the total sequences for each genus. However, in both cases the non-dominant OTUs clustered with the dominant OTUs by date, lake, and depth. All Planktothrix OTUs and a single Cyanobium OTU were detected below the oxycline. All other Cyanobium and Microcystis OTUs were detected above the oxycline. The distribution of Cyanobium OTUs between lakes and seasons can be explained by an epidemic-like response where individual OTUs clonally rise from a diverse hypolimnion population when conditions are appropriate. The importance of using 99% identity over the more commonly used 97% is discussed with respect to cyanobacterial community structure. The approach described here can provide another valuable tool for assessing cyanobacterial populations and provide greater insight into the controls of cyanobacterial blooms.

Stability Assessment of the Rumen Bacterial and Archaeal Communities in Dairy Cows Within a Single Lactation and Its Association With Host Phenotype.

Better characterization of changes in the rumen microbiota in dairy cows over the lactation period is crucial for understanding how microbial factors may potentially be interacting with host phenotypes. In the present study, we characterized the rumen bacterial and archaeal community composition of 60 lactating Holstein dairy cows (33 multiparous and 27 primiparous), sampled twice within the same lactation with a 122 days interval. Firmicutes and Bacteroidetes dominated the rumen bacterial community and showed no difference in relative abundance between samplings. Two less abundant bacterial phyla (SR1 and Proteobacteria) and an archaeal order (Methanosarcinales), on the other hand, decreased significantly from the mid-lactation to the late-lactation period. Moreover, between-sampling stability assessment of individual operational taxonomic units (OTUs), evaluated by concordance correlation coefficient (C-value) analysis, revealed the majority of the bacterial OTUs (6,187 out of 6,363) and all the 79 archaeal OTUs to be unstable over the investigated lactation period. The remaining 176 stable bacterial OTUs were mainly assigned to Prevotella, unclassified Prevotellaceae, and unclassified Bacteroidales. Milk phenotype-based screening analysis detected 32 bacterial OTUs, mainly assigned to unclassified Bacteroidetes and Lachnospiraceae, associated with milk fat percentage, and 6 OTUs, assigned to Ruminococcus and unclassified Ruminococcaceae, associated with milk protein percentage. These OTUs were only observed in the multiparous cows. None of the archaeal OTUs was observed to be associated with the investigated phenotypic parameters, including methane production. Co-occurrence analysis of the rumen bacterial and archaeal communities revealed Fibrobacter to be positively correlated with the archaeal genus vadinCA11 (Pearson r = 0.76) and unclassified Methanomassiliicoccaceae (Pearson r = 0.64); vadinCA11, on the other hand, was negatively correlated with Methanobrevibacter (Pearson r = –0.56). In conclusion, the rumen bacterial and archaeal communities of dairy cows displayed distinct stability at different taxonomic levels. Moreover, specific members of the rumen bacterial community were observed to be associated with milk phenotype parameters, however, only in multiparous cows, indicating that dairy cow parity could be one of the driving factors for host–microbe interactions.

Particle Collection in Imhoff Sedimentation Cones Enriches Both Motile Chemotactic and Particle-Attached Bacteria.

Marine heterotrophic microorganisms remineralize about half of the annual primary production, with the microbiomes on and around algae and particles having a major contribution. These microbiomes specifically include free-living chemotactic and particle-attached bacteria, which are often difficult to analyze individually, as the standard method of size-selective filtration only gives access to particle-attached bacteria. In this study, we demonstrated that particle collection in Imhoff sedimentation cones enriches microbiomes that included free-living chemotactic bacteria and were distinct from particle microbiomes obtained by filtration or centrifugation. Coastal seawater was collected during North Sea phytoplankton spring blooms, and the microbiomes were investigated using 16S rRNA amplicon sequencing and fluorescence microscopy. Enrichment factors of individual operational taxonomic units (OTUs) were calculated for comparison of fractionated communities after separation with unfractionated seawater communities. Filtration resulted in a loss of cells and yielded particle fractions including bacterial aggregates, filaments, and large cells. Centrifugation had the lowest separation capacity. Particles with a sinking rate of >2.4 m day–1 were collected in sedimentation cones as a bottom fraction and enriched in free-living chemotactic bacteria, i.e., Sulfitobacter, Pseudoalteromonas, and Vibrio. Subfractions of these bottom fractions, obtained by centrifugation, showed enrichment of either free-living or particle-attached bacteria. We identified five distinct enrichment patterns across all separation techniques: mechano-sensitive and mechano-stable free-living bacteria and three groups of particle-attached bacteria. Simultaneous enrichment of particle-attached and chemotactic free-living bacteria in Imhoff sedimentation cones is a novel experimental access to these groups providing more insights into the diversity, structure, and function of particle-associated microbiomes, including members of the phycosphere.

Comparison of Effects of Trichuris muris and Spontaneous Colitis on the Proximal Colon Microbiota in C3H/HeJ and C3Bir IL10-/- Mice.

The nematode Trichuris muris has been shown to interact with specific enteric bacteria, but its effects on the composition of its host's microbial community are not fully understood. We hypothesized that Trichuris muris-infected mice would have altered colon microbiota as compared with uninfected mice. Colon histopathology and microbial community structure and composition were examined in mouse models of colitis (C3BirTLR4-/- IL10-/- and C3H/HeJ TLR4-/- IL10+/+ mice) with and without T. muris infection, in uninfected C3BirIL10-/- mice with and without spontaneous colitis, and in normal C3H/ HeJ mice. T. muris-infected mice developed colon lesions that were more severe than those seen in IL10-deficient mice. Ap- proximately 80% of infected IL10-/- mice had colon neutrophilic exudates, and some had extraintestinal worms and bacteria. The composition and structure of proximal colon microbiota were assessed by using terminal restriction fragment length polymorphism analysis targeting the bacterial 16S rRNA gene. Colon microbiota in C3BirIL10-/- and C3H/HeJ mice differed both qualitatively and quantitatively. Trichuris infection significantly altered the relative abundance of individual operational taxonomic units [OTU] but not the composition (presence or absence of OTU) of colon microbiota in the 2 mouse genotypes. When C3BirIL10-/- and C3H/HeJ mouse OTU were considered separately, Trichuris was found to affect the microbiota of C3BirIL10-/- mice but not of C3H/HeJ mice. Even though 34 of the 75 (45%) C3BirIL10-/- mice had spontaneous colitis, neither qualitative nor quantitative differences were detected in microbiota between colitic or noncolitic C3BirIL10-/- mice or noncolitic C3H/HeJ mice. Therefore, Trichuris-infected mice developed distinct microbial communities that were influenced by host background genes; these alterations cannot be attributed solely to colonic inflammation.

PSVIII-3 Can the fermentation of insoluble corn fiber be improved in the pig? – An investigation into the in vivo mode of action of xylanase

Abstract Xylanase may improve fermentability of corn co-products through the alteration of hemicellulose, but the mode of action (MOA) is incompletely understood. The experimental objective was to investigate the in vivo MOA of xylanase in growing pigs fed insoluble fiber. Sixty gilts (25.4 ± 0.9 kg BW; L337 X Camborough), were blocked by weight, housed individually, and randomly assigned to one of four dietary treatments: a low-fiber control (LF; 8.45% NDF), a 30% corn bran high-fiber control (HF; 24.5% NDF), HF + 100 mg of xylanase/kg (HF+XY; Econase XT 25P; AB Vista, Marlborough, UK), and HF + 50 mg of arabinoxylan-oligosaccharide/kg (HF+AX; 3-7 degrees of polymerization). Gilts were fed ad libitum for 36 d, followed by 10-d of metabolism crate housing and limit feeding (80% of average ad libitum intake). On d 46, pigs were necropsied and ileal, cecal, and colonic digesta were collected for short-chain fatty acid (SCFA) analysis, and 16s rRNA gene amplicon sequencing. Data were analyzed as a mixed model with random effects of replicate and block, and fixed effect of treatment. Differences in individual operational taxonomic units (OTUs) were compared using Linear Discriminant Analysis Effect Size. Acetate, propionate, butyrate, and total SCFA in the ileum did not differ (P &amp;gt;0.05), but HF+XY had 10 significantly different OTUs compared to HF in the ileum (P&amp;lt; 0.05). In the cecum, compared to LF, HF reduced total SCFA concentration (91.7 vs. 82.8 mM/L; P&amp;lt; 0.01). However, HF+XY and HF+AX increased total SCFA concentration by 23% and 12% over HF, respectively (P&amp;lt; 0.05). This is likely due to increased cecal acetate concentration (54.0, 53.2, 74.4, 61.2 mM/L for LF, HF, HF+XY, and HF+AX, respectively; P&amp;lt; 0.01). Total colonic SCFA concentration did not differ (P=0.72), but xylanase increased molar proportions of butyrate (P&amp;lt; 0.01). One MOA of xylanase could be the release of fermentable substrates from insoluble fiber.

A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination.

Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) toward a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526mg kg-1) soil compared to corresponding communities extracted from moderately (458mg kg-1) Cu contaminated soil and a low Cu reference soil (15mg kg-1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.