Добірка наукової літератури з теми "Patescibacteria"

Although the anaerobic ammonium oxidation (anammox) process has attracted attention regarding its application in ammonia wastewater treatment based on its efficiency, the physiological characteristics of anammox bacteria remain unclear because of the lack of pure-culture representatives. The coexistence of heterotrophic bacteria has often been observed in anammox reactors, even in those fed with synthetic inorganic nutrient medium. In this study, we recovered 37 draft genome bins from a long-term-operated anammox column reactor and predicted the metabolic pathway of coexisting bacteria, especially Patescibacteria (also known as Candidate phyla radiation). Genes related to the nitrogen cycle were not detected in Patescibacterial bins, whereas nitrite, nitrate, and nitrous oxide-related genes were identified in most of the other bacteria. The pathway predicted for Patescibacteria suggests the lack of nitrogen marker genes and its ability to utilize poly-N-acetylglucosamine produced by dominant anammox bacteria. Coexisting Patescibacteria may play an ecological role in providing lactate and formate to other coexisting bacteria, supporting growth in the anammox reactor. Patescibacteria-centric coexisting bacteria, which produce anammox substrates and scavenge organic compounds produced within the anammox reactor, might be essential for the anammox ecosystem.

Members of the Candidate phylum Patescibacteria, also called Candidate Phyla Radiation (CPR), are described as ultramicrobacteria with limited metabolic capacities. Wide diversity and relative abundances up to 80% in anaerobic habitats, e.g., in groundwater or sediments are characteristic for Candidatus Patescibacteria. However, only few studies exist for marine surface water. Here, we report the presence of 40 patescibacterial candidate clades at air-sea interfaces, including the upper water layer, floating foams and the sea-surface microlayer (SML), a < 1 mm layer at the boundary between ocean and atmosphere. Particle-associated (>3 µm) and free-living (3–0.2 µm) samples were obtained from the Jade Bay, North Sea, and 16S rRNA (gene) amplicons were analyzed. Although the abundance of Cand. Patescibacteria representatives were relatively low (<1.3%), members of Cand. Kaiserbacteria and Cand. Gracilibacteria were found in all samples. This suggests profound aerotolerant capacities of these phylogenetic lineages at the air-sea interface. The presence of ultramicrobacteria in the >3 µm fraction implies adhesion to bigger aggregates, potentially in anoxic niches, and a symbiotic lifestyle. Due to their small sizes, Cand. Patescibacteria likely become aerosolized to the atmosphere and dispersed to land with possible implications for affecting microbial communities and associated processes in these ecosystems.

Abstract Declining health and cognition are hallmarks of advanced age that reduce both the quality and length of the lifespan. While caloric restriction has been highlighted as a strategy for increasing healthspan, time-restricted feeding and changes in dietary macronutrient composition may be more feasible alternatives with similar health outcomes. Furthermore, age-related changes in gut microbiome composition may reciprocally interact with several physiological systems – providing a good target for future therapeutic interventions. To begin to investigate the potential utility of a ketogenic (high fat, low carbohydrate) diet and/or time-restricted feeding, fully mature young (5 mo) and older (22 mo) adult male Fischer Brown Norway Hybrid rats were placed on a time-restricted feeding regimen of a ketogenic or micronutrient and calorically matched control diet for 7 months. A third group of rats was permitted to eat standard chow ad libitum. Fecal samples collected at the conclusion of the study were submitted for 16S microbiome analysis, which revealed significant differences across age and diet groups, as well as across feeding paradigms. Beta diversity analysis demonstrated distinct microbiome composition across the three diet groups regardless of age. Furthermore, diet group significantly impacted abundance in expression of several microbiota at the phylum level, including Verrucomicrobia, Cyanobacteria, Actinobacteria and Patescibacteria, though age did not. Verrucomicrobia was significantly increased (p=0.02) and Actinobacteria and Patescibacteria (p&lt;0.01) were significantly decreased in animals fed in a time-restricted fashion. These results indicate the value of both altered macronutrient composition and altered feeding methodology for therapeutic interventions targeting the gut microbiome.

Abstract This study evaluated the effect of heat stress abatement strategies on the faecal microbiome of finishing beef steers in the Southeastern United States. The study was designed as a completely randomized block using 32 steers (BW 453k 4 kg) stratified by weight and randomly assigned to one of four treatment groups: covered with fans (CWF), covered no fans (CNF), outside with shade (SHADE), and outside without shade (OUT). All steers were housed outside from June to July and were brought up on a common feedlot ration. After-which steers were placed into treatments on d -10 and covered steers were given 10 days to acclimate Calan-gate system. During the acclimation phase, both covered and outside steers were brought up at a similar rate. Steers were weighed and faecal samples were collected on d 0, 50, and 85. Microbial DNA was extracted from the samples using a combination of mechanical and enzymatic processes, and the DNA sequences were analyzed using QIIME v2.0. There was a treatment x day interaction for Actinobacteriota, Bacteroidota, and Patescibacteria phyla. Additionally, there was a day effect for all three phyla (P &lt; 0.001), but there was only a treatment effect (P &lt; 0.001) for Patescibacteria. There was not an interaction for Fibrobacterota, Firmicutes, or Proteobacteria (P &gt; 0.226), but there was a day effect (P &lt; 0.019) for all three phyla. There was a treatment effect (P = 0.036) for Fibrobacterota, however there was not a treatment effect for Firmicutes and Proteobacteria (P &gt; 0.394). Moreover, there was no interaction, treatment, or day effect (P &gt; 0.39) for the Firmicutes to Bacteroidota ratio. These results suggest that stress abatement strategies may influence the fecal microbiome over time, and they might help better understand how stress affects the microbiome and nutrient digestibility in the lower gut.

Objectives. The experiment aimed to explore the effects of curcumin on motor impairment, dopamine neurons, and gut microbiota in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mice model. Methods. Mice were randomly assigned to six groups: normal control group, solvent control group, MPTP group, curcumin-low-dose group (40 mg/kg), curcumin-medium-dose group (80 mg/kg), and curcumin-high-dose group (160 mg/kg). After 14 days, each group of mice was subjected to the pole text, the hanging test, and the open-field test. Tyrosine hydroxylase (TH) immunohistochemistry was used to observe the survival of nigrostriatal dopamine neurons. Moreover, ultrastructural changes were observed with a transmission electron microscope in mice striatal tissue cells. Then, 16S rRNA was used to assess changes in the gut microbiota. Results. (1) Each dose of curcumin reduced pole climbing time and increased suspension score and total distance moved dose-dependently. (2) All curcumin groups improved cell wrinkling and vacuolar degeneration, increased the number of TH positives, improved cell survival, and the higher the dose of curcumin, the better the effect. (3) There were differences in microbiota composition and a relative abundance among the groups. The relative abundance of Patescibacteria, Proteobacteria, and Verrucomicrobia was higher in the MPTP group. The relative abundance of Patescibacteria, Enterobacteriaceae, Enterococcaceae all decreased in all curcumin groups. In addition, the Kyoto Encyclopedia of Genes and Genomes pathways showed a reduction in the superpathway of N-acetylneuraminate degradation after medium- and high-dose curcumin administration. Conclusions. Curcumin regulates gut microbiota and exerts a neuroprotective effect in the MPTP mice model. This preliminary study demonstrates the therapeutic potential of curcumin for Parkinson’s disease, providing clues for microbially targeted therapies for Parkinson’s disease.

Biofertilizers have been suggested as alternatives to synthetic fertilizers, which could reduce soil degradation brought on by excessive chemical fertilization and have an impact on the bacterial diversity and community in the soil. The diversity and community of soil bacteria in tea plantations treated with wheat straw compost have, however, received relatively little attention. In this research, a two-year field trial was run to examine the effects of applying wheat straw compost on the characteristics of the soil and the quality of the tea. We also used high-throughput sequencing to investigate the response of the soil bacterial community, and Spearman’s rank correlation was used to estimate the relationship between the soil bacterial community, soil characteristics, and tea quality. It was noticed that applying chemical fertilizer along with compost increased the fertility of the soil and the quality of the tea. Based on a two-year thorough data analysis, the T4 treatment (compost fertilizers 15,000 kg ha−1 + chemical fertilizers 1050 kg ha−1, chemical fertilizer reduction 30%) was determined to be the best group. The diversity and community makeup of soil bacteria were impacted by fertilization management. After the initial compost replacement, soils with compost had a greater bacterial richness than soils with inorganic fertilizers. After the second compost substitution, PCoA analysis revealed that compost fertilizer could be easily differentiated from chemical fertilizer. In 2019, Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, and Patescibacteria were the most prevalent bacterial phyla. In 2020, Firmicutes and Chloroflexi overtook Bacteroidetes and Patescibacteria as the two major bacterial phyla. In addition to increasing the diversity of soil bacteria and having an impact on the bacterial population, the application of wheat straw compost mixed with chemical fertilizers can also control the soil’s characteristics and the quality of the tea produced in tea plantations. So, as a fertilization way with less environmental impact, wheat straw compost fertilization can be used in tea plantations.

Under irrigation with saline wastewater, SO42−, Cl−, and Ca2+ aggregated in the topsoil, and Mg2+ was significantly higher in the deeper soil than in the topsoil and 40 cm soil layers. The abundance of Zoopagomycota, Ascomycota, Mortierellomycota, Basidiomycota, Chytridiomycota, Rozellomycota, Blastocladiomycota, Monoblepharomycota, Mucoromycota and Olpidiomycota in the surface soil was influenced by Mg2+, whereas Ca2+ affected the abundance of Zoopagomycota and Chytridiomycota. In the 40 cm soil layer, Mg2+ and Cl− promoted Actinobacteria, Proteobacteria, Nitrospirae, Firmicutes, Entotheonellaeota, Myxococcota, Gemmatimonadota and Methylomirabilota, whereas they inhibited Planctomycetota, Acidobacteria, Chloroflexi, Patescibacteria and Bacteroidota. In the 80 cm soil layer, SO42− and Cl− promoted Rozellomycota, Mortierellomycota, Chytridiomycota, Ascomycota, and Mucoromycota, but had a negative effect on Glomeromycota, Blastocladiomycota, Olpidiomycota and Monoblepharomy-cota. The increase in salinity significantly reduced the abundance of the Actinomycetes phylum and the Amoebozoa phylum. Both saprophytic and symbiotic fungi decreased with increasing salinity.

Les Patescibacteria forment un phylum bactérien très diversifié, comprenant au moins 25 % de la diversité bactérienne. On trouve des représentants de ce clade dans de nombreux environnements, allant des écosystèmes d'eau douce et marin aux microbiomes animaux et aux sédiments. Très peu de cultures de Patescibacteria sont disponibles à ce jour. En raison de ce manque de représentants cultivés, ils ont été largement étudiés par l’approche métagénomique. Ces études ont révélé, qu'en général, ils présentent de petits génomes avec des manques significatifs de gènes codant pour des fonctions métaboliques, ce qui amène à émettre l’hypothèse qu'ils dépendent d'un hôte pour survivre. Il n'y a cependant aucune preuve que tous les Patescibacteria soient réellement des symbiotes. De plus, environ la moitié de leurs gènes ne peuvent pas être annotés fonctionnellement par des approches de similarité. Il est nécessaire d'obtenir davantage de représentants cultivés pour mieux comprendre l'écologie de ce phylum bactérien. Les Patescibacteria ont récemment été identifiés comme apparentés aux Chloroflexota et Dormibacterota, qui présentent un mode de vie libre. L'évolution des Patescibacteria, en particulier leur mode de vie symbiotique, et leur diversification par rapport à leur groupe sœur vivant librement, ne sont pas entièrement compris. Ici, nous avons obtenu une culture enrichie d'un nouveau représentant à l’échelle du genre de Patescibacteria, qui est un épibionte de protéobactéries oxydant le méthanol, un type d'hôte jamais observé auparavant associé à ce clade. De plus, en utilisant une correspondance d’espaceurs CRISPR, nous avons identifié un nouveau phage ciblant potentiellement cet épibionte. Ainsi, nous avons caractérisé la première interaction potentielle tripartite entre un représentant du phylum Patescibacteria, son hôte et un phage. De plus, nous avons reconstruit le contenu génique ancestral des différentes classes de Patescibacteria pour décrypter les premières étapes de l'évolution du mode de vie symbiotique dans ce clade et les bases de leur diversification. Nos résultats suggèrent que le dernier ancêtre commun des Patescibacteria était déjà dépendant d’un hôte. La diversification des Patescibacteria qui a suivi est due à une combinaison de pertes indépendantes et substansielles de gènes métaboliques, complétée par l'acquisition de nouveaux gènes aux fonctions inconnues
Patescibacteria is a highly diverse bacterial phylum, including at least 25% of the bacterial diversity. Representatives of this clade can be found in many environments, ranging from freshwater and marine ecosystems to animal microbiomes and sediments. Very few Patescibacteria cultures are available to date. Due to this lack of cultured representatives, they have been extensively studied using metagenomics. These investigations revealed that, overall, they present small genomes with significant gaps in the genes coding for metabolic functions, and thus, they are hypothesized to depend on a host for survival. There is no evidence, however, that all Patescibacteria are actual symbionts. Besides, about half of their genes cannot be functionally annotated by similarity approaches. More cultured representatives are needed to better understand the ecology of this bacterial phylum. Patescibacteria have been recently reported to be a sister group to the free-living phyla Chloroflexota and Dormibacterota. The evolution of the Patescibacteria, particularly their symbiotic lifestyle, and diversification from their free-living sister group, is not fully comprehended. Here, we obtained an enriched culture of a representative of a new genus-level patescibacterium, which is an epibiont of methanol-oxidizing proteobacteria, a type of host never observed before to be associated with this clade. Additionally, using a CRISPR-spacer match, we identified a new potential phage targeting this patescibacterium. Thus, we characterized the first potential three-partite interaction between a patescibacterium, its host, and a phage. Furthermore, we reconstructed the ancestral gene content of the different Patescibacteria classes to decipher the early steps of the evolution of the symbiotic lifestyle in the clade and the basis of their diversification. Our results suggest that the last common ancestor of Patescibacteria was already host-dependent. The subsequent patescibacterial diversification appears driven by a combination of independent and substantial losses of metabolic genes, complemented by the acquisition of novel genes with functions yet to be identified