Microbiome Community Composition Research Articles

High-fat diet, microbiome-gut-brain axis signaling, and anxiety-like behavior in male rats

Obesity, associated with the intake of a high-fat diet (HFD), and anxiety are common among those living in modern urban societies. Recent studies suggest a role of microbiome-gut-brain axis signaling, including a role for brain serotonergic systems in the relationship between HFD and anxiety. Evidence suggests the gut microbiome and the serotonergic brain system together may play an important role in this response. Here we conducted a nine-week HFD protocol in male rats, followed by an analysis of the gut microbiome diversity and community composition, brainstem serotonergic gene expression (tph2, htr1a, and slc6a4), and anxiety-related defensive behavioral responses. We show that HFD intake decreased alpha diversity and altered the community composition of the gut microbiome in association with obesity, increased brainstem tph2, htr1a and slc6a4 mRNA expression, including in the caudal part of the dorsomedial dorsal raphe nucleus (cDRD), a subregion previously associated with stress- and anxiety-related behavioral responses, and, finally, increased anxiety-related defensive behavioral responses. The HFD increased the Firmicutes/Bacteroidetes ratio relative to control diet, as well as higher relative abundances of Blautia, and decreases in Prevotella. We found that tph2, htr1a and slc6a4 mRNA expression were increased in subregions of the dorsal raphe nucleus in the HFD, relative to control diet. Specific bacterial taxa were associated with increased serotonergic gene expression in the cDRD. Thus, we propose that HFD-induced obesity is associated with altered microbiome-gut-serotonergic brain axis signaling, leading to increased anxiety-related defensive behavioral responses in rats.

Plants attacked above-ground by leaf-mining flies change below-ground microbiota to enhance plant defense

Abstract Root-associated microbiomes play a crucial role in plant responses to biotic and abiotic stresses. Plants can recruit beneficial microbes to increase their stress-relieving ability. Above-ground insect herbivory is among the most detrimental stresses for plants, especially to crop production. However, few studies have explored how root-associated microbiomes respond to herbivores and influence plant-defense functions under herbivory stress. We investigate the changes and functional role of root-associated microbial communities under herbivory stress using leafminer (Liriomyza trifolii) and cowpea (Vigna unguiculata) as a focal system. We did this by using a combination of 16S ribosomal RNA gene profiling and metagenomic sequencing to test for differences in co-occurrence networks and functions between cowpea plants infested and noninfested with leafminers. The results demonstrated that leafminer infestation caused a shift in the rhizosphere microbiome, which was characterized by a significant variation in microbiome community structure and composition, the selection of hub microbes involved in nitrogen (N) metabolism, and functional enrichment related to N metabolism. Notably, nitrogen-fixing bacteria Bradyrhizobium species were actively recruited and selected to be hubs in the rhizosphere. Inoculation with Bradyrhizobium enhanced cowpea performance under leafminer stress and increased protease inhibitor levels to decrease leafminer fitness. Overall, our study characterized the changes of root-associated microbiota between leafminer-infested and noninfested cowpea plants and revealed the mechanisms underlying the rhizosphere microbiome shift that enhance plant performance and defense against herbivory. Our findings provide further support for the notion that plants recruit rhizosphere microbes to counteract aboveground insect herbivores.

Quantification of microbial community assembly processes during degradation on diverse plastispheres based on physicochemical characters and phylogenetic bin-based null model analysis

To understand the differences in degradation processes depending on the chemical properties of polymers, it is necessary to both quantify the microbiome composition and evaluate the process of microbial turnover (i.e., community assembly processes) in a variety of polymer materials. In this study, using a phylogenetic bin-based null model analysis (i.e., iCAMP), we evaluated community assembly processes from original estuary water to 37 types of polymers, which provide overwhelmingly diverse niches for microbes, in 14-day incubation experiments. First, we evaluated the polymer properties related to degradation rates. Polymers with higher adipic acid (AdA) monomer exhibited higher motility, hydrophilicity, and degradation rates, whereas those with higher aromatic monomer exhibited the opposite trends. Second, microbiome composition analysis was performed, and the microbiomes were significantly changed by the AdA or aromatic content. This was consistent with the polymer properties, suggesting that polymer motility and hydrophilicity attributable to the first-order structure modify the accessibility of the enzyme to the reaction site and hence the degradation rate, resulting in differences in microbiome community composition. Finally, we determined community assembly processes from estuary water to plastics using a phylogenetic bin-based null model analysis. The importance of heterogeneous selection was higher in mobile, hydrophilic, and fast-degrading polymers, while that of homogeneous selection was lower. This suggests that the environmental difference between before and after incubation becomes significant under rapid degradation, which select microbes adapted to biofilm environments. In addition, the more stochastic turnover prevailed, the more variation in the communities (i.e., β-diversity) increased. This suggests that turnover processes not dictated by the environment lead to instability in community compositions.

Nutrient availability and plant phenological stage influence the substrate microbiome in container-grown Impatiens walleriana ‘Xtreme Red’

BackgroundThe microbiome plays a fundamental role in plant health and performance. Soil serves as a reservoir of microbial diversity where plants attract microorganisms via root exudates. The soil has an important impact on the composition of the rhizosphere microbiome, but greenhouse ornamental plants are commonly grown in soilless substrates. While soil microbiomes have been extensively studied in traditional agriculture to improve plant performance, health, and sustainability, information about the microbiomes of soilless substrates is still limited. Thus, we conducted an experiment to explore the microbiome of a peat-based substrate used in container production of Impatiens walleriana, a popular greenhouse ornamental plant. We investigated the effects of plant phenological stage and fertilization level on the substrate microbiome.ResultsImpatiens plants grown under low fertilization rates were smaller and produced more flowers than plants grown under optimum and high fertilization. The top five bacterial phyla present in the substrate were Proteobacteria, Actinobacteria, Bacteriodota, Verrucomicrobiota, and Planctomycetota. We found a total of 2,535 amplicon sequence variants (ASV) grouped into 299 genera. The substrate core microbiome was represented by only 1.8% (48) of the identified ASV. The microbiome community composition was influenced by plant phenological stage and fertilizer levels. Phenological stage exhibited a stronger influence on microbiome composition than fertilizer levels. Differential abundance analysis using DESeq2 identified more ASVs significantly affected (enriched or depleted) in the high fertilizer levels at flowering. As observed for community composition, the effect of plant phenological stage on microbial community function was stronger than fertilizer level. Phenological stage and fertilizer treatments did not affect alpha-diversity in the substrate.ConclusionsIn container-grown ornamental plants, the substrate serves as the main microbial reservoir for the plant, and the plant and agricultural inputs (fertilization) modulate the microbial community structure and function of the substrate. The differences observed in substrate microbiome composition across plant phenological stage were explained by pH, total organic carbon (TOC) and fluoride, and across fertilizer levels by pH and phosphate (PO4). Our project provides an initial diversity profile of the bacteria occurring in soilless substrates, an underexplored source of microbial diversity.

Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products

Abstract Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. By analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiome. The CSMD included over 49 million non-redundant genes and 3175 metagenome-assembled genomes (MAGs), which represented 1895 species spanning 105 phyla. In addition, beta diversity analysis indicated that both the sampling site and cold seep type had a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms were prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicated that at least 98.81% of the sequences potentially encoded novel natural products, with ribosomal processing peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.

Linking microbiome and stress hormone responses in wild tropical treefrogs across continuous and fragmented forests

The amphibian skin microbiome is an important component of anti-pathogen defense, but the impact of environmental change on the link between microbiome composition and host stress remains unclear. In this study, we used radiotelemetry and host translocation to track microbiome composition and function, pathogen infection, and host stress over time across natural movement paths for the forest-associated treefrog, Boana faber. We found a negative correlation between cortisol levels and putative microbiome function for frogs translocated to forest fragments, indicating strong integration of host stress response and anti-pathogen potential of the microbiome. Additionally, we observed a capacity for resilience (resistance to structural change and functional loss) in the amphibian skin microbiome, with maintenance of putative pathogen-inhibitory function despite major temporal shifts in microbiome composition. Although microbiome community composition did not return to baseline during the study period, the rate of microbiome change indicated that forest fragmentation had more pronounced effects on microbiome composition than translocation alone. Our findings reveal associations between stress hormones and host microbiome defenses, with implications for resilience of amphibians and their associated microbes facing accelerated tropical deforestation.

Effects of maternal type 1 diabetes and confounding factors on neonatal microbiomes

Aims/hypothesisBody niche-specific microbiota in maternal–neonatal dyads from gravidae with type 1 diabetes have not been quantitatively and functionally examined. Similarly, the impact of pregnancy-specific factors, such as the presence of comorbidities known to occur more frequently among gravidae with type 1 diabetes, including Caesarean delivery, as well as antibiotic prophylaxis, level of glycaemic control during each trimester of pregnancy and insulin administration, has not been adequately considered. The aims of this study were to characterise the maternal and neonatal microbiomes, assess aspects of microbiota transfer from the maternal microbiomes to the neonatal microbiome and explore the impact of type 1 diabetes and confounding factors on the microbiomes.MethodsIn this observational case–control study, we characterised microbiome community composition and function using 16S rRNA amplicon sequencing in a total of 514 vaginal, rectal and ear-skin swabs and stool samples derived from 92 maternal–neonatal dyads (including 50 gravidae with type 1 diabetes) and in-depth clinical metadata from throughout pregnancy and delivery.ResultsType 1 diabetes-specific microbiota were identified among gravidae with type 1 diabetes and their neonates. Neonatal microbiome profiles of ear-skin swabs and stool samples were established, indicating the taxa more prevalent among neonates born to mothers with type 1 diabetes compared with neonates born to control mothers. Without taking into account the type 1 diabetes status of mothers, both delivery mode and intrapartum antibiotic prophylaxis were found to have an influence on neonatal microbiota composition (both p=0.001). In the logistic regression analysis involving all confounding variables, neonatal ear-skin microbiome variation was explained by maternal type 1 diabetes status (p=0.020) and small for gestational age birthweight (p=0.050). Moreover, in women with type 1 diabetes, a relationship was found between HbA1c levels >55 mmol/mol (>7.2%) measured in the first trimester of pregnancy and neonatal ear-skin microbiota composition (p=0.008). In the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) assessment, pathways concerning carbohydrate biosynthesis were predicted as key elements of the microbial functional profiles dysregulated in type 1 diabetes. Additionally, in SourceTracker analysis, we found that, on average, 81.0% of neonatal microbiota was attributed to maternal sources. An increase in the contribution of maternal rectum microbiota and decrease in the contribution of maternal cervix microbiota were found in ear-skin samples of vaginally delivered neonates of mothers with type 1 diabetes compared with neonates born to control mothers (83.2% vs 59.5% and 0.7% vs 5.2%, respectively).Conclusions/interpretationThese findings indicate that, in addition to maternal type 1 diabetes, glycaemic dysregulation before/in the first trimester of pregnancy, mode of delivery and intrapartum antibiotic prophylaxis may contribute to the inoculation and formation of the neonatal microbiomes.Data availabilityThe BioProject (PRJNA961636) and associated SRA metadata are available at http://www.ncbi.nlm.nih.gov/bioproject/961636. Processed data on probiotic supplementation and the PICRUSt analysis are available in the Mendeley Data Repository (https://doi.org/10.17632/g68rwnnrfk.1).Graphical

Influence of organic plant breeding on the rhizosphere microbiome of common bean (Phaseolus vulgaris L.).

We now recognize that plant genotype affects the assembly of its microbiome, which in turn, affects essential plant functions. The production system for crop plants also influences the microbiome composition, and as a result, we would expect to find differences between conventional and organic production systems. Plant genotypes selected in an organic regime may host different microbiome assemblages than those selected in conventional environments. We aimed to address these questions using recombinant inbred populations of snap bean that differed in breeding history. Rhizosphere microbiomes of conventional and organic common beans (Phaseolus vulgaris L.) were characterized within a long-term organic research site. The fungal and bacterial communities were distinguished using pooled replications of 16S and ITS amplicon sequences, which originated from rhizosphere samples collected between flowering and pod set. Bacterial communities significantly varied between organic and conventional breeding histories, while fungal communities varied between breeding histories and parentage. Within the organically-bred populations, a higher abundance of a plant-growth-promoting bacteria, Arthrobacter pokkalii, was identified. Conventionally-bred beans hosted a higher abundance of nitrogen-fixing bacteria that normally do not form functional nodules with common beans. Fungal communities in the organically derived beans included more arbuscular mycorrhizae, as well as several plant pathogens. The results confirm that the breeding environment of crops can significantly alter the microbiome community composition of progeny. Characterizing changes in microbiome communities and the plant genes instrumental to these changes will provide essential information about how future breeding efforts may pursue microbiome manipulation.

Food desert residence has limited impact on veteran fecal microbiome composition: a U.S. Veteran Microbiome Project study.

Social and economic inequities can have a profound impact on human health. The inequities could result in alterations to the gut microbiome, an important factor that may have profound abilities to alter health outcomes. Moreover, the strong correlations between social and economic inequities have been long understood. However, to date, limited research regarding the microbiome and mental health within the context of socioeconomic inequities exists. One particular inequity that may influence both mental health and the gut microbiome is living in a food desert. Persons living in food deserts may lack access to sufficient and/or nutritious food and often experience other inequities, such as increased exposure to air pollution and poor access to healthcare. Together, these factors may confer a unique risk for microbial perturbation. Indeed, external factors beyond a food desert might compound over time to have a lasting effect on an individual's gut microbiome. Therefore, adoption of a life-course approach is expected to increase the ecological validity of research related to social inequities, the gut microbiome, and physical and mental health.

Metal transporter SLC39A14/ZIP14 modulates regulation between the gut microbiome and host metabolism.

Metal transporter SLC39A14/ZIP14 is localized on the basolateral side of the intestine, functioning to transport metals from blood to intestine epithelial cells. Deletion of Slc39a14/Zip14 causes spontaneous intestinal permeability with low-grade chronic inflammation, mild hyperinsulinemia, and greater body fat with insulin resistance in adipose. Importantly, antibiotic treatment reverses the adipocyte phenotype of Slc39a14/Zip14 knockout (KO), suggesting a potential gut microbial role in the metabolic alterations in the Slc39a14/Zip14 KO mice. Here, we investigated the hypothesis that increased intestinal permeability and subsequent metabolic alterations in the absence of Zip14 could be in part due to alterations in gut microbial composition. Dietary metals have been shown to be involved in the regulation of gut microbial diversity and composition. However, studies linking the action of intestinal metal transporters to gut microbial regulation are lacking. We showed the influence of deletion of metal transporter Slc39a14/Zip14 on gut microbiome composition and how ZIP14-linked changes to gut microbiome community composition are correlated with changes in host metabolism. Deletion of Slc39a14/Zip14 generated Zn-deficient epithelial cells and luminal content in the entire intestinal tract, a shift in gut microbial composition that partially overlapped with changes previously associated with obesity and inflammatory bowel disease (IBD), increased the fungi/bacteria ratio in the gut microbiome, altered the host metabolome, and shifted host energy metabolism toward glucose utilization. Collectively, our data suggest a potential predisease microbial susceptibility state dependent on host gene Slc39a14/Zip14 that contributes to intestinal permeability, a common trait of IBD, and metabolic disorders such as obesity and type 2 diabetes.NEW & NOTEWORTHY Metal dyshomeostasis, intestinal permeability, and gut dysbiosis are emerging signatures of chronic disorders, including inflammatory bowel diseases, type-2 diabetes, and obesity. Studies in reciprocal regulations between host intestinal metal transporters genes and gut microbiome are scarce. Our research revealed a potential predisease microbial susceptibility state dependent on the host metal transporter gene, Slc39a14/Zip14, that contributes to intestinal permeability providing new insight into understanding host metal transporter gene-microbiome interactions in developing chronic disease.

Microbial signatures of vertebrate visitation in floral nectar: a case study with two endemic Aotearoa New Zealand plant species

ABSTRACT Microbes found in nectar and dispersed by animal visitors can mediate pollination and host fitness. While previous studies have characterised floral nectar microbiomes and their effects on invertebrate pollinators, fewer studies have focused on vertebrate pollinators, especially outside of the Northern Hemisphere. In Aotearoa New Zealand, vertebrates, such as birds and bats, are critical pollinators for many native plant species. Here, we present nectar microbiome profiles for two endemic, vertebrate-pollinated plant species in Aotearoa New Zealand, wharariki, mountain flax (Phormium cookianum), and pua o te Rēinga, wood rose (Dactylanthus taylorii). We used vertebrate exclusion treatments and camera traps to monitor visitation. Camera trap footage revealed silvereye (Zosterops lateralis), ship rat (Rattus rattus), and possum (Trichosurus vulpecula) visitation. We detected shifts in microbial species turnover in wood rose and varying relative abundances of fungal and bacterial taxa across the vertebrate exclusion treatments for both mountain flax and wood rose. However, we did not detect strong effects on floral nectar microbiome community composition or richness. Future work should move beyond profiling the microbial communities and identify fitness consequences and pollination outcomes, which could affect conservation and management decisions.

Comparative analysis of microbial community structure in different times of Panax ginseng Rhizosphere microbiome and soil properties under larch forest

BackgroundPanax ginseng cultivated under the forest is popular because its shape and effective ingredients are similar to wild ginseng. The growth of P. ginseng in the larch forest is generally better than in the broad-leaved forest, and the incidence rate of diseases is low. Therefore, the selection of forest species is one of the basic factors in the successful cropping of P. ginseng.MethodsIllumina HiSeq high-throughput sequencing was used to analyze the 16S rRNA/ITS gene sequence of P. ginseng rhizosphere soil under larch forest to study the rhizosphere microbiome's diversity and community composition structure.ResultsThe species classification and richness of rhizosphere bacterial and fungal communities in the same-aged P. ginseng were similar. Consistent with the soil system of commonly cultivated crops, Proteobacteria, Actinobacteriota, Acidobacteriota, Verrucomicrobiota, Chloroflexi, and Basidiomycota, Ascomycota were the dominant phylum of bacteria and fungi, respectively. Compared with the soil without planting P. ginseng, the diversity of microorganisms and community structure of continuous planting for 2 years, 5 years, and 18 years of P. ginseng rhizosphere soil had little change. The accumulation levels of Ilyonectria, Fusarium, Gibberella, and Cylindrocarpon were not significantly increased with planting P. ginseng and the increased age of cropping P. ginseng.ConclusionsThe results of this study showed that the soil function of the larch forest was good, which provided a theoretical basis for the land selection and soil improvement of cultivating P. ginseng under the larch forest.

Crop rotational diversity enhances soil microbiome network complexity and multifunctionality

Although it is widely accepted that crop rotations can alleviate the adverse effects of agricultural intensification on ecosystem functioning, the influence of rotational diversification on soil microbial diversity, network complexity, and their associations with multifunctionality remains unclear. Here, we used a 16-year field experiment to assess the effect of six cropping regimes, and their respective crop diversity index (CDI, i.e., the number of crop species in a rotation multiplied by the species per year) and management intensity (MI, i.e., the anthropogenic inputs including fertilizer use, pesticide use and fuel consumption across a 2-year cycle), on soil microbial community (bacteria, fungi and protists) and soil multifunctionality. We used 20 soil functions related to soil properties, soil basal respiration, soil enzymatic activities and soil nitrogen cycling potential to characterize soil multifunctionality. Diversified crop rotation was shown to enhance soil multifunctionality. Also, soil multifunctionality and microbial diversity increased with CDI, but were negatively correlated or had a hump-shaped relationship with MI. With the increase in CDI, microbiome network nodes, edges and degree increased, but betweenness and average path length decreased. An increase in MI was found to have a hump-shaped relationship with the topological properties of the network. Soil microbiome network complexity had a stronger effect on multifunctionality than microbiome diversity and community composition. This study illustrates that more diverse rotations under intermediate MI promoted soil multifunctionality, and highlights the crucial role of network complexity in maintaining soil functions.

Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum.

Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.

Hybrids with heterosis possess a more diverse intestinal microbiome than that of carnivorous and herbivorous parental fishes in controlled conditions

The intestinal microbiome plays critical, interactive roles in host nutrition and metabolism and may be involved in the known growth advantage of hybrids. In a previous study, we obtained healthy F1 hybrids (PS) by crossing carnivorous Percocypris pingi (PP, male) and herbivorous Schizothorax wangchiachii (SW, female) and found that the PS hybrids exhibited a growth advantage and that their feeding traits were similar to those of omnivorous S. davidi (SD). In this study, we compared the intestinal histology and anatomy of four fish lines (PP, PS, SW, SD) and, using 16S rRNA gene sequencing, constructed a map of their intestinal microbiome to explore host-influenced intestinal microbiome community composition among them under the same diet. We found that the intestinal anatomical and histological traits of PS and SD were similar, and intermediate between PP and SW, but closer to SW. Although PS and SD have similar feeding traits, their intestinal microbiome composition varied remarkably and, notably, the SD microbiome was closer to that of SW, indicating that phylogenetic effects may play a stronger role in gut microbiome development than the effects of feeding traits. Cetobacterium and Aeromonas were the predominant components of the intestinal microbiome in the four fishes, the former was more abundant in PP, and the latter was more abundant in SW and SD. The relative abundances of Cetobacterium and Aeromonas were lower in PS than in the other three fish lines, but the relative abundances of other microorganisms were generally higher in the PS microbiome, which led to more OTUs and higher alpha diversity. In addition, trypsin activity and amylase activity were strongly positively correlated with the relative abundance of Cetobacterium and Aeromonas, respectively. Although the digestive enzyme activities of PS showed hybrid weakness, its intestinal microbial diversity was higher, which may be related to its growth advantage.

Oral Microbiome Community Composition in Head and Neck Squamous Cell Carcinoma.

The impact of the oral microbiome on head and neck cancer pathogenesis and outcomes requires further study. 16s rRNA was isolated and amplified from pre-treatment oral wash samples for 52 cases and 102 controls. The sequences were binned into operational taxonomic units (OTUs) at the genus level. Diversity metrics and significant associations between OTUs and case status were assessed. The samples were binned into community types using Dirichlet multinomial models, and survival outcomes were assessed by community type. Twelve OTUs from the phyla Firmicutes, Proteobacteria, and Acinetobacter were found to differ significantly between the cases and the controls. Beta-diversity was significantly higher between the cases than between the controls (p < 0.01). Two community types were identified based on the predominant sets of OTUs within our study population. The community type with a higher abundance of periodontitis-associated bacteria was more likely to be present in the cases (p < 0.01), in older patients (p < 0.01), and in smokers (p < 0.01). Significant differences between the cases and the controls in community type, beta-diversity, and OTUs indicate that the oral microbiome may play a role in HNSCC.

Soil Suppressiveness Against Pythium ultimum and Rhizoctonia solani in Two Land Management Systems and Eleven Soil Health Treatments.

The soil microbiome is known to be crucial for the control of soil-borne plant diseases. However, there is still little knowledge on how to modify the soil microbiome to induce or increase disease suppressiveness. In the present study, we applied eleven soil health treatments combined with conventional and organic agricultural management in a long-term field experiment. Suppressiveness against Pythium ultimum and Rhizoctonia solani was assessed in bioassays for 2 years. In addition, the microbiome community composition and microbial abundance were determined. We found that while several treatments changed the microbial community composition compared to the control, only a combination treatment of anaerobic soil disinfestation, hair meal, and compost addition resulted in suppressiveness against P. ultimum. Pythium suppressiveness is likely to have been caused by an increased microbial abundance and activity. Moreover, the increased abundance of several bacterial taxa, such as Pseudomonas sp., Chryseobacterium sp., members of the family Chitinophagaceae, and the fungal genus Mortierella sp. and family Trichosporonaceae, was measured. There was no overall difference in suppressiveness between conventional and organic land management. Also, no suppressiveness against R. solani could be detected. Our results indicate that a treatment combining the reduction of microorganisms followed by a recovery phase with high amounts of organic amendments may be more effective in inducing suppressiveness than treatments consisting of only one of these measures.

Interactive effects of depth and differential irrigation on soil microbiome composition and functioning

Two factors that are well-known to influence soil microbiomes are the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil microbiome composition and functioning down the depth profile. Here, we investigated soil and wheatgrass rhizosphere microbiomes in a single common field setting under four different levels of irrigation (100%, 75%, 50%, and 25%) and three depths (0-5 cm, 5-15 cm, and 15-25 cm from the surface). We demonstrated that there is a significant interactive effect between depth and irrigation, where changes in soil moisture more strongly affect soil microbiomes at the surface layer than at deeper layers. This was true for not only microbiome community composition and diversity metrics, but also for functional profiles (transcriptomic and metabolomic datasets). Meanwhile, in rhizosphere communities the influence of irrigation was similar across the different depths. However, for the ‘Alkar’ wheatgrass cultivar, the rhizosphere microbial communities responded more strongly to changes in irrigation level than did the communities for the ‘Jose’ cultivar rhizosphere. The lessened response of deeper soil microbiomes to changes in irrigation may be due to higher incidence of slow-growing, stress-resistant microbes. These results demonstrate that the soil microbiome response to moisture content is depth-dependent. As such, it will be optimal for soil microbiome studies to incorporate deeper as well as surface soils, to get a more accurate picture of the soil microbiome response to stress.

Time is a stronger predictor of microbiome community composition than tissue in external mucosal surfaces of Atlantic salmon (Salmo salar) reared in a semi-natural freshwater environment

Time is a stronger predictor of microbiome community composition than tissue in external mucosal surfaces of Atlantic salmon (Salmo salar) reared in a semi-natural freshwater environment

The First Next-Generation Sequencing Metabarcoding Dataset on Faecal Bacterial Diversity from the Southern River Terrapin, Batagur affinis ssp.

The Southern River terrapin, Batagur affinis ssp., has the first data on faecal bacterial diversity from next-generation sequencing (NGS). This dataset describes the bacterial diversity of the Southern River terrapin, locally known as Tuntung. Batagur affinis spp. are freshwater turtles listed as critically endangered on the International Union for Conservation of Nature (IUCN) Red List since 2000. This is the first dataset on the faecal bacterial diversity of Batagur affinis ssp., and the data provided here can be used to comprehensively understand the microbiome's community composition. Seven faeces samples were collected aseptically from captive (N = 5) and wild (N = 2) adult B. affinis ssp. while crossing Peninsular Malaysia's east and west coasts. The data was acquired by metabarcoding using 16S rRNA. The amplicons were further analysed using the SILVA and DADA2 pipelines. The V3-V4 of the 16S rRNA gene region was amplified, and the amplicons were sequenced on the Illumina MiSeq system. In total, 297 bacterial communities' taxonomic profiles (phylum to genus) have been determined. The data for this metagenome can be found in the BioSample Submission Portal as Bio-Project PRJNA767629 and Sequence Read Archive (SRA) accession numbers from SAMN21919713 to SAMN21919722.