The Red and Orange Complex Subgingival Microbiome of Cognitive Impairment and Cognitively Normal Elderly with Periodontitis

Increasing evidence has shown an association between periodontitis and cognitive impairment. Subgingival microbiota play a great role in periodontitis pathogenesis. However, the correlation between the subgingival microbiome and cognitive impairment remains unclear. This study aimed to evaluate the red and orange complex subgingival microbiome of cognitively impaired and cognitively normal elderly Indonesian subjects with periodontitis. Twenty-eight elderly subjects diagnosed with periodontitis underwent two cognitive examinations using the Hopkins Verbal Learning Test and the Mini-Mental State Examination. Gingival crevicular fluid taken from the periodontal pocket, at a depth between 5 and 7 mm, using a paper point was used as the subgingival samples. The subgingival microbiome in the cognitive impairment group (n = 14) and cognitively normal group (n = 14) was compared using the 16S rRNA Metagenomic iSeq™ 100 Sequencing System. There was β-diversity in the subgingival microbiota between the cognitively impaired and cognitively normal subjects. The metagenomic analysis showed a higher abundance of Porphyromonas and Treponema bacteria in the cognitive impairment group than in the normal cognitive group (p < 0.05). The abundance of Porphyromonas gingivalis and Treponema denticola was higher in the cognitively impaired elderly subjects. The role of P. gingivalis and T. denticola in the pathogenesis of cognitive impairment needs further investigation.

Explaining the microbial diversity conundrum: can microbiome composition be crucial for host fitness, while highly divergent among healthy individuals?

Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term the microbial β-diversity conundrum: it has been shown that the microbiome is crucial for host wellbeing and survival. At the same time, different healthy individuals' microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the notion that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes, even microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. Here we suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers, relating to factors such as host population size, the specific mode of contribution of the microbes to host fitness, and the typical microbiome richness, offer solutions to the conundrum by creating scenarios where even when a host's fitness is determined in full by its microbiome composition, this composition has little or no effect on the natural selection dynamics of the population.

Bacterial Succession during Vermicomposting of Silver Wattle (Acacia dealbata Link)

Vermicomposting is the process of organic waste degradation through interactions between earthworms and microbes. A variety of organic wastes can be vermicomposted, producing a nutrient-rich final product that can be used as a soil biofertilizer. Giving the prolific invasive nature of the Australian silver wattle Acacia dealbata Link in Europe, it is important to find alternatives for its sustainable use. However, optimization of vermicomposting needs further comprehension of the fundamental microbial processes. Here, we characterized bacterial succession during the vermicomposting of silver wattle during 56 days using the earthworm species Eisenia andrei. We observed significant differences in α- and β-diversity between fresh silver wattle (day 0) and days 14 and 28, while the bacterial community seemed more stable between days 28 and 56. Accordingly, during the first 28 days, a higher number of taxa experienced significant changes in relative abundance. A microbiome core composed of 10 amplicon sequence variants was identified during the vermicomposting of silver wattle (days 14 to 56). Finally, predicted functional profiles of genes involved in cellulose metabolism, nitrification, and salicylic acid also changed significantly during vermicomposting. This study, hence, provides detailed insights of the bacterial succession occurring during vermicomposting of the silver wattle and the characteristics of its final product as a sustainable plant biofertilizer.

Waterbird assemblages of inland wetlands in Chile: A meta-analysis

Chile has a large number of wetlands that offer a wide variety of refuges and food to waterbird assemblages. This research hypothesises that these assemblages differ according to the structural characteristics of each type of inland wetland. The object is to identify the structure of these assemblages, evaluating their richness, alpha α diversity and some ecological characteristics, taxonomic structures and trophic guilds. We performed a meta-analysis by submitting pre-selected articles to multivariate reliability analysis. The selected articles were used to characterise the assemblages by alpha α diversity: species richness, Shannon-Wiener index, Pielou’s Evenness Index, relative abundance and taxonomic distinctiveness Δ + and beta β diversity: Bray-Curtis with analysis of similarity percentage. Diversity and evenness differed in the seven wetlands studied, among 12 to 45 species, Shannon-Wiener index H’= 0.08 to 0.94 bits and Pielou’s Evenness Index J’= 0.06 to 0.71. Four wetlands were below and three above the expected value for taxonomic distinctiveness (Δ +) (73.2 units). Two clusters were identified using the β diversity: one consisting of the High-Andean wetlands (Huasco and Negro Francisco); and the other of El Peral lagoon, the Cruces River wetlands complex and the Tranque San Rafael man-made wetland. The most remarkable dissimilarity was provided by three species (Cygnus melancoryphus, Phoenicoparrus jamesi and Phoenicoparrus andinus). Zoophagous species that eat invertebrates by the first choice are the dominant group, while in lagoon wetlands phytophages and omnivores are more evenly represented.

Patterns of grassland community composition and structure along an elevational gradient on the Qinghai-Tibet Plateau

Aims Grasslands in the Qinghai-Tibet Plateau play an important role in preserving ecological security and high biodiversity in this region. However, the distribution of the composition and structure of plant community and the mechanism by which it maintains itself in this region is still poorly understood. Methods Here, we designed 195 grassland plots in 39 grassland sites along an approximately 1700-m elevation gradient on the Northeastern Qinghai-Tibet Plateau. Important findings We found that the grassland community height decreased significantly with the increase of elevation, while community coverage did not demonstrate significant changes. With the increase of elevation, the plant species richness (α diversity) increased significantly, but the community variability (β diversity) decreased significantly. The constrained clustering analysis suggested that the α- and β-diversity in the grasslands transformed gradually with elevation, and three discontinuous points (based on community structure) were observed at elevation of 3640, 4252 and 4333 m. Structural equation modeling (SEM) indicated that the increase of precipitation and the decrease of temperature significantly positively influenced α diversity, which was negatively correlated with β diversity. These results demonstrate that the community composition and structure presented a quantitative-to-qualitative change along this elevational gradient on the Qinghai-Tibet Plateau.

Dietary Fiber Influences Bacterial Community Assembly Processes in the Gut Microbiota of Durco × Bamei Crossbred Pig

Several studies have shown that dietary fiber can significantly alter the composition and structure of the gut bacterial community in humans and mammals. However, few researches have been conducted on the dynamics of the bacterial community assembly across different graded levels of dietary fiber in different gut regions. To address this, 24 Durco × Bamei crossbred pigs were randomly assigned to four experimental chows comprising graded levels of dietary fiber. Results showed that the α-and β-diversity of the bacterial community was significantly different between the cecum and the jejunum. Adding fiber to the chow significantly increased the α-diversity of the bacterial community in the jejunum and cecum, while the β-diversity decreased. The complexity of the bacterial network increased with the increase of dietary fiber in jejunal content samples, while it decreased in cecal content samples. Furthermore, we found that stochastic processes governed the bacterial community assembly of low and medium dietary fiber groups of jejunal content samples, while deterministic processes dominated the high fiber group. In addition, deterministic processes dominated all cecal content samples. Taken together, the variation of gut community composition and structure in response to dietary fiber was distinct in different gut regions, and the dynamics of bacterial community assembly across the graded levels of dietary fiber in different gut regions was also distinct. These findings enhanced our knowledge on the bacterial community assembly processes in gut ecosystems of livestock.

Host Genetic Associations with Salivary Microbiome in Oral Cancer

Despite the growing recognition of a host genetic effect on shaping gut microbiota composition, the genetic determinants of oral microbiota remain largely unexplored, especially in the context of oral diseases. Here, we performed a microbiome genome-wide association study in 2 independent cohorts of patients with oral squamous cell carcinoma (OSCC, n = 144 and 67) and an additional group of noncancer individuals ( n = 104). Besides oral bacterial dysbiosis and signatures observed in OSCC, associations of 3 loci with the abundance of genus-level taxa and 4 loci with β diversity measures were detected ( q < 0.05) at the discovery stage. The most significant hit (rs10906082 with the genus Lachnoanaerobaculum, P = 3.55 × 10–9 at discovery stage) was replicated in a second OSCC cohort. Moreover, the other 2 taxonomical associations, rs10973953 with the genus Kingella ( P = 1.38 × 10–9) and rs4721629 with the genus Parvimonas ( P = 3.53 × 10–8), were suggestive in the meta-analysis combining 2 OSCC cohorts. Further pathway analysis revealed that these loci were enriched for genes in regulation of oncogenic and angiogenic responses, implicating a genetic anchor to the oral microbiome in estimation of casual relationships with OSCC. Our findings delineate the role of host genotypes in influencing the structure of oral microbial communities.

Host Factors Affect the Gut Microbiome More Significantly than Diet Shift

The determining factors of the composition of the gut microbiome are one of the main interests in current science. In this work, we compared the effect of diet shift (DS) from heavily relying on meatatarian diets to vegetarian diets and physical exercise (EX) on the composition of the gut microbiome after 3 months. Although both DS and EX affected the composition of the gut microbiome, the patterns of alteration were different. The α-diversity analyzed by InvSimpson, Shannon, Simpson, and Evenness showed that both EX and DS affected the microbiome, causing it to become more diverse, but EX affected the gut microbiome more significantly than DS. The β-diversity analyses indicated that EX and DS modified the gut microbiome in two different directions. Co-occurrence network analysis confirmed that both EX and DS modified the gut microbiome in different directions, although EX modified the gut microbiome more significantly. Most notably, the abundance of Dialister succinatiphilus was upregulated by EX, and the abundances of Bacteroides fragilis, Phascolarctobacterium faecium, and Megasphaera elsdenii were downregulated by both EX and DS. Overall, EX modulated the composition of the gut microbiome more significantly than DS, meaning that host factors are more important in determining the gut microbiome than diets. This work also provides a new theoretical basis for why physical exercise is more health-beneficial than vegetarian diets.

Changes in Ciliate Communities Reveal Modification of Lake Functioning Over the Last Century

Ciliates are unicellular heterotrophic organisms that play a key role in the planktonic and benthic food webs of lakes, and represent a great potential as bioindicator. In this study, we used the top-bottom paleolimnological approach to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located along an elevation gradient using metabarcoding techniques applied on sedimentary DNA (sed-DNA). Our results show an overall decline in the β-diversity in recent time, especially in lowland lakes which are more strongly expose to local human pressure. Analyses of the functional groups indicate important restructuration of the trophic food web and changes that are consistent with several well documented environmental changes such as the widespread increase in deep water anoxia, changes in thermal stability and nutrient cycling. Our study demonstrates the potential offered by sed-DNA to uncover information about past ciliate communities on a wide variety of lakes and the potential of using ciliates as valuable indicators, integrating information from the pelagic to the benthic profundal (and littoral) zones. Through trait-based functional community approach, the ciliates provide additional valuable information on ecosystem functioning, thus offering more a holistic view on the long-term changes of aquatic ecosystems.

CUMS and dexamethasone induce depression-like phenotypes in mice by differentially altering gut microbiota and triggering macroglia activation

BackgroundAlthough the link between gut microbiota and depression has been suggested, changes of gut microbiota vary largely among individuals with depression.AimsExplore the heterogeneity of microbiota–gut–brain axis and new pathogenic characteristics in murine models of depression.MethodsAdolescent female mice were randomly divided into control (CON) group (n=10), chronic unexpected mild stress (CUMS) group (n=15) and dexamethasone (DEX) group (n=15). Mice in the DEX group were gavaged twice a day with 0.2 mg/kg of DEX for 5 weeks, whereas CON mice were given the same amount of solvent. Mice in the CUMS group were exposed to stressors. After behavioural evaluations, all mice were sacrificed for harvesting tissues and blood samples. Enzyme-linked immunosorbent assay (ELISA) was conducted for measuring levels of corticosterone (CORT) and interleukin-1β (IL-1β) in sera, whereas levels of protein expression in colon and hippocampal tissues were examined by western blot. Faecal microbial communities were analysed by sequencing 16S rDNAs.ResultsMice in CUMS and DEX groups exhibited severe depression-like behaviours. Compared with CON mice, CUMS-exposed mice showed a significant increase in both α and β diversity. Prevotellaceae and Desulfovibrio were enriched, whereas Bacilli were decreased in the faeces of mice in the CUMS group. DEX-treated mice had a decrease in the abundance of Clostridium XVIII. Levels of occludin in colon tissue of DEX-treated mice were reduced. Relative to mice in the CON and CUMS groups, DEX-treated mice contained higher serum levels of CORT and IL-1β. Compared with CON mice, mice in the DEX and CUMS groups had higher levels of IL-1β in sera and lower levels of glial fibrillary acidic protein (GFAP), Nestin, Synapsin-1 and P2Y12 receptor in the hippocampus.ConclusionsChanges of gut microbiota diversity, intestinal integrity and neuroinflammation in the brain contribute to CUMS-induced depression, whereas pathobionts and excessive immunosuppression with damaged neuronal synapses is a basis of the DEX-induced depression.