Family Taxonomic Level Research Articles

512 Divergence of the sow vaginal microbiome based on fertility status

Abstract The need for alternative biomarkers of reproductive potential in the pork industry is apparent as the current selection approach for sow fertility is not keeping up with the improvement of other production-related traits. To date, the vaginal microbiome has been overlooked as a source of potential biomarkers of sow fertility status. We aimed to elucidate a possible divergence of the vaginal microbiome between sows of differing fertility status and identify possible microbial biomarkers that classify the fertility potential of a sow. Microbial DNA was extracted from vaginal microbiome samples originating from highly reproductive sows (HRP, n = 41) with the number of piglets born alive ≥ 13 or infertile sows (INF, n = 22), that failed to become pregnant after two rounds of consecutive artificial insemination. Our 16S rRNA sequencing results revealed significant (P < 0.05) beta diversity divergence at the family and genus taxonomic levels between HRP and INF vaginal communities. INF vaginal communities displayed significantly greater (P < 0.05) alpha diversity at both the family and genus levels and had a significantly (P < 0.05) greater number of unique OTUs identified at the genus level. The composition of the vaginal microbiome diverges between HRP and INF sows, with INF sows experiencing a disruption of their communities via the colonization of opportunistic pathogens reducing the abundance of normal microbiota seen in HRP. The genera Streptococcus, Lachnospiraceae XPB1014 group, Staphylococcus and Treponema were selected to test as potential biomarkers due to their univariate significance, contribution to partial least squares discriminant analysis (PLS-DA) and selection in a recursive feature elimination model (RFE). The resultant support-vector machine model was diagnostic (achieving an ROC-AUC = 0.86), supporting the selected biomarkers as diagnostic markers for sow fertility status. Overall, there was an apparent shift from a normal vaginal microbiota in HRP sows to a dysbiotic vaginal microbiota in INF sows dominated by potentially pathogenic, more anaerobic and short-chain fatty acid (SCFA)-producing microbiota that may play damaging and pro-inflammatory roles in the vaginal canal. Lactobacillus, known to be the dominant genus in a majority of healthy human vaginal microbiomes, was not the dominating genus in either INF or HRP vaginal microbiomes, suggesting the uniqueness of pig vaginal microbiomes. This also emphasizes the need for pig-specific vaginal microbiome research. Investigations regarding the application of the potential vaginal microbial biomarkers identified in this study to a large, novel population of sow and gilt vaginal microbiome samples to test their on-farm accuracy are underway. In addition, the mechanistic and physiologic role of SCFAs and the bacteria that produce them in the sow vaginal microbiome should be further investigated to understand how they may influence or be a product of fertility status.

Selective and non-selective evolutionary signatures found in the simplest replicative biological entities.

Mitoviruses, which are considered evolutionary relics of extinct alpha-proteobacteria RNA phages, represent one of the simplest self-replicating biological systems. This study aims to quantitatively describe genomes and identify potential genomic signatures that support the protein phylogenetic-based classification criterion. Genomic variables, such as mononucleotide and dinucleotide composition, codon usage bias, and minimal free energy derived from optimized predicted RNA secondary structure, were analyzed. From the values obtained, the main evolutionary pressures were discussed, indicating that natural selection plays a significant role in shaping mitovirus genomes. However, neutral evolution also makes a significant contribution. This study reveals a significant discovery of structural divergence in Kvaramitovirus. The energy minimization approach employed to study 2D folding in this study reveals a distinct spatial organization of their genomes, providing evidence for the hypothesis of a single evolutionary event of circularization in the most recent common ancestor of the lineage. This hypothesis was discussed in light of recent discoveries by other researchers that partially support the existence of mitoviruses with circular genomes. Finally, this study represents a significant advancement in the understanding of mitoviruses, as it quantitatively describes the nucleotide sequence at the family and genus taxonomic levels. Additionally, we provide hypotheses that can be experimentally validated to inspire new research and address the gaps in knowledge of this fascinating, basally divergent RNA virus lineage.

The effect of anthelmintic treatment and efficacy on the faecal microbiota of healthy adult horses

Changes to the faecal microbiota of horses associated with administration of anthelmintic drugs is poorly defined. This study included horses with cyathostomin infection where susceptibility and resistance to oxfendazole and abamectin was known. This study assessed the changes to the faecal microbiota associated with administration of two different anthelmintics in this population. Twenty-four adult horses were included. Faecal egg counts were performed on all horses prior to random allocation into abamectin (n=8), oxfendazole (n=8) or Control groups (n=8) and at Day 14 post treatment. Faecal samples were collected for microbiota analysis prior to anthelmintic administration and on Day 3 and Day 14. From each faecal sample, DNA was extracted prior to PCR amplification, next generation sequencing and analysis using QIIME2. Anthelmintic treatment was associated with changes in alpha diversity (p <0.05), with increased evenness and diversity at Day 14 and increased richness at Day 3 within the abamectin group. Differences in relative abundance of bacteria at the phyla, family and genus taxonomic levels occurred after treatment; indicating that the microbiota was altered with anthelmintic administration. The results support that anthelmintic administration and removal of cyathostomins from the large intestine of horses is associated with changes in the faecal microbiota. The results suggest that removal of cyathostomins is associated with greater differences in microbiota, compared to anthelmintic drug administration that is ineffective in reducing cyathostomin infection. Cyathostomin removal was supported by adequate reduction of faecal egg counts, determined by faecal egg count reduction testing.

Effects of sustainable agricultural practices on soil microbial diversity, composition, and functions

Soil microorganisms can provide multiple benefits to agroecosystems, which are assumed to be promoted by sustainable agricultural practices. However, the mechanisms that explain this relationship have not been clearly elucidated. Although studies have reported that sustainable agricultural practices promote microbial biomass, the broader implications for soil microbial composition and functions remain uncertain. Accordingly, we searched field experiments worldwide contrasting soil microbial communities under conventional and sustainable agricultural practices. We analysed 924 results of relative abundance of bacteria or fungi (using 16 S and ITS rRNA amplicon sequencing, respectively) at the Family taxonomic level obtained from 46 articles. We found higher soil bacterial richness and higher abundance of copiotrophic bacteria under sustainable agricultural practices. Organic fertilisation promoted the abundance of bacteria involved in C and N cycling, while conservation tillage decreased those involved in the decomposition of plant residue. While sustainable agricultural practices had a minor effect on the overall fungal structure, they led to increases in symbiotic fungi abundance (e.g., Geoglossaceae). Additionally, we observed a slight increase in arbuscular mycorrhizal fungi and a slight reduction in pathogenic fungi associated with plant disease (e.g., Botryosphaeriaceae). Higher soil microbial taxonomic diversity did not lead to increased soil multifunctionality; however, it could safeguard resilience for soil functions via the diversity insurance effect. This study establishes that sustainable agricultural practices can significantly influence microbial communities, leading to compositional and structural changes, as well as promoting relevant functions for agroecosystems. Altogether, these results highlight the importance of integrating concepts of community ecology into agricultural management practices for reaching sustainable agricultural systems.

Microbiome composition and presence of cultivable commensal groups of Southern Tamanduas (Tamandua tetradactyla) varies with captive conditions

Southern Tamanduas (Tamandua tetradactyla) belong to the specialized placental myrmecophages. There is not much information about their intestinal microbiome. Moreover, due to their food specialization, it is difficult to create an adequate diet under breeding conditions. Therefore, we used 16S rDNA amplicon sequencing to analyze the fecal microbiome of captive Southern Tamanduas from four locations in the Czech Republic and evaluated the impact of the incoming diet and facility conditions on microbiome composition. Together with the microbiome analysis, we also quantified and identified cultivable commensals. The anteater fecal microbiome was dominated by the phyla Bacillota and Bacteroidota, while Pseudomonadota, Spirochaetota, and Actinobacteriota were less abundant. At the taxonomic family level, Lachnospiraceae, Prevotellaceae, Bacteroidaceae, Oscillospiraceae, Erysipelotrichaceae, Spirochaetaceae, Ruminococcaceae, Leuconostocaceae, and Streptococcaceae were mainly represented in the fecal microbiome of animals from all locations. Interestingly, Lactobacillaceae dominated in the location with a zoo-made diet. These animals also had significantly lower diversity of gut microbiome in comparison with animals from other locations fed mainly with a complete commercial diet. Moreover, captive conditions of analyzed anteater included other factors such as the enrichment of the diet with insect-based products, probiotic interventions, the presence of other animals in the exposure, which can potentially affect the composition of the microbiome and cultivable microbes. In total, 63 bacterial species from beneficial commensal to opportunistic pathogen were isolated and identified using MALDI-TOF MS in the set of more than one thousand selected isolates. Half of the detected species were present in the fecal microbiota of most animals, the rest varied across animals and locations.

Seasonal variation in marine bird distribution in the northeast Pacific Ocean

Human activities have profound influences on marine ecosystems. Marine birds are particularly sensitive to these impacts and, given their ease of observation and diverse life histories, often represent good indicators of ecosystem health. Conserving marine birds and their ecosystems requires robust predictions of species distribution to help mitigate human disturbance in areas where large aggregations of diverse species occur. We modelled variation in marine bird species diversity (Shannon-Wiener Index) and taxonomic family level probability of occurrence to map the intensity and extent of highly diverse ‘hotspots’ in Canada’s Pacific Exclusive Economic Zone. To do so, we paired 20 yr of survey data from the North Pacific Pelagic Seabird Database (1997-2017) and remote sensing data describing marine conditions and local geography (sea surface temperature, chlorophyll a, bathymetry, distance to shore, and benthic substrate type). These data were used to illustrate how seasonality within years and the El Niño-Southern Oscillation (ENSO) across years influenced spatial patterns in diversity. Hotspots were most persistent in Hecate Strait, off the west coast of Vancouver Island, and surrounding the Scott Islands in most seasons. Changes in hotspot locations and intensity were observed across seasons and within season under varying ENSO conditions. Our results provide a template for mapping marine species distribution for the purpose of identifying hotspots of diversity, and thereby facilitate planning to minimize harmful impacts in highly diverse and dynamic systems.

Anticoagulant Rodenticide Toxicity in Terrestrial Raptors: Tools to Estimate the Impact on Populations in North America and Globally.

Anticoagulant rodenticides (ARs) have caused widespread contamination and poisoning of predators and scavengers. The diagnosis of toxicity proceeds from evidence of hemorrhage, and subsequent detection of residues in liver. Many factors confound the assessment of AR poisoning, particularly exposure dose, timing and frequency of exposure, and individual and taxon-specific variables. There is a need, therefore, for better AR toxicity criteria. To respond, we compiled a database of second-generation anticoagulant rodenticide (SGAR) residues in liver and postmortem evaluations of 951 terrestrial raptor carcasses from Canada and the United States, 1989 to 2021. We developed mixed-effects logistic regression models to produce specific probability curves of the toxicity of ∑SGARs at the taxonomic level of the family, and separately for three SGARs registered in North America, brodifacoum, bromadiolone, and difethialone. The ∑SGAR threshold concentrations for diagnosis of coagulopathy at 0.20 probability of risk were highest for strigid owls (15 ng g-1 ) lower and relatively similar for accipitrid hawks and eagles (8.2 ng g-1 ) and falcons (7.9 ng g-1 ), and much lower for tytonid barn owls (0.32 ng g-1 ). These values are lower than those we found previously, due to compilation and use of a larger database with a mix of species and source locations, and also to refinements in the statistical methods. Our presentation of results on the family taxonomic level should aid in the global applicability of the numbers. We also collated a subset of 440 single-compound exposure events and determined the probability of SGAR-poisoning symptoms as a function of SGAR concentration, which we then used to estimate relative SGAR toxicity and toxic equivalence factors: difethialone, 1, brodifacoum, 0.8, and bromadiolone, 0.5. Environ Toxicol Chem 2024;00:1-11. © 2024 His Majesty the King in Right of Canada and The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC Reproduced with the permission of the Minister of Environment and Climate Change Canada.

P081 The integration of transcriptomic and microbiomic data links several intestinal bacterial families with key biological functions in the development of postoperative recurrence in Crohn's disease

Abstract Background Crohn's disease (CD) is characterized by an imbalance between the microbiota and the host. The severity of CD leads to intestinal resection. However, more than half of the patients not receiving prophylaxis experience post-operative recurrence (POR) within one year. The main objective of this study has been to improve the knowledge of the pathophysiological bases of POR through the integration of transcriptome and microbiome data. Methods Samples of inflamed and microscopically non-inflamed ileal mucosa were collected from patients with CD undergoing intestinal resection. The severity of POR was classified according to the Rutgeerts endoscopic index: without recurrence (i0+i1, n=12) and with recurrence (i2+i3+i4, n=8). Samples of healthy ileal tissue were also obtained from patients with colorectal cancer (n=10). Gene expression was evaluated by microarrays and organized into co-expression modules. By sequencing the V3-V4 region of the 16S rRNA gene, intestinal bacteria were identified and classified at the genus and family taxonomic level. The differential expression and correlations between the two sources of omics information were studied. Next, the analysis of pathway enrichment and clustering was carried out according to the severity of the POR and the intestinal area affected or not (graphical abstract A). Results The results of the integrative analysis in the uninflamed area of patients without recurrence showed that Actinomycetales negatively correlated with COX6A1 and MTRF1L, related to mitochondrial respiration (GO:0098803; q=0.004) and protein synthesis (R-HSA-72766; q=0.034) (B). These genes and bacteria also played a key role in modules 3 and 25 related to the respiratory chain. In contrast, the inflamed area of recurrent patients showed a positive correlation of the Xanthomonadaceae family in the regulation of neutrophil granules (GO:0035579; q=0.011), with the key participation of the ITGAM transcript (C). This transcript was also related to integrins (R-HSA-216083; q=0.007) in the transcriptomic analyses. In addition, Porphyromonadaceae correlated with LSR and TFF1, involved in epithelium maintenance (GO:0010669; q=0.012) and A group in the Lachnospiradaceae family correlated with CDC20 and CDT1, linked to the cell cycle (q=0.019). Conclusion Bacterial families, involved in butyrate production, such as Porphyromonadaceae and Lachnospiradaceae, could influence functions that remember to epithelial regeneration in recurrent patients, while Actinomycetales are associated with a normalization in energy production in uninflamed areas of resections of patients without POR. These findings reveal a potential interaction between the microbiota and the pathophysiology of POR in patients with CD.

Avaliando a suficiência taxonômica das comunidades de macroinvertebrados e seu potencial para distinguir os impactos do uso da terra em riachos de terras baixas no Uruguai

Abstract: Aim Macroinvertebrates are extensively employed as bioindicators for evaluating how stream ecosystems respond to alterations in physical and chemical habitats caused by human activity. Although family-taxonomic level is usually used to identify macroinvertebrates in biomonitoring programs, coarser taxonomic resolution may provide similar information. We aim to evaluate taxonomic sufficiency by comparing macroinvertebrate communities at the order and family levels to differentiate the effects of different land uses. Methods We conducted colonization experiments using artificial substrates in streams representing three land use types: urban (U, n=3), intensive agriculture - dairy production (AD, n=4), and extensive cattle ranching (CR, n=4). Results We obtained similar results using both taxonomic levels, which effectively distinguished the impacts of different land uses. In the sites examined, the majority of indicator groups exhibited only one family per order, with the exception of Ephemeroptera (Leptophlebiidae, Baetidae, and Caenidae). Notably, Baetidae and Caenidae were more prevalent in streams associated with extensive cattle ranching (CR). Conclusions Although this study provides a clear precedent, further investigation of these systems and other land uses (e.g., afforestation) is needed to validate this pattern. Coarser taxonomic assessment holds potential as a cost-effective method for stream monitoring and assessment in Uruguay.

Edaphic Beetles (Insecta: Coleoptera) in Three Different Land Use Systems in the Eastern Amazon

Objective: The objective of this study was to evaluate edaphic beetles’ abundance, diversity indexes and composition dependence in different land-use systems (LUS) under tropical climate conditions. Method: We surveyed three different LUS such as primary forest fragment (FFP), agroforestry system (SAF) and conventional agricultural cultivation (CAC) in Eastern Amazon. The edaphic beetles were collected using pitfall traps, identified to the family taxonomic level and classified into trophic guilds (carnivore, detritivore, fungivore, and/or herbivore). Results and conclusion: All LUS showed strong dominance by Scarabaeidae and Staphylinidae families. The edaphic beetles community is influenced by the LUS, since the highest rates of abundance, average richness, diversity and evenness were found in the CAC. Edaphic beetles’ composition is dependent to natural vegetation, which accumulated richness is the greatest parameter related to natural vegetation. Research implications: No-tillage cultivation, with homogeneous vegetation formed by decayed plant material from the last culture cycle, can improve and preserve beetles’ detritivore trophic guild. Due to the edaphic beetles’ composition dependence to natural vegetation, is important to preserve forest fragments near altered landscapes to ensure better conditions for this organism’s reestablishment. Originality/value: Edaphic beetles have rarely been studied under different LUS with tropical conditions, particularly in the Eastern Amazon. Comprising these organisms distribution pattern after land-use changes is essential for ecological conservation implications.

Diversity of fishes of the Napo and Arajuno rivers, with potential of handling, in the Parish Ahuano, Canton Tena, Napo Province

The study is carried out to establish the diversity of fish in the Napo and Arajuno rivers in the segments that cross the Ahuano parish of the Tena Canton, Napo Province in the Ecuadorian Amazon. Several studies indicate that the Napo River basin would have up to 680 species of fish (Barriga, 2012). A monitoring effort was carried out for 12 months. Trammel and trawl nets were used to collect the specimens. Sampling was carried out at five stations in each river, every 1,000 meters, once a month during the 11 months of study. As a general result, the record of 27 species of bony fish was obtained. Of the order Characiformes, 16 species were obtained, being the most diverse, while at the taxonomic family level, Characidae was more frequent with 9 corresponding species. Additionally, a survey was carried out among 5 indigenous and peasant communities on the banks of the two rivers to establish the preference for fish consumption and the potential species for management, which were: Prochilodus nigricans for 28%, followed by Pimelodus blochii 18%, Mylosoma duriventre, Leporinus pearsoni, Hypostomus oculeus, Aguarunichthys torosus, Leporinus friederici and Triportheus angulatus with 9% each.

Comprehensive analysis of water quality in the middle and lower basin of the Marquesote River Colombian

Different biotic indices have been used for the integral analysis of hydrographic basins in Colombia, using benthic microinverters and physicochemical parameters. A comprehensive analysis of water quality was performed in the low Marquesote river basin, using benthic macroinvertebrates and the ETP index (Ephemeroptera-Trichoptera-Plecoptera) as a biological indicator and some physicochemical parameters. Work was worked on the middle and lower basin on the Marquesote River at two times of the year (dry and rainy); standardized methods for water physicochemical variables were applied, for benthic fauna collected using a Surber network, and identifying them up to the taxonomic level of family. The study observed 22 families and 1388 individuals, where 49 % represent PTSD, indicating regular water quality; however, physicochemical variables had wide variation, noting that pH showed the greatest variability based on an analysis of major components. Environmental quality in the Marquesote river basin is compromised according to the indicators used, a more detailed study of the sources of pollution and dynamics of macroinvertebrates could provide a greater ecological knowledge of the basin

Characterization of gut microbiota associated with metabolic syndrome and type-2 diabetes mellitus in Mexican pediatric subjects

BackgroundChildhood obesity is a serious public health concern that confers a greater risk of developing important comorbidities such as MetS and T2DM. Recent studies evidence that gut microbiota may be a contributing factor; however, only few studies exist in school-age children. Understanding the potential role of gut microbiota in MetS and T2DM pathophysiology from early stages of life might contribute to innovative gut microbiome-based interventions that may improve public health. The main objective of the present study was to characterize and compare gut bacteria of T2DM and MetS children against control subjects and determine which microorganisms might be potentially related with cardiometabolic risk factors to propose gut microbial biomarkers that characterize these conditions for future development of pre-diagnostic tools.ResultsStool samples from 21 children with T2DM, 25 with MetS, and 20 controls (n = 66) were collected and processed to conduct 16S rDNA gene sequencing. α- and β-diversity were studied to detect microbial differences among studied groups. Spearman correlation was used to analyze possible associations between gut microbiota and cardiometabolic risk factors, and linear discriminant analyses (LDA) were conducted to determine potential gut bacterial biomarkers. T2DM and MetS showed significant changes in their gut microbiota at genus and family level. Read relative abundance of Faecalibacterium and Oscillospora was significantly higher in MetS and an increasing trend of Prevotella and Dorea was observed from the control group towards T2DM. Positive correlations were found between Prevotella, Dorea, Faecalibacterium, and Lactobacillus with hypertension, abdominal obesity, high glucose levels, and high triglyceride levels. LDA demonstrated the relevance of studying least abundant microbial communities to find specific microbial communities that were characteristic of each studied health condition.ConclusionsGut microbiota was different at family and genus taxonomic levels among controls, MetS, and T2DM study groups within children from 7 to 17 years old, and some communities seemed to be correlated with relevant subjects’ metadata. LDA helped to find potential microbial biomarkers, providing new insights regarding pediatric gut microbiota and its possible use in the future development of gut microbiome-based predictive algorithms.

Heartworm (Dirofilaria immitis) in carnivores kept in zoos in Texas, USA: risk perception, practices, and antigen detection

BackgroundDirofilaria immitis is the causative agent of heartworm disease in wild and domestic canids, felids, and mustelids. Recent studies demonstrate that additional families in the order Carnivora are also susceptible to infection. Therefore, the objectives of this study were to (1) better understand current practices surrounding heartworm prevention and diagnostics in zoological facilities located in the state of Texas, USA, and (2) assess archival serum samples of carnivores kept in these facilities for the presence D. immitis antigen and/or antibody.MethodsA questionnaire was completed by veterinarians or veterinary technicians representing 10 zoological facilities across Texas. This questionnaire was designed at the taxonomic family level, encompassing the 12 terrestrial carnivore families Ailuridae, Canidae, Eupleridae, Felidae, Herpestidae, Hyaenidae, Mephitidae, Mustelidae, Prionodontidae, Procyonidae, Ursidae, and Viverridae. The second objective was achieved with the use of archival serum samples made available by six zoo facilities.ResultsRisk perception varied across facilities for every family, including among species belonging to Canidae. All facilities used monthly heartworm prevention in canids and felids, with more variation existing in the other families. The use of diagnostic testing and type and route of administration of preventive varied by facility, with oral ivermectin the most commonly used preventive. A total of 217 archival serum samples, belonging to 211 individual animals encompassing 11 families and 39 species, were tested with a commercial heartworm antigen ELISA test, pre- and post-immune-complex dissociation. A subset of samples was also assessed for the presence of feline anti-heartworm antibodies using a commercial ELISA test. Two animals, both of which were Asian small-clawed otters from the same facility, had antigen detected (0.95%).ConclusionsThis study demonstrates that while the zoo veterinary community is aware of the risk and health impact of heartworm disease in canids and felids, there is still a great deal of uncertainty regarding the risks and ideal strategies for prevention in other carnivore families. The low proportion of antigen detection may serve as a baseline for future prevalence studies across the southern United States, where there is an emerging concern of macrocyclic lactone resistance in heartworm.Graphical

Anti-PD-L1 Antibody and/or 17β-Estradiol Treatment Induces Changes in the Gut Microbiome in MC38 Colon Tumor Model.

17β-Estradiol (E2) supplementation suppresses MC38 tumor growth by downregulating the expression of programmed death-ligand 1 (PD-L1). This study aims to figure out the gut microbiota that respond to anti-PD-L1 and/or estrogen treatment in MC38 colon cancer model. A syngeneic colon tumor model was developed by injection of MC38 cells into C57BL/6 background male and female mice. Three days before MC38 cells injection, E2 was supplemented to male mice daily for 1 week. Male and female mice with MC38 tumors (50-100 mm3) were injected with anti-PD-L1 antibody. Fresh feces were collected 26 days after injection of MC38 cells and 16S rRNA metagenomics sequencing of DNA extracted from feces was used to assess gut microbial composition. At the taxonomic family level, Muribaculaceae was enriched only in the MC38 male control group. In male mice, linear discriminant analysis effect size analysis at the species level revealed that the four microorganisms were commonly regulated in single and combination treatment with anti-PD-L1 and/or E2; a decrease in PAC001068_g_uc and PAC001070_s (family Muribaculaceae) and increase in PAC001716_s and PAC001785_s (family Ruminococcaceae). Interestingly, in the anti-PD-L1 plus E2 group, a decrease in opportunistic pathogens (Enterobacteriaceae group) and an increase in commensal bacteria (Lactobacillus murinus group and Parabacteroides goldsteinii) were observed. Furthermore, the abundance of Parabacteroides goldsteinii was increased in both males and females in the anti-PD-L1 group. Our results suggest that gut microbial changes induced by the pretreatment of estrogen before anti-PD-L1 might contribute to treatment of MC38 colon cancer.

Micronutrient Biosynthesis Potential of Spontaneous Grain Fermentation Microbiomes.

Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics. The purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analyses were conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) were generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipelines with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were differences in the relative abundances of the dominant taxa of bacteria that are involved in the spontaneous fermentation of millet namely Lactobacillaceae, Burkholderiaceae, Streptococcaceae, Leuconostocaceae, and Acetobacteraceae. Clostridiaceae was the dominant family in one dataset. The incidence of Lactobacillaceae and Bifidobacteriaceae suggest the probiotic characteristics of fermented millet. The datasets were collected with fermentations that were mediated by autochthonous microorganisms and the presence of some potential pathogens such as Enterobacteriaceae, Clostridiaceae, Aeromonadaceae, Microbacteiaceae, Pseudomonadaceae, and Neisseriaceae which suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as essential amino acids and vitamins, suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.

Identification of fish species through tRNA-based primer design

BackgroundThe correct establishment of the barcode classification system for fish can facilitate biotaxonomists to distinguish fish species, and it can help the government to verify the authenticity of the ingredients of fish products or identify unknown fish related samples. The Cytochrome c oxidation I (COI) gene sequence in the mitochondria of each species possesses unique characteristics, which has been widely used as barcodes in identifying species in recent years. Instead of using COI gene sequences for primer design, flanking tRNA segments of COI genes from 2618 complete fish mitochondrial genomes were analyzed to discover suitable primers for fish classification at taxonomic family level. The minimal number of primer sets is designed to effectively distinguish various clustered groups of fish species for identification applications. Sequence alignment analysis and cross tRNA segment comparisons were applied to check and ensure the primers for each cluster group are exclusive.ResultsTwo approaches were applied to improve primer design and re-cluster fish species. The results have shown that exclusive primers for 2618 fish species were successfully discovered through in silico analysis. In addition, we applied sequence alignment analysis to confirm that each pair of primers can successfully identify all collected fish species at the taxonomic family levels.ConclusionsThis study provided a practical strategy to discover unique primers for each fishery species and a comprehensive list of exclusive primers for extracting COI barcode sequences of all known fishery species. Various applications of verification of fish products or identification of unknown fish species could be effectively achieved.

Construcción de un índice integral basado en macroinvertebrados para determinar la calidad del agua con influencia agroindustrial

The physicochemical and biological indices have been used in isolation; if the parameters of these indices were applied in an integrated manner, they would bring together in a single measure the functional and structural variability of the biotic and abiotic components of water quality. The aim of this study was to build a comprehensive water quality index. Eleven sampling points were selected considering different degrees of agro-industrial intervention. 21 abiotic variables and 27 biological metrics were measured. Macroinvertebrates were quantitatively collected and identified to family taxonomic level. Using Principal Component Analysis, after standardization and exclusion of uncorrelated variables (VIF ≤ 10), the abiotic gradient was determined, which represented the abiotic variables that explained the disturbances in the water; with the abiotic gradient and the biological metrics, a Pearson correlation was performed, and those biological metrics that presented a high and non-redundant correlation were selected (Pearson 0.6 ≤ r ≤ 0.8); with the selected biological metrics, we proceeded to formulate and categorize the index; finally, by means of simple linear regression, the proposed index was compared with five other indexes (ICA, ICOMO, EPT, BMWP/col. and ASPT). The results showed that the abiotic gradient was defined by CP 1 which explained 65.5% of the accumulated variance, represented by altitude (r = 0.411), iron (r = 0.345) and dissolved oxygen (r = 0.329). The biological metrics used for the index design were: % scrapers, % swimmers, NEF of order 2, Ephemeroptera and Trichoptera tolerance. It was concluded that the integral index presents a higher predictive level (R2 = 0.87) of water quality, compared to the other indices: ASPT (R2 = 0.79), BMWP/col. (R2 = 0.68), EPT (R2 = 0.61), ICOMO (R2 = 0.35) and ICA (R2 = 0.27).

Nutritional Intake and Gut Microbiome Composition Predict Parkinson's Disease.

BackgroundModels to predict Parkinson’s disease (PD) incorporating alterations of gut microbiome (GM) composition have been reported with varying success.ObjectiveTo assess the utility of GM compositional changes combined with macronutrient intake to develop a predictive model of PD.MethodsWe performed a cross-sectional analysis of the GM and nutritional intake in 103 PD patients and 81 household controls (HCs). GM composition was determined by 16S amplicon sequencing of the V3-V4 region of bacterial ribosomal DNA isolated from stool. To determine multivariate disease-discriminant associations, we developed two models using Random Forest and support-vector machine (SVM) methodologies.ResultsUsing updated taxonomic reference, we identified significant compositional differences in the GM profiles of PD patients in association with a variety of clinical PD characteristics. Six genera were overrepresented and eight underrepresented in PD patients relative to HCs, with the largest difference being overrepresentation of Lactobacillaceae at family taxonomic level. Correlation analyses highlighted multiple associations between clinical characteristics and select taxa, whilst constipation severity, physical activity and pharmacological therapies associated with changes in beta diversity. The random forest model of PD, incorporating taxonomic data at the genus level and carbohydrate contribution to total energy demonstrated the best predictive capacity [Area under the ROC Curve (AUC) of 0.74].ConclusionThe notable differences in GM diversity and composition when combined with clinical measures and nutritional data enabled the development of a predictive model to identify PD. These findings support the combination of GM and nutritional data as a potentially useful biomarker of PD to improve diagnosis and guide clinical management.

Dynamics of the Queensland Fruit Fly Microbiome through the Transition from Nature to an Established Laboratory Colony.

The transition from nature to laboratory or mass rearing can impose significant physiological and evolutionary impact on insects. The Queensland fruit fly (also known as ‘Qfly’), Bactrocera tryoni (Froggatt) (Diptera: Tephritidae), is a serious economic pest that presents major challenges for horticulture industries in Australia. The sterile insect technique (SIT) is being developed to manage outbreaks in regions that remain free of Qfly and to suppress populations in regions where this species is endemic. The biology of Qfly is intimately connected to its microbiome. Therefore, changes in the microbiome that occur through domestication have implications for SIT. There are numerous studies of the microbiome in Qfly larvae and adults, but there is little information on how the microbiome changes as Qfly laboratory colonies are established. In this study, high-throughput Illumina sequencing was used to assess the Qfly microbiome in colonies reared from wild larvae, collected from fruit, for five generations, on a gel-based larval diet. Beta diversity analysis showed that the bacterial communities from Generation 5 (G5) clustered separately from earlier generations. At the genus level, bacterial communities were significantly different between the generations and mostly altered at G5. However, communities were found similar at phyla to family taxonomic levels. We observed high abundance of Morganella and Burkholderia at the genus level in the larval and pupal stages respectively at G5, but these were not detected in earlier generations. Overall, our findings demonstrate that the domestication process strongly affects the Qfly microbiome and prompts questions about the functional relationship between the Qfly and its microbiome, as well as implications for the performance of insects that have been domesticated and mass-reared for SIT programs.