Biodiversity metrics on ecological networks: Demonstrated with animal gastrointestinal microbiomes

Biodiversity has become a terminology familiar to virtually every citizen in modern societies.It is said that ecology studies the economy of nature,and economy studies the ecology of humans;then measuring biodiversity should be similar with measuring national wealth.Indeed,there have been many parallels between ecology and economics,actually beyond analogies.For example,arguably the second most widely used biodiversity metric,Simpson(1949)’s diversity index,is a function of familiar Gini-index in economics.One of the biggest challenges has been the high“diversity”of diversity indexes due to their excessive“speciation”-there are so many indexes,similar to each country’s sovereign currency-leaving confused diversity practitioners in dilemma.In 1973,Hill introduced the concept of“numbers equivalent”,which is based on Renyi entropy and originated in economics,but possibly due to his abstruse interpretation of the concept,his message was not widely received by ecologists until nearly four decades later.What Hill suggested was similar to link the US dollar to gold at the rate of$35 per ounce under the Bretton Woods system.The Hill numbers now are considered most appropriate biodiversity metrics system,unifying Shannon,Simpson and other diversity indexes.Here,we approach to another paradigmatic shift-measuring biodiversity on ecological networks-demonstrated with animal gastrointestinal microbiomes representing four major invertebrate classes and all six vertebrate classes.The network diversity can reveal the diversity of species interactions,which is a necessary step for understanding the spatial and temporal structures and dynamics of biodiversity across environmental gradients.

Interactions between maternal parity and feed additives drive the composition of pig gut microbiomes in the post‑weaning period

Background Nursery pigs undergo stressors in the post-weaning period that result in production and welfare chal-lenges.These challenges disproportionately impact the offspring of primiparous sows compared to those of mul-tiparous counterparts.Little is known regarding potential interactions between parity and feed additives in the post-weaning period and their effects on nursery pig microbiomes.Therefore,the objective of this study was to investigate the effects of maternal parity on sow and offspring microbiomes and the influence of sow parity on pig fecal microbi-ome and performance in response to a prebiotic post-weaning.At weaning,piglets were allotted into three treat-ment groups:a standard nursery diet including pharmacological doses of Zn and Cu(Con),a group fed a commercial prebiotic only(Preb)based on an Aspergillus oryzae fermentation extract,and a group fed the same prebiotic plus Zn and Cu(Preb+ZnCu).Results Although there were no differences in vaginal microbiome composition between primiparous and mul-tiparous sows,fecal microbiome composition was different(R^(2)=0.02,P=0.03).The fecal microbiomes of primiparous offspring displayed significantly higher bacterial diversity compared to multiparous offspring at d 0 and d 21 post-weaning(P<0.01),with differences in community composition observed at d 21(R^(2)=0.03,P=0.04).When analyzing the effects of maternal parity within each treatment,only the Preb diet triggered significant microbiome distinc-tions between primiparous and multiparous offspring(d 21:R^(2)=0.13,P=0.01;d 42:R^(2)=0.19,P=0.001).Composi-tional differences in pig fecal microbiomes between treatments were observed only at d 21(R^(2)=0.12,P=0.001).Pigs in the Con group gained significantly more weight throughout the nursery period when compared to those in the Preb+ZnCu group.Conclusions Nursery pig gut microbiome composition was influenced by supplementation with an Aspergillus oryzae fermentation extract,with varying effects on performance when combined with pharmacological levels of Zn and Cu or for offspring of different maternal parity groups.These results indicate that the development of nursery pig gut microbiomes is shaped by maternal parity and potential interactions with the effects of dietary feed additives.

Core and variable antimicrobial resistance genes in the gut microbiomes of Chinese and European pigs

Monitoring the prevalence of antimicrobial resistance genes(ARGs)is vital for addressing the global crisis of antibiotic-resistant bacterial infections.Despite its importance,the characterization of ARGs and microbiome structures,as well as the identification of indicators for routine ARG monitoring in pig farms,are still lacking,particularly concerning variations in antimicrobial exposure in different countries or regions.Here,metagenomics and random forest machine learning were used to elucidate the ARG profiles,microbiome structures,and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe.Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs(P<0.05).ANT(6)-Ib,APH(3')-IIIa,and tet(40)were identified as shared core ARGs between the two pig populations.Furthermore,the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions.Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs,respectively.Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100%and 98.7%,respectively.Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy(r=0.72-0.88).Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs.The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.

The roles of phosphate in shaping the structure and dynamics of Antarctic soil microbiomes

One major consequence of global warming in the Antarctic region is increased ice-free zones.Subsequent colonization of these ice-free areas by penguins alters their biogeochemistry,with one prominent example being elevation of inorganic phosphate concentrations around feces depositions.The complex soil biochemistry in the region makes it difficult to define the causal factors of these changes using common research approaches.Here,we addressed the effects of phosphate alone on microbiome structure and dynamics over time by adding external phosphate to selected soils in the Antarctic region.We then analyzed the soil bacterial community composition and diversity using 16S rRNA amplicon sequencing and compared these data with phosphate levels.Parallel geochemical analysis revealed changes in nine soil geochemical factors upon phosphate addition,all of which were relevant to microbiome structure,with soil pH showing the highest correlation.Links between geochemical factors and composition were identified,as were interactions between bacterial taxa.Additionally,Sphingobacteriia,Sphingobacteriales and Chitinophagaceae were found to be more abundant in phosphate-treated soils.Co-occurrence network analysis revealed significantly increased levels of associations in all major network properties over time after phosphate supplementation.Therefore,we conclude phosphate addition has diverse effects on Antarctic soil microbiomes.

Plant microbiomes and their role in plant health

Microorganisms are integral inhabitants of plants,playing a crucial role in plant growth,development,and health.The composition and diversity of microorganisms in plants can be influenced by several factors,including environmental factors such as soil type,temperature,and water availability.The plant microbiome serves essential functions,including nutrient acquisition,disease resistance,and stress tolerance,achieved through complex interactions between microorganisms and plants.Understanding these interactions and the impact of environmental factors can provide valuable insights into developing sustainable agricultural practices.The use of plant microbiomes in agriculture has the potential to improve crop yield,reduce fertilizer and pesticide use,and enhance soil health and sustainability,but scaling up these technologies poses several challenges.The potential benefits of using plant microbiomes in agriculture are significant and could revolutionize the industry.However,scaling up these technologies presents several challenges that require further research and innovation.In conclusion,studying plant microbiomes has the potential to bring about positive impacts for farmers,consumers,and the environment.

Meeting report: a close look at oral biofilms and microbiomes

The "Biofilms, Microbiomes and Oral Diseases: Challenges and Future Perspectives" symposium jointly organized by Penn Dental Medicine and West China School of Stomatology was held on 30 September 2017 at Penn Wharton China Center(PWCC) in Beijing,China. The topics included the pathogenicity of oral biofilms, novel strategies for the control of biofilm-related diseases, oral microbiome and single-cell approaches, and the link between oral diseases and overall health. Researchers from a number of disciplines, representing institutions from China and Penn Dental Medicine, gathered to discuss advances in our understanding of biofilms, as well as future directions for the control of biofilm-related oral and systemic diseases.

Microbiomes of Top and Sub-Layers of Semi-Arid Soils in North-Eastern Nigeria Are Rich in Firmicutes and Proteobacteria with Surprisingly High Diversity of Rare Species

Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46?C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32?C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria;however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility, suggest that revegetation efforts could be improved by shifting the gradient of these microbiota upwards using shades and micro-irrigation. Soils in semi-arid regions in Nigeria contain numerous operational taxonomic bacterial groups with potential thermophilic and drought genetic resources to be mined. Microbial community structure beneath the top soil appears stable and should be the target sample for the assessments of climatic change impact on microbial community structure in environments like this.

The vaginal and fecal microbiomes are related to pregnancy status in beef heifers

Background:The greatest impact on profitability of a commercial beef operation is reproduction.However,in beef heifers,little is known about the vaginal and fecal microbiota with respect to their relationship with fertility.To this end,we followed heifers through gestation to examine the dynamics of vaginal and fecal microbial composition throughout pregnancy.Results:Heifers were exposed to an estrus synchronization protocol,observed over a 12-day period,artificially inseminated 12 h to 18 h after observed estrus,and subsequently exposed to bulls for a 50-day breeding season.Vaginal samples were taken at pre-breeding(n=72),during the first(n=72),and second trimester(n=72)for all individuals,and third trimester for individuals with confirmed pregnancies(n=56).Fecal samples were taken at prebreeding(n=32)and during the first trimester(n=32),including bred and open individuals.Next generation sequencing of the V4 region of the 16 S rRNA gene via the Illumina Mi Seq platform was applied to all samples.Shannon indices and the number of observed bacterial features were the same in fecal samples.However,significant differences in vaginal microbiome diversity between gestation stages were observed.No differences in beta-diversity were detected in vaginal or fecal samples regarding pregnancy status,but such differences were seen with fecal microbiome over time.Random Forest was developed to identify predictors of pregnancy status in vaginal(e.g.,Histophilus,Clostridiaceae,Campylobacter)and fecal(e.g.,Bacteroidales,Dorea)samples.Conclusions:Our study shows that bovine vaginal and fecal microbiome could be used as biomarkers of bovine reproduction.Further experiments are needed to validate these biomarkers and to examine their roles in a female’s ability to establish pregnancy.

Distinct gut microbiomes in Thai patients with colorectal polyps

BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence[e.g.,tubular adenoma(TA)]often progress to malignancy and are closely associated with changes in the composition of the gut microbiome.There is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway,such as hyperplastic polyps(HP).Exploration of microbiome alterations asso-ciated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal carcinogenesis.AIM To investigate gut microbiome signatures,microbial associations,and microbial functions in HP and TA patients.METHODS Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps[control group(CT),n=40],patients with HP(n=52),and patients with TA(n=60).Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or TA.Analytical techniques in this study included differential abundance analysis,co-occurrence network analysis,and differential pathway analysis.RESULTS Colorectal cancer(CRC)-associated bacteria,including Streptococcus gallolyticus(S.gallolyticus),Bacteroides fragilis,and Clostridium symbiosum,were identified as characteristic microbial species in TA patients.Mediterraneibacter gnavus,associated with dysbiosis and gastrointestinal diseases,was significantly differentially abundant in the HP and TA groups.Functional pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively,whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis(e.g.,mevalonate);S.gallolyticus was a major contributor.Co-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients,whereas TA patients exhibited co-occurrence of CRC-associated bacteria.Furthermore,the co-occurrence of SCFA-producing bacteria was lower in TA patients than HP patients.CONCLUSION This study revealed distinct gut microbiome signatures associated with pathways of colorectal polyp development,providing insights concerning the roles of microbial species,functional pathways,and microbial interactions in colorectal carcinogenesis.

Interspecific plant interaction via root exudates structures the disease suppressiveness of rhizosphere microbiomes

Terrestrial plants can affect the growth and health of adjacent plants via interspecific interaction.Here,we studied the mechanism by which plant root exudates affect the recruitment of the rhizosphere microbiome in adjacent plants—with implications for plant protection—using a tomato(Solanum lycopersicum)–potatoonion(Allium cepa var.agrogatum)intercropping system.First,we showed that the intercropping system results in a disease-suppressive rhizosphere microbiome that protects tomato plants against Verticillium wilt disease caused by the soilborne pathogen Verticillium dahliae.Second,16S rRNA gene sequencing revealed that intercropping with potatoonion altered the composition of the tomato rhizosphere microbiome by promoting the colonization of specific Bacillus sp.This taxon was isolated and shown to inhibit V.dahliae growth and induce systemic resistance in tomato plants.Third,a belowground segregation experiment found that root exudates mediated the interspecific interaction between potatoonion and tomato.Moreover,experiments using split-root tomato plants found that root exudates from potatoonion,especially taxifolin—a flavonoid compound—stimulate tomato plants to recruit plant-beneficial bacteria,such as Bacillus sp.Lastly,ultra-high-pressure liquid chromatography–mass spectrometry analysis found that taxifolin alters tomato root exudate chemistry;thus,this compound acts indirectly in modulating root colonization by Bacillus sp.Our results revealed that this intercropping system can improve tomato plant fitness by changing rhizosphere microbiome recruitment via the use of signaling chemicals released by root exudates of potatoonion.This study revealed a novel mechanism by which interspecific plant interaction modulates the establishment of a disease-suppressive microbiome,thus opening up new avenues of research for precision plant microbiome manipulations.

An integrative bioinformatics pipeline shows that honeybee-associated microbiomes are driven primarily by pollen composition

The microbiomes associated with bee nests influence colony health through various mechanisms,although it is not yet clear how honeybee congeners differ in microbiome assembly processes,in particular the degrees to which floral visitations and the environment contribute to different aspects of diversity.We used DNA metabarcoding to sequence bacterial 16S rRNA from honey and stored pollen from nests of 4 honeybee species(Apis cerana,A.dorsata,A.florea,and A.laboriosa)sampled throughout Yunnan,China,a global biodiversity hotspot.We developed a computational pipeline integrating multiple databases for quantifying key facets of diversity,including compositional,taxonomic,phylogenetic,and functional ones.Further,we assessed candidate drivers of observed microbiome dissimilarity,particularly differences in floral visitations,habitat disturbance,and other key environmental variables.Analyses revealed that microbiome alpha diversity was broadly equivalent across the study sites and between bee species,apart from functional diversity which was very low in nests of the reclusive A.laboriosa.Turnover in microbiome composition across Yunnan was driven predominantly by pollen composition.Human disturbance negatively impacted both compositional and phylogenetic alpha diversity of nest microbiomes,but did not correlate with microbial turnover.We herein make progress in understanding microbiome diversity associated with key pollinators in a biodiversity hotspot,and provide a model for the use of a comprehensive informatics framework in assessing pattern and drivers of diversity,which enables the inclusion of explanatory variables both subtly and fundamentally different and enables elucidation of emergent or unexpected drivers.

Oral microbiomes： more and more importance in oral cavity and whole body

Microbes appear in every corner of human life, and microbes affect every aspect of human life. The human oral cavity contains a number of different habitats. Synergy and interaction of variable oral microorganisms help human body against invasion of undesirable stim- ulation outside. However, imbalance of microbial flora contributes to oral diseases and systemic diseases. Oral microbiomes play an important role in the human microbial community and human health. The use of recently developed molecular methods has greatly expanded our knowledge of the composition and function of the oral microbiome in health and disease. Studies in oral microbiomes and their interactions with microbiomes in variable body sites and variable health condition are critical in our cognition of our body and how to make effect on human health improvement.

Plant specialized metabolites modulate root microbiomes

Plants are surrounded by myriad microbes during their growth,death,and importantly,evolution(Zhang et al.,2018).It is well known that the interaction between plantassociated microbes and their hosts greatly impacts host development and health(Verbon and Liberman,2016;Berendsen et al.,2012).One of the strategies employed by plants to defend themselves against pathogens and adapt to adverse conditions is to selectively recruit specific host-associated microbial communities possessing beneficial functions.Thus far,numerous attempts have been made to elucidate the ways by which plants regulate host-associated microbiota.Plant immune signaling(Lebeis et al.,2015)and phosphate starvation responses(Castrillo et al.,2017)have been identified to be involved in this process.

Soil microbiomes divergently respond to heavy metals and polycyclic aromatic hydrocarbons in contaminated industrial sites

Contaminated sites from electronic waste(e-waste)dismantling and coking plants feature high concentrations of heavy metals(HMs)and/or polycyclic aromatic hydrocarbons(PAHs)in soil.Mixed contamination(HMsþPAHs)hinders land reclamation and affects the microbial diversity and function of soil microbiomes.In this study,we analyzed HM and PAH contamination from an e-waste dismantling plant and a coking plant and evaluated the influences of HM and PAH contamination on soil microbiomes.It was noticed that HMs and PAHs were found in all sites,although the major contaminants of the e-waste dismantling plant site were HMs(such as Cu at 5,947.58±433.44 mg kg^(-1),Zn at 4,961.38±436.51 mg kg^(-1),and Mn at 2,379.07±227.46 mg kg^(-1)),and the major contaminants of the coking plant site were PAHs(such as fluorene at 11,740.06±620.1 mg kg^(-1),acenaphthylene at 211.69±7.04 mg kg^(-1),and pyrene at 183.14±18.89 mg kg^(-1)).The microbiomes(diversity and abundance)of all sites were determined via high-throughput sequencing of 16S rRNA genes,and redundancy analysis was conducted to investigate the relations between soil microbiomes and contaminants.The results showed that the microbiomes of the contaminated sites divergently responded to HMs and PAHs.The abundances of the bacterial genera Sulfuritalea,Pseudomonas,and Sphingobium were positively related to PAHs,while the abundances of the bacterial genera Bryobacter,Nitrospira,and Steroidobacter were positively related to HMs.This study promotes an understanding of how soil microbiomes respond to single and mixed contamination with HMs and PAHs.

肠上皮细胞Axin1缺失可调节肠道微生态预防结肠炎

Intestinal homeostasis is maintained by specialized host cells and the gut microbiota.Wnt/β-catenin signaling is essential for gastrointestinal development and homeostasis,and its dysregulation has been implicated in inflammation and colorectal cancer.Axin1 negatively regulates activated Wnt/β-catenin signaling,but little is known regarding its role in regulating host–microbial interactions in health and disease.Here,we aim to demonstrate that intestinal Axin1 determines gut homeostasis and host response to inflammation.Axin1 expression was analyzed in human inflammatory bowel disease datasets.To explore the effects and mechanism of intestinal Axin1 in regulating intestinal homeostasis and colitis,we generated new mouse models with Axin1 conditional knockout in intestinal epithelial cell(IEC;Axin1^(ΔIEC))and Paneth cell(PC;Axin1^(ΔPC))to compare with control(Axin1^(LoxP);LoxP:locus of X-over,P1)mice.We found increased Axin1 expression in the colonic epithelium of human inflammatory bowel disease(IBD).Axin1^(ΔIEC) mice exhibited altered goblet cell spatial distribution,PC morphology,reduced lysozyme expression,and enriched Akkermansia muciniphila(A.muciniphila).The absence of intestinal epithelial and PC Axin1 decreased susceptibility to dextran sulfate sodium(DSS)-induced colitis in vivo.Axin1^(ΔIEC) and Axin1^(ΔPC)mice became more susceptible to DSS-colitis after cohousing with control mice.Treatment with A.muciniphila reduced DSS-colitis severity.Antibiotic treatment did not change the IEC proliferation in the Axin1Loxp mice.However,the intestinal proliferative cells in Axin1^(ΔIEC)mice with antibiotic treatment were reduced compared with those in Axin1^(ΔIEC) mice without treatment.These data suggest non-colitogenic effects driven by the gut microbiome.In conclusion,we found that the loss of intestinal Axin1 protects against colitis,likely driven by epithelial Axin1 and Axin1-associated A.muciniphila.Our study demonstrates a novel role of Axin1 in mediating intestinal homeostasis and the microbiota.Further mechanistic studies using specific Axin1 mutations elucidating how Axin1 modulates the microbiome and host inflammatory response will provide new therapeutic strategies for human IBD.

Microbiome changes in esophageal cancer:implications for pathogenesis and prognosis

Esophageal cancer(EC)is an aggressive malignancy with a poor prognosis.Various factors,including dietary habits,and antacid and antibiotic use,have been shown to influence the esophageal microbiome.Conversely,enrichment and diversity of the esophageal microbiome can also impact its function.Recent studies have revealed prevalent changes in the esophageal microbiome among patients with EC,thus suggesting the potential contribution of the esophageal microbiome to EC development.Additionally,distinct microbiome compositions have been observed in patients with different responses to radiotherapy and chemotherapy,indicating the role of the esophageal microbiome in modulating treatment outcomes.In this review,we have examined previous studies on the esophageal microbiome in healthy individuals and patients with EC or other esophageal diseases,with a focus on identifying microbial communities associated with EC pathogenesis and prognosis.Understanding the role of the microbiome in EC may aid in early detection and optimized treatment strategies,ultimately leading to better outcomes for patients.

Multi-omics analysis reveals the molecular regulatory network underlying the prevention of Lactiplantibacillus plantarum against LPS-induced salpingitis in laying hens

Background Salpingitis is one of the common diseases in laying hen production, which greatly decreases the economic outcome of laying hen farming. Lactiplantibacillus plantarum was effective in preventing local or systemic inflammation, however rare studies were reported on its prevention against salpingitis. This study aimed to investigate the preventive molecular regulatory network of microencapsulated Lactiplantibacillus plantarum(MLP) against salpingitis through multi-omics analysis, including microbiome, transcriptome and metabolome analyses.Results The results revealed that supplementation of MLP in diet significantly alleviated the inflammation and atrophy of uterus caused by lipopolysaccharide(LPS) in hens(P < 0.05). The concentrations of plasma IL-2 and IL-10 in hens of MLP-LPS group were higher than those in hens of LPS-stimulation group(CN-LPS group)(P < 0.05). The expression levels of TLR2, MYD88, NF-κB, COX2, and TNF-α were significantly decreased in the hens fed diet supplemented with MLP and suffered with LPS stimulation(MLP-LPS group) compared with those in the hens of CN-LPS group(P < 0.05). Differentially expressed genes(DEGs) induced by MLP were involved in inflammation, reproduction, and calcium ion transport. At the genus level, the MLP supplementation significantly increased the abundance of Phascolarctobacterium, whereas decreased the abundance of Candidatus_Saccharimonas in LPS challenged hens(P < 0.05). The metabolites altered by dietary supplementation with MLP were mainly involved in galactose, uronic acid, histidine, pyruvate and primary bile acid metabolism. Dietary supplementation with MLP inversely regulates LPSinduced differential metabolites such as Lyso PA(24:0/0:0)(P < 0.05).Conclusions In summary, dietary supplementation with microencapsulated Lactiplantibacillus plantarum prevented salpingitis by modulating the abundances of Candidatus_Saccharimonas, Phascolarctobacterium, Ruminococcus_torques_group and Eubacterium_hallii_group while downregulating the levels of plasma metabolites, p-tolyl sulfate, o-cresol and N-acetylhistamine and upregulating S-lactoylglutathione, simultaneously increasing the expressions of CPNE4, CNTN3 and ACAN genes in the uterus, and ultimately inhibiting oviducal inflammation.

Evaluation of ruminal methane and ammonia formation and microbiota composition as affected by supplements based on mixtures of tannins and essential oils using Rusitec

Background Dietary supplements based on tannin extracts or essential oil compounds(EOC)have been repeatedly reported as a promising feeding strategy to reduce the environmental impact of ruminant husbandry.A previous batch culture screening of various supplements identified selected mixtures with an enhanced potential to mitigate ruminal methane and ammonia formation.Among these,Q-2(named after quebracho extract and EOC blend 2,composed of carvacrol,thymol,and eugenol)and C-10(chestnut extract and EOC blend 10,consisting of oregano and thyme essential oils and limonene)have been investigated in detail in the present study with the semi-continuous rumen simulation technique(Rusitec)in three independent runs.For this purpose,Q-2 and C-10,dosed according to the previous study,were compared with a non-supplemented diet(negative control,NC)and with one supplemented with the commercial EOC-based Agolin^(R) Ruminant(positive control,PC).Results From d 5 to 10 of fermentation incubation liquid was collected and analysed for pH,ammonia,protozoa count,and gas composition.Feed residues were collected for the determination of ruminal degradability.On d 10,samples of incubation liquid were also characterised for bacterial,archaeal and fungal communities by high-throughput sequencing of 16S rRNA and 26S ribosomal large subunit gene amplicons.Regardless of the duration of the fermentation period,Q-2 and C-10 were similarly efficient as PC in mitigating either ammonia(-37%by Q-2,-34%by PC)or methane formation(-12%by C-10,-12%by PC).The PC was also responsible for lower feed degradability and bacterial and fungal richness,whereas Q-2 and C-10 effects,particularly on microbiome diversities,were limited compared to NC.Conclusions All additives showed the potential to mitigate methane or ammonia formation,or both,in vitro over a period of 10 d.However,several differences occurred between PC and Q-2/C-10,indicating different mechanisms of action.The pronounced defaunation caused by PC and its suggested consequences apparently determined at least part of the mitigant effects.Although the depressive effect on NDF degradability caused by Q-2 and C-10 might partially explain their mitigation properties,their mechanisms of action remain mostly to be elucidated.

Comparative analysis of the microbiome of sympatric wintering Bean Geese,Domestic Ducks,humans,and soil at Shengjin Lake of China reveals potential public risk to human health

The gut microbiota of migratory waterbirds is affected by various complex factors,including cross-species transmission,which increases the risk of pathogen spreading among sympatric animals and poses a potential public health risk to humans.In this study,we investigated the microbial communities of wintering Bean Geese(Anser fabalis),Domestic Ducks(A.platyrhynchos domesticus),humans,and soil using high-throughput sequencing of the 16S rRNA gene region in Shengjin Lake,China.In total,6,046,677 clean reads were obtained,representing 41,119 operational taxonomic units(OTUs)across the four groups.The dominant microbial phyla were the Proteobacteria,Firmicutes,Bacteroidota,and Actinobacteriota.The Sorensen similarity index and alpha and beta diversity results showed that the gut microbial communities of Bean Geese and Domestic Ducks were more similar to those of the other pairs.Network analysis revealed that Faecalibacterium prausnitzii,Pseudomonas fragi,and Bradyrhizobium elkanii were hubs of the three major modules.Fourteen common microbiomes were iden-tified in Bean Geese,Domestic Ducks,humans,and soil in Shengjin Lake.A total of 96 potential pathogens were identified among the four groups,with 20 specific potentially pathogenic microbiomes found in the gut of Bean Geese.Some of these pathogens are responsible for significant financial losses in the poultry industry and pose risks to human health.Klebsiella pneumoniae,Morganella morganii,Escherichia coli,and Ralstonia insidiosa are potential core pathogens found in the four groups at Shengjin Lake that can cause diseases in humans and an-imals and facilitate cross-species transmission through various media.Therefore,humans are at risk of con-tracting these pathogens from migratory birds because of their frequent contact with domestic poultry.However,further studies are required to explore the potential pathogenic species and transmission pathways among sympatric wintering Bean Geese,Domestic Ducks,humans,and soil.

Unraveling the gut-brain axis:the impact of steroid hormones and nutrition on Parkinson's disease

This comprehensive review explores the intricate relationship between nutrition,the gut microbiome,steroid hormones,and Parkinson's disease within the context of the gut-brain axis.The gut-brain axis plays a pivotal role in neurodegenerative diseases like Parkinson's disease,encompassing diverse components such as the gut microbiota,immune system,metabolism,and neural pathways.The gut microbiome,profoundly influenced by dietary factors,emerges as a key player.Nutrition during the first 1000 days of life shapes the gut microbiota composition,influencing immune responses and impacting both child development and adult health.High-fat,high-sugar diets can disrupt this delicate balance,contributing to inflammation and immune dysfunction.Exploring nutritional strategies,the Mediterranean diet's anti-inflammatory and antioxidant properties show promise in reducing Parkinson's disease risk.Microbiome-targeted dietary approaches and the ketogenic diet hold the potential in improving brain disorders.Beyond nutrition,emerging research uncovers potential interactions between steroid hormones,nutrition,and Parkinson's disease.Progesterone,with its anti-inflammatory properties and presence in the nervous system,offers a novel option for Parkinson's disease therapy.Its ability to enhance neuroprotection within the enteric nervous system presents exciting prospects.The review addresses the hypothesis thatα-synuclein aggregates originate from the gut and may enter the brain via the vagus nerve.Gastrointestinal symptoms preceding motor symptoms support this hypothesis.Dysfunctional gut-brain signaling during gut dysbiosis contributes to inflammation and neurotransmitter imbalances,emphasizing the potential of microbiota-based interventions.In summary,this review uncovers the complex web of interactions between nutrition,the gut microbiome,steroid hormones,and Parkinson's disease within the gut-brain axis framework.Understanding these connections not only offers novel therapeutic insights but also illuminates the origins of neurodegenerative diseases such as Parkinson's disease.