Do Oil and Gas Lease Stipulations in the Northwestern Gulf of Mexico Need Expansion to Better Protect Vulnerable Coral Communities? How Low Relief Habitats Support High Coral Biodiversity

The continental shelf of the northwestern Gulf of Mexico harbors extensive reefs and banks that support diverse coral reefs and mesophotic communities. Mesophotic communities range in depth from 40 to 200 m and, in this region, foster some of the densest coral forests [aggregations of mesophotic octocoral, antipatharian, and branching stony coral communities] reported in published literature (10.23 ± 9.31 col/m2). The geologic features underlying the exposed substrates that harbor mesophotic communities are targeted for extensive hydrocarbon exploration and extraction, as they often contain oil and/or natural gas. The Bureau of Ocean Energy Management regulates offshore energy development in the United States and is tasked with protecting sensitive biological communities from impacts related to oil and gas activities. This study analyzed alpha and beta diversity of mesophotic coral forests on fourteen topographic banks in the northwestern Gulf of Mexico. The objective of the study was to examine differences in structure and community in relation to lease stipulations established by the Bureau of Ocean and Energy Management. It was determined that dense and diverse mesophotic coral forests and carbonate producers exist in present regulatory zones that prohibit oil and gas activities; however, the coral communities exist in higher densities, diversity, and richness in low relief substrates outside of these regulatory zones. Our findings suggest low relief hard substrates serve as important habitat for mesophotic coral forests; thus, we suggest the expansion of current stipulations should be considered to provide better protection to vulnerable coral communities on low relief features. Furthermore, additional studies to refine the relationship between low relief structures and biodiversity are needed to develop more meaningful habitat definitions to support resource management and improve resource protection in the future.

Comparison of the Respiratory Tractmicrobiome in Hospitalized COVID-19 Patients with Different Disease Severity

Background: Little is known about the characteristics of respiratory tract microbiome in Coronavirus disease 2019 (COVID-19) inpatients with different severity. Methods: A cross-sectional study was conducted to characterize respiratory tract microbial communities of 69 COVID-19 inpatients from 64 nasopharyngeal swabs and 5 sputum specimens using 16S ribosomal RNA (rRNA) gene V3-V4 region sequencing. The bacterial profiles were used to find potential biomarkers by the two-step method, the combination of random forest model and the linear discriminant analysis effect size (LEfSe), and explore the connections with clinical characteristics by Spearman’s rank test.Results: Compared with mild COVID-19 patients, severe patients had significantly decreased bacterial diversity (Pvalues were less than 0.05 in the alpha and beta diversity) and relative lower abundance of opportunistic pathogens, including Actinomyces, Prevotella, Rothia, Streptococcus, Veillonella. Eight potential biomarkers including Treponema, Lachnoanaerobaculum, Parvimonas, Selenomonas, Alloprevotella, Porphyromonas, GemellaandStreptococcus were found to distinguish the mild COVID-19 patients from the severe COVID-19 patients. The genera of Actinomyces andPrevotella were negatively correlated with age and inpatient days. Intensive Care Unit (ICU) admission, neutrophil count (GRA) and lymphocyte count (LYMPH) were significantly correlated with different genera in the two groups. In addition, there were a positive correlation between Klebsiella and white blood cell count (WBC) in two groups.Conclusion: The respiratory tract microbiome had significant difference in COVID-19 patients with different severity. The value of the respiratory tract microbiome as predictive biomarkers for COVID-19 severity merits further exploration.

The rumen liquid metatranscriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula

Background Targeted modification of the dairy calf ruminal microbiome has been attempted through rumen fluid inoculation to alter productive phenotypes later in life. However, sustainable effects of the early life interventions have not been well studied, particularly on the metabolically active rumen microbiota and its functions. This study investigated the sustained effects of adult-derived rumen fluid inoculations in pre-weaning dairy calves on the active ruminal microbiome of post-weaned dairy calves analyzed via RNA-sequencing. Results Two different adult-derived microbial inocula (bacterial- or protozoal-enriched rumen fluid; BE or PE, respectively) were administered in pre-weaned calves (3–6 weeks) followed by analyzing active rumen microbiome of post-weaned calves (9 weeks). The shared bacterial community at the genus level of 16S amplicon-seq and RNA-seq datasets was significantly different (P = 0.024), 21 out of 31 shared major bacterial genera differed in their relative abundance between the two analytic pipelines. No significant differences were found in any of the prokaryotic alpha- and beta-diversity measurements (P > 0.05), except the archaeota that differed for BE based on the Bray–Curtis dissimilarity matrix (P = 0.009). Even though the relative abundances of potentially transferred microbial and functional features from the inocula were minor, differentially abundant prokaryotic genera significantly correlated to various fermentation and animal measurements including butyrate proportion, body weight, and papillae length and counts. The overall microbial functions were affected quantitatively by BE and qualitatively by PE (P < 0.05), and this might be supported by the individual KEGG module and CAZymes profile differences. Exclusive networks between major active microbial (bacterial and archaeal genera) and functional features (KEGG modules) were determined which were differed by microbial inoculations. Conclusions This study demonstrated that actively transcribed microbial and functional features showed reliable connections with different fermentations and animal development responses through adult rumen fluid inoculations compared to our previous 16S amplicon sequencing results. Exclusive microbial and functional networks of the active rumen microbiome of dairy calves created by BE and PE might also be responsible for the different ruminal and animal characteristics. Further understanding of the other parts of the gastrointestinal tract (e.g., abomasum, omasum, and small intestine) using metatranscriptomics will be necessary to elucidate undetermined biological factors affected by microbial inoculations.

Parasite-Probiotic Interactions in the Gut: Bacillus sp. and Enterococcus faecium Regulate Type-2 Inflammatory Responses and Modify the Gut Microbiota of Pigs During Helminth Infection

Dietary probiotics may enhance gut health by directly competing with pathogenic agents and through immunostimulatory effects. These properties are recognized in the context of bacterial and viral pathogens, but less is known about interactions with eukaryotic pathogens such as parasitic worms (helminths). In this study we investigated whether two probiotic mixtures (comprised of Bacillus amyloliquefaciens, B. subtilis, and Enterococcus faecium [BBE], or Lactobacillus rhamnosus LGG and Bifidobacterium animalis subspecies Lactis Bb12 [LB]) could modulate helminth infection kinetics as well as the gut microbiome and intestinal immune responses in pigs infected with the nodular worm Oesophagostomum dentatum. We observed that neither probiotic mixture influenced helminth infection levels. BBE, and to a lesser extent LB, changed the alpha- and beta-diversity indices of the colon and fecal microbiota, notably including an enrichment of fecal Bifidobacterium spp. by BBE. However, these effects were muted by concurrent O. dentatum infection. BBE (but not LB) significantly attenuated the O. dentatum-induced upregulation of genes involved in type-2 inflammation and restored normal lymphocyte ratios in the ileo-caecal lymph nodes that were altered by infection. Moreover, inflammatory cytokine release from blood mononuclear cells and intestinal lymphocytes was diminished by BBE. Collectively, our data suggest that selected probiotic mixtures can play a role in maintaining immune homeostasis during type 2-biased inflammation. In addition, potentially beneficial changes in the microbiome induced by dietary probiotics may be counteracted by helminths, highlighting the complex inter-relationships that potentially exist between probiotic bacteria and intestinal parasites.

Butterfly Community Diversity in the Qinling Mountains

The Qinling Mountains are one of the oldest mountain ranges in China and a global biodiversity research and conservation hotspot. However, there is a lack of systematic research and survey of butterfly diversity in this region. Based on the butterfly taxa, combined with the changes in natural climate, altitude gradient and season in the Qinling Mountains, the butterfly diversity and community structure changes in 12 counties in the middle Qinling Mountains were analyzed by transect surveys and platform data analyses. A total of 9626 butterflies were observed, belonging to 427 species across 175 genera and 5 families. The species richness on the southern slope of the Qinling Mountains was higher than on the northern slope. We also studied the variation in alpha and beta diversity of butterflies. The results show that butterfly species were abundant and the highest diversity was found at the middle altitudes (1000–2000 m). Moreover, there were obvious seasonal differences in both species and number of butterflies. The community similarity in spring, summer and autumn was low, with limited species co-existing. The butterflies in the Qinling Mountains reserve area were the most abundant, exhibiting no significant difference with those in the ecotone and the farm area. Finally, we did an assessment of butterflies as endangered and protected species. In conclusion, our long-term butterfly survey data show that human disturbance and climate and environmental changes jointly shape the butterfly diversity in the middle of the Qinling Mountains.

Alfa and beta diversity of thrips (Thysanoptera) and biological control agents in chrysanthemum flowers (Chrysanthemum sp.) of two ecoregions in Jujuy province, Argentina

The objectives of this study are to identify thrips and their biological controllers, to analyze their abundance in three flower opening stages stages of chrysanthemum crops, and to determine alpha and beta diversity in two ecoregions of Jujuy province (Argentina). The study was carried out in the Chaco ecoregion (ECH) in October and November 2016, and in the Prepuna ecoregion (EP) in February and March 2018. On each date, six replicates of five flowers were excised in the stages: flower bud , semi-open flower and open flower. Diversity profiles and rank-abundance curves were built, and Jaccard's coefficient of similarity was applied. The diversity profiles showed significant differences in thrips communities. In the ECH, 15 thrips species were identified; the dominant and permanent species were Microcephalothrips abdominalis (Crawford) and Frankliniella occidentalis (Pergande). Five species were recorded in the EP, although Frankliniella gemina Bagnall and Thrips tabaci Lindeman on their own represented 78% of the total abundance. In the ECH, 20 entomophagous species/morphospecies were recognized, and 19 in the EP; antocorids were dominant in both ecoregions. The thrips and the entomophagous communities of chrysanthemum flowers were different (34%) between the ecoregions studied.

LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis

Background: Amplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (Less OTU Scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences. Results: In LotuS2, six different sequence clustering algorithms as well as extensive pre- and post-processing options allow for flexible data analysis by both experts, where parameters can be fully adjusted, and novices, where defaults are provided for different scenarios. We benchmarked three independent gut and soil datasets, where LotuS2 was on average 29 times faster compared to other pipelines - yet could better reproduce the alpha- and beta-diversity of technical replicate samples. Further benchmarking a mock community with known taxa composition showed that, compared to the other pipelines, LotuS2 recovered a higher fraction of correctly identified genera and species (98% and 57%, respectively). At ASV/OTU level, precision and F-score were highest for LotuS2, as was the fraction of correctly reconstructed 16S sequences. Conclusion: LotuS2 is a lightweight and user-friendly pipeline that is fast, precise and streamlined. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. Availability: LotuS2 is available from GitHub, conda or via a Galaxy web interface, documented at http://lotus2.earlham.ac.uk/.

Colorectal Cancer-Associated Microbiome Patterns and Signatures

The gut microbiome is dynamic and shaped by diet, age, geography, and environment. The disruption of normal gut microbiota (dysbiosis) is closely related to colorectal cancer (CRC) risk and progression. To better identify and characterize CRC-associated dysbiosis, we collected six independent cohorts with matched normal pairs (when available) for comparison and exploration of the microbiota and their interactions with the host. Comparing the microbial community compositions between cancerous and adjacent noncancerous tissues, we found that more microbes were depleted than enriched in tumors. Despite taxonomic variations among cohorts, consistent depletion of normal microbiota (members of Clostridia and Bacteroidia) and significant enrichment of oral-originated pathogens (such as Fusobacterium nucleatum and Parvimonas micra) were observed in CRC compared to normal tissues. Sets of hub and hub-connecting microbes were subsequently identified to infer microbe-microbe interaction networks in CRC. Furthermore, biclustering was used for identifying coherent patterns between patients and microbes. Two patient-microbe interaction patterns, named P0 and P1, can be consistently identified among the investigated six CRC cohorts. Characterization of the microbial community composition of the two patterns revealed that patients in P0 and P1 differed significantly in microbial alpha and beta diversity, and CRC‐associated microbiota changes consist of continuous populations of widespread taxa rather than discrete enterotypes. In contrast to the P0, the patients in P1 have reduced microbial alpha diversity compared to the adjacent normal tissues, and P1 possesses more oral-related pathogens than P0 and controls. Collectively, our study investigated the CRC-associated microbiome changes, and identified reproducible microbial signatures across multiple independent cohorts. More importantly, we revealed that the CRC heterogeneity can be partially attributed to the variety and compositional differences of microbes and their interactions to humans.

The impact of gastric acid suppression on the developing intestinal microbiome of a child

Gastric acid suppressing medications have been associated with an increased risk of Clostridioides difficile (C. difficile) infection, hypothesized to be due to underlying intestinal microbiome changes. Our goal is to characterize these changes in children as their microbiome is undergoing critical development. Our study included 5 children (< 3 years old) who were started on clinically indicated gastric acid suppression and 15 healthy age-matched controls. Stool samples were collected before and after 2 months of treatment. We analyzed the microbiome using 16S rRNA sequencing. Quantitative-PCR was used to detect C. difficile toxins. Subjects and controls had similar alpha and beta diversity. We found no significant change in alpha or beta diversity of subjects after treatment. C. difficile toxins were not found and there was no increase in C. difficile carriage after treatment. A significant increase in Lactobacillus was found after treatment, which has been associated with C. difficile in adults.

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Aquatic environmental DNA (eDNA) surveys are transforming how we monitor marine ecosystems. The time-consuming pre-processing step of active filtration, however, remains a bottleneck. Hence, new approaches omitting active filtration are in great demand. One exciting prospect is to use the filtering power of invertebrates to collect eDNA. While proof-of-concept has been achieved, comparative studies between aquatic and filter feeder eDNA signals are lacking. Here, we investigated the differences among four eDNA sources (water; bivalves; sponges; and ethanol in which filter-feeding organisms were stored) along a vertical transect in Doubtful Sound, New Zealand using three metabarcoding primers (fish (16S); MiFish-E/U). While concurrent SCUBA diver observations validated eDNA results, laboratory trials corroborated in-field bivalve eDNA detection results. Combined, eDNA sources detected 59 vertebrates, while divers observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was detected in ethanol, although only a reduced number of species were detected. Bivalves failed to reliably detect eDNA in both field and mesocosm experiments. While additional research into filter feeder eDNA accumulation efficiency is essential, our results provide strong evidence for the potential of incorporating sponges into eDNA surveys.