Journal articles on the topic 'Patescibacteria'
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1
Hosokawa, Suguru, Kyohei Kuroda, Takashi Narihiro, Yoshiteru Aoi, Noriatsu Ozaki, Akiyoshi Ohashi, and Tomonori Kindaichi. "Cometabolism of the Superphylum Patescibacteria with Anammox Bacteria in a Long-Term Freshwater Anammox Column Reactor." Water 13, no. 2 (January 16, 2021): 208. http://dx.doi.org/10.3390/w13020208.
Abstract:
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.
2
Rahlff, Janina, Helge-Ansgar Giebel, Christian Stolle, Oliver Wurl, Alexander J. Probst, and Daniel P. R. Herlemann. "Overlooked Diversity of Ultramicrobacterial Minorities at the Air-Sea Interface." Atmosphere 11, no. 11 (November 10, 2020): 1214. http://dx.doi.org/10.3390/atmos11111214.
Abstract:
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.
3
Sánchez-Osuna, Miquel, Jordi Barbé, and Ivan Erill. "Comparative genomics of the DNA damage-inducible network in the Patescibacteria." Environmental Microbiology 19, no. 9 (July 21, 2017): 3465–74. http://dx.doi.org/10.1111/1462-2920.13826.
4
Lemos, Leandro, Lokeshwaran Manoharan, Lucas Mendes, Andressa Venturini, Victor Pylro, and Siu Mui Tsai. "Metagenome assembled‐genomes reveal similar functional profiles of CPR /Patescibacteria phyla in soils." Environmental Microbiology Reports 12, no. 6 (September 7, 2020): 651–55. http://dx.doi.org/10.1111/1758-2229.12880.
5
Hernandez, Abbi, Sara Burke, Thomas Buford, and Christy Carter. "Influence of aging, macronutrient composition and time-restricted feeding on the rat gut microbiome." Innovation in Aging 4, Supplement_1 (December 1, 2020): 888. http://dx.doi.org/10.1093/geroni/igaa057.3278.
Abstract:
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<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.
6
Hernandez, Shane R., Alexander M. Stelzleni, Wil Sims, Dylan B. Davis, Jeferson M. Lourenco, and R. Lawton Stewart. "2 Measuring the Impact of Heat Stress Abatement Strategies on Fecal Microbiome in Finishing Steers During the Summer Months in the Southeast United States." Journal of Animal Science 99, Supplement_3 (October 8, 2021): 4–5. http://dx.doi.org/10.1093/jas/skab235.007.
Abstract:
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 < 0.001), but there was only a treatment effect (P < 0.001) for Patescibacteria. There was not an interaction for Fibrobacterota, Firmicutes, or Proteobacteria (P > 0.226), but there was a day effect (P < 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 > 0.394). Moreover, there was no interaction, treatment, or day effect (P > 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.
7
Zhu, Hong, Houwen Zhang, Bonan Hou, Bin Xu, Liting Ji, and You Wu. "Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson’s Disease." Evidence-Based Complementary and Alternative Medicine 2022 (November 24, 2022): 1–16. http://dx.doi.org/10.1155/2022/9110560.
Abstract:
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.
8
Fu, Haiyan, Dapeng Song, Kunpeng Wang, Fengxiang Fang, Shunying Han, Fengshan Yang, and Shibo Ding. "Application of Wheat Straw Compost Mixed with Chemical Fertilizer Regulates Soil Bacterial Community Diversity in Tea (Camellia sinensis) Plantation." Diversity 15, no. 4 (April 20, 2023): 580. http://dx.doi.org/10.3390/d15040580.
Abstract:
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.
9
Lemos, Leandro N., Julliane D. Medeiros, Francisco Dini‐Andreote, Gabriel R. Fernandes, Alessandro M. Varani, Guilherme Oliveira, and Victor S. Pylro. "Genomic signatures and co‐occurrence patterns of the ultra‐small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle." Molecular Ecology 28, no. 18 (September 2019): 4259–71. http://dx.doi.org/10.1111/mec.15208.
10
Wang, Weihan, Dandan Zhang, Hao Kong, Gengtao Zhang, Feng Shen, and Zhiping Huang. "Effects of Salinity Accumulation on Physical, Chemical, and Microbial Properties of Soil under Rural Domestic Sewage Irrigation." Agronomy 14, no. 3 (March 1, 2024): 514. http://dx.doi.org/10.3390/agronomy14030514.
Abstract:
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.
11
Kagemasa, Shuka, Kyohei Kuroda, Ryosuke Nakai, Yu-You Li, and Kengo Kubota. "Diversity of <i>Candidatus</i> Patescibacteria in Activated Sludge Revealed by a Size-Fractionation Approach." Microbes and Environments 37, no. 2 (2022): n/a. http://dx.doi.org/10.1264/jsme2.me22027.
12
Liu, Bin, Zhenghua Ding, Junhui Xiong, Xing Heng, Huafu Wang, and Weihua Chu. "Gut Microbiota and Inflammatory Cytokine Changes in Patients with Ankylosing Spondylitis." BioMed Research International 2022 (August 19, 2022): 1–6. http://dx.doi.org/10.1155/2022/1005111.
Abstract:
Ankylosing spondylitis (AS) is a chronic inflammatory disease characterized by sacroiliac joint lesions and spinal ascending involvement. The aim of this work was at investigating the gut microbiota profile and proinflammatory cytokines in AS patients. Gut microbiota of AS patients was clearly different from that of healthy human controls. 16S rRNA sequencing analysis demonstrated a changed microbial diversity in the AS patients, and there was a significant increase in the abundance of Cyanobacteria, Deinococcota, Patescibacteria, Actinobacteriota, and Synergistota at a phyla level increased in AS, while the relative abundance of Acidobacteriota, Bdellovibrionota, Campylobacterota, Chloroflexi, Gemmatimonadota, Myxococcota, Nitrospirota, Proteobacteria, and Verrucomicrobiota declined in AS patients. ELISA results for the markers of inflammation in the AS patients revealed increased concentrations of proinflammatory cytokines such as IL-23, IL-17, and IFN-γ. Our findings support the fact that the intestinal microbiota are altered in AS with an inflammatory status, which indicates that gut microbiota should be a potential target for ankylosing spondylitis therapy.
13
Gu, Yaqiong, Beiying Li, Xiang Zhong, Conghe Liu, and Bin Ma. "Bacterial Community Composition and Function in a Tropical Municipal Wastewater Treatment Plant." Water 14, no. 10 (May 11, 2022): 1537. http://dx.doi.org/10.3390/w14101537.
Abstract:
Bacterial diversity and community composition are of great importance in wastewater treatment; however, little is known about the diversity and community structure of bacteria in tropical municipal wastewater treatment plants (WWTPs). Therefore, in this study, activated sludge samples were collected from the return sludge, anaerobic sludge, anoxic sludge, and aerobic sludge of an A2O WWTP in Haikou, China. Illumina MiSeq high-throughput sequencing was used to examine the 16S ribosomal RNA (rRNA) of bacteria in the samples. The microbial community diversity in this tropical WWTP was higher than in temperate, subtropical, and plateau WWTPs. Proteobacteria, Bacteroidota, Patescibacteria, and Chloroflexi were the dominant phyla. Nitrification bacteria Nitrosomonas, and Nitrospira were also detected. Tetrasphaera, instead of Candidatus Accumulibacter, were the dominant polyphosphate accumulating organisms (PAOs), while, glycogen accumulating organisms (GAOs), such as Candidatus Competibacter and Defluviicoccus were also detected. The bacterial community functions predicted by PICRUSt2 were related to metabolism, genetic information processing, and environmental information processing. This study provides a reference for the optimization of tropical municipal WWTPs.
14
Alqaderi, Hend, Meganathan P. Ramakodi, Rasheeba Nizam, Sindhu Jacob, Sriraman Devarajan, Muthukrishnan Eaaswarkhanth, and Fahd Al-Mulla. "Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot Study." Microorganisms 9, no. 6 (June 4, 2021): 1222. http://dx.doi.org/10.3390/microorganisms9061222.
Abstract:
The potential role of the salivary microbiome in human diseases has increasingly been explored. The salivary microbiome has been characterized in several global populations, except the Arabian Gulf region. Hence, in this pilot study, we profiled the salivary microbiome of Kuwaiti adolescents with varied body mass indexes (BMI). The analyses of core microbiome composition showed Firmicutes, Bacteroidota, Proteobacteria, Patescibacteria, Fusobacteriota, Actinobacteriota, and Campylobacterota as the common phylum found in the Kuwaiti adolescent population. We also illustrated a diverse microbial community among the sampled individuals grouped according to their BMI. Notably, the overweight group was found with a higher number of distinct taxa than other groups. As such, the core microbiome composition was found to be significantly different (p-value < 0.001) across different BMI groups. Overall, this pilot investigation outlined the microbial diversity and suggested that changes in salivary microbiome composition in people with obese or overweight BMI might reflect their susceptibility to oral diseases.
15
Yi, Xin, Baoyun Wu, Jinglei Ma, Xiaojing Cui, Ziqi Deng, Sanlong Hu, Wei Li, et al. "Effects of Dietary Capsaicin and Yucca schidigera Extracts as Feed Additives on Rumen Fermentation and Microflora of Beef Cattle Fed with a Moderate-Energy Diet." Fermentation 9, no. 1 (December 30, 2022): 30. http://dx.doi.org/10.3390/fermentation9010030.
Abstract:
Capsaicin (CAP) and Yucca schidigera extract (YSE) are two types of plant extracts that can change rumen fermentation. This study was conducted to investigate whether supplementation of beef cattle diets with CAP and YSE for 90 days would affect rumen fermentation and microflora. Forty-five healthy Angus steers (initial body weight = 510.54 ± 41.27 kg) were divided into three groups: control (CON), CAP, and YSE. Ammonia nitrogen (NH3-N) and total volatile fatty acid (TVFA) concentrations were significantly higher in the YSE group than in the CON group and significantly lower in the CAP group than in the CON group. At the phylum level, YSE increased the relative abundances of Bacteroidota and Patescibacteria and reduced that of Bacillota. At the genus level, CAP and YSE both increased the relative abundances of genera subordinate to Bacteroidota and decreased the relative abundances of genera subordinate to Bacillota. Our study shows that YSE and CAP have different effects on rumen fermentation and microflora after long-term supplementation.
16
Zhao, Z., S. Yu, X. Han, and S. Yang. "Influence of drought and dry-wet alternation on nitrogen transformation and low abundance microorganisms in tea garden soil." Journal of Environmental Biology 43, no. 2 (March 11, 2022): 231–38. http://dx.doi.org/10.22438/jeb/43/2/mrn-2068.
Abstract:
Aim: The soil water availability seriously limits the growth and development of tea plants, and soil microorganisms are an important medium to regulate soil nutrient cycling. In this study, the effects of water supply mode on soil nitrogen nutrition and soil microbes in tea gardens were investigated. Methodology: This experiment set up consisted two water supply modes (consecutive drought and dry-wet alternation) by using the soil microcosm incubation experiment, and four treatments were set: 20% water holding capacity for 21day (D21); 20% water holding capacity for 1-7 days and 60% water holding capacity for 8-21 days (D7W14); 20% water holding capacity for 1-14 day and 60% water holding capacity for 15-21 days (D14W7); 20% water holding capacity for 1-7 days, 60% water holding capacity for 8-14 days, 20% water holding capacity for 15-21 days (D7W7D7). Destructive sampling was carried out to determine soil NH4+-N, NO3--N, soil enzyme activities. 16S rRNA sequencing technique was used to determine the change in soil microbial diversity. Results: The results showed that the consecutive drought reduced the content of soil NH4+-N to 13.97 mg kg-1, and the net nitrogen mineralization was negative (-2.75 mg kg-1) after 21 days of incubation. Dry-wet alternation promoted the increase in of soil net nitrogen mineralization quantity and net nitrification quantity, which rose to 3.48-26.41 mg kg-1 and 8.07-23.11 mg kg-1, respectively. Different water supply modes had no significant impact on the structure of dominant soil microbial community, and the effect mainly focused on relative abundance, especially dry-wet alternation mode. Compared with the continuous drought treatment, the relative abundance of Nitrospirae, Actinobacteria, Chloroflexi, Patescibacteria, Latescibacteria, Rokubacteria, Acidobacteria were significantly different in different dry-wet alternation treatments, while the relative abundance of Nitrospirae, Acidobacteria, Latescibacteria, Gemmatimonadetes, Patescibacteria and Chloroflexi also increased or decreased significantly among different dry-wet alternation treatments. Among the physical and chemical factors of tea garden soil, NO3- had the most significant effect on the structure of microbial community. Interpretation: Different water supply can significantly affect the transformation of soil nitrogen and the change in soil bacterial community in tea garden, which provided a theoretical basis for tea garden to cope with adverse weather changes and maintain the stability of tea garden soil ecosystem.
17
Sonthiphand, Prinpida, Pasunun Rattanaroongrot, Kasarnchon Mek-yong, Kanthida Kusonmano, Chalida Rangsiwutisak, Pichahpuk Uthaipaisanwong, Srilert Chotpantarat, and Teerasit Termsaithong. "Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes." PeerJ 9 (January 8, 2021): e10653. http://dx.doi.org/10.7717/peerj.10653.
Abstract:
The microbiomes of deep and shallow aquifers located in an agricultural area, impacted by an old tin mine, were explored to understand spatial variation in microbial community structures and identify environmental factors influencing microbial distribution patterns through the analysis of 16S rRNA and aioA genes. Although Proteobacteria, Cyanobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Epsilonbacteraeota were widespread across the analyzed aquifers, the dominant taxa found in each aquifer were unique. The co-dominance of Burkholderiaceae and Gallionellaceae potentially controlled arsenic immobilization in the aquifers. Analysis of the aioA gene suggested that arsenite-oxidizing bacteria phylogenetically associated with Alpha-, Beta-, and Gamma proteobacteria were present at low abundance (0.85 to 37.13%) and were more prevalent in shallow aquifers and surface water. The concentrations of dissolved oxygen and total phosphorus significantly governed the microbiomes analyzed in this study, while the combination of NO3--N concentration and oxidation-reduction potential significantly influenced the diversity and abundance of arsenite-oxidizing bacteria in the aquifers. The knowledge of microbial community structures and functions in relation to deep and shallow aquifers is required for further development of sustainable aquifer management.
18
Parihar, Jagdish, Suraj P. Parihar, Prashanth Suravajhala, and Ashima Bagaria. "Spatial Metagenomic Analysis in Understanding the Microbial Diversity of Thar Desert." Biology 11, no. 3 (March 17, 2022): 461. http://dx.doi.org/10.3390/biology11030461.
Abstract:
The arid and semi-arid regions of Rajasthan are one of the most extreme biomes of India, possessing diverse microbial communities that exhibit immense biotechnological potential for industries. Herein, we sampled study sites from arid and semi-arid regions of Thar Desert, Rajasthan, India and subjected them to chemical, physical and metagenomics analysis. The microbial diversity was studied using V3–V4 amplicon sequencing of 16S rRNA gene by Illumina MiSeq. Our metagenomic analyses revealed that the sampled sites consist mainly of Proteobacteria (19–31%) followed by unclassified bacteria (5–21%), Actinobacteria (3–25%), Planctomycetes (5–13%), Chloroflexi (2–14%), Bacteroidetes (3–12%), Firmicutes (3–7%), Acidobacteria (1–4%) and Patescibacteria (1–4%). We have found Proteobacteria in abundance which is associated with a range of activities involved in biogeochemical cycles such as carbon, nitrogen, and sulphur. Our study is perhaps the first of its kind to explore soil bacteria from arid and semi-arid regions of Rajasthan, India. We believe that the new microbial candidates found can be further explored for various industrial and biotechnological applications.
19
Sonthiphand, Prinpida, Pasunun Rattanaroongrot, Kasarnchon Mek-yong, Kanthida Kusonmano, Chalida Rangsiwutisak, Pichahpuk Uthaipaisanwong, Srilert Chotpantarat, and Teerasit Termsaithong. "Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes." PeerJ 9 (January 8, 2021): e10653. http://dx.doi.org/10.7717/peerj.10653.
Abstract:
The microbiomes of deep and shallow aquifers located in an agricultural area, impacted by an old tin mine, were explored to understand spatial variation in microbial community structures and identify environmental factors influencing microbial distribution patterns through the analysis of 16S rRNA and aioA genes. Although Proteobacteria, Cyanobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Epsilonbacteraeota were widespread across the analyzed aquifers, the dominant taxa found in each aquifer were unique. The co-dominance of Burkholderiaceae and Gallionellaceae potentially controlled arsenic immobilization in the aquifers. Analysis of the aioA gene suggested that arsenite-oxidizing bacteria phylogenetically associated with Alpha-, Beta-, and Gamma proteobacteria were present at low abundance (0.85 to 37.13%) and were more prevalent in shallow aquifers and surface water. The concentrations of dissolved oxygen and total phosphorus significantly governed the microbiomes analyzed in this study, while the combination of NO3--N concentration and oxidation-reduction potential significantly influenced the diversity and abundance of arsenite-oxidizing bacteria in the aquifers. The knowledge of microbial community structures and functions in relation to deep and shallow aquifers is required for further development of sustainable aquifer management.
20
Zhang, Yangbo, Jianan Huang, Yifan Xiong, Xiangna Zhang, Yong Lin, and Zhonghua Liu. "Jasmine Tea Attenuates Chronic Unpredictable Mild Stress-Induced Depressive-like Behavior in Rats via the Gut-Brain Axis." Nutrients 14, no. 1 (December 27, 2021): 99. http://dx.doi.org/10.3390/nu14010099.
Abstract:
The number of depressed people has increased worldwide. Dysfunction of the gut microbiota has been closely related to depression. The mechanism by which jasmine tea ameliorates depression via the brain-gut-microbiome (BGM) axis remains unclear. Here, the effects of jasmine tea on rats with depressive-like symptoms via the gut microbiome were investigated. We first established a chronic unpredictable mild stress (CUMS) rat model to induce depressive symptoms and measured the changes in depression-related indicators. Simultaneously, the changes in gut microbiota were investigated by 16S rRNA sequencing. Jasmine tea treatment improved depressive-like behaviors and neurotransmitters in CUMS rats. Jasmine tea increased the gut microbiota diversity and richness of depressed rats induced by CUMS. Spearman’s analysis showed correlations between the differential microbiota (Patescibacteria, Firmicutes, Bacteroidetes, Spirochaetes, Elusimicrobia, and Proteobacteria) and depressive-related indicators (BDNF, GLP-1, and 5-HT in the hippocampus and cerebral cortex). Combined with the correlation analysis of gut microbiota, the result indicated that jasmine tea could attenuate depression in rats via the brain- gut-microbiome axis.
21
Satjarak, Anchittha, Jittra Piapukiew, Wikrom Chanthapatchot, Karnjana Ruen-Pham, and Alisa S. Vangnai. "Hercide Atrazine Alters the Microbiota of the Filametous Green Alga Cladophora sp. Cultured from Thailand." Sains Malaysiana 50, no. 5 (May 31, 2021): 1255–65. http://dx.doi.org/10.17576/jsm-2021-5005-06.
Abstract:
The attached green alga Cladophora known to harbor microbiota that play important roles in ecosystem, is one of the most common freshwater filamentous green algae in rivers globally, including those in the northern part of Thailand. These rivers mostly run through agricultural regions where herbicides are heavily used to improve crop quality and quantity. The extensively-used herbicide atrazine persists in soil sediments through transport by surface runoff to rivers. The effect of such herbicide contamination on Cladophora microbiota in Thailand have not been investigated. To acquire this information, 16S rDNA amplicons were used to compare microbiota of Cladophora sp. cultures treated with a spectrum of atrazine concentrations. The results showed that the Cladophora microbiome included at least 106 possible Operational taxonomic units (OTUs) representing twelve bacterial phyla which are Acidobacteria, Actinobacteria, Armatimonadetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Epsilonbacteraeota, Nitrospirae, Patescibacteria, Planctomycetes, Proteobacteria, and WPS-2, representing both core and local algal bacteria. The presence of atrazine was also correlated with changes in richness of bacterial taxa suggesting that these algal epibiotic bacteria were differently affected by atrazine treatments.
22
Li, Mengwei, Faizul Hassan, Lijuan Peng, Huade Xie, Xin Liang, Jiaxiang Huang, Feng Huang, Yanxia Guo, and Chengjian Yang. "Mulberry flavonoids modulate rumen bacteria to alter fermentation kinetics in water buffalo." PeerJ 10 (December 14, 2022): e14309. http://dx.doi.org/10.7717/peerj.14309.
Abstract:
Mulberry flavonoids can modulate the composition of rumen microbiota in ruminants to improve nutrient digestibility, owing to their strong biological activities. This study aimed to explore the effect of mulberry leaf flavonoids (MLF) on rumen bacteria, fermentation kinetics, and metagenomic functional profile in water buffalo. Forty buffaloes (4 ± 1 lactations) with almost same body weight (av. 600 ± 50 Kg) and days in milk (90 ± 20 d) were randomly allocated to four treatments having different levels of MLF: 0 g/d (control), 15 g/d (MLF15), 30 g/d (MLF30), and 45 g/d (MLF45) supplemented in a basal diet. After 35 days of supplementation, rumen contents were collected to determine rumen fermentation parameters. The 16S rRNA gene sequencing was performed to elucidate rumen bacteria composition. The obtained taxonomic data were analyzed to explore the rumen bacteriome and predict the associated gene functions and metabolic pathways. Results demonstrated a linear increase (p < 0.01) in rumen acetate, propionate, and total VFAs in the MLF45 group as compared to control. No effect of treatment was observed on rumen pH and butyrate contents. Acetate to propionate ratio in the MLF45 group linearly and quadratically decreased (p = 0.001) as compared to MLF15 and control groups. Similarly, MLF45 linearly increased (p < 0.05) the microbial protein (MCP) and NH3-N as compared to other treatments. Treatment adversely affected (p < 0.01) almost all alpha diversity parameters of rumen bacteria except Simpson index. MLF promoted the abundance of Proteobacteria while reducing the relative abundances of Actinobacteria, Acidobacteria, Chloroflexi, and Patescibacteria. The MLF supplementation tended to substantially reduce (0.05 < p < 0.1) the abundance of Actinobacteria, and Patescibacteria while completely eliminating Acidobacteria (p = 0.029), Chloroflexi (p = 0.059), and Gemmatimonadetes (p = 0.03) indicating the negative effect of flavonoids on the growth of these bacteria. However, MLF45 tended to substantially increase (p = 0.07) the abundance (~21.5%) of Acetobacter. The MLF treatment exhibited negative effect on five genera by significantly reducing (Sphingomonas) or eliminating (Arthobactor, unclassified_c__Actinobacteria, norank_c__Subgroup_6, norank_o__Saccharimonadales, and Nocardioides) them from the rumen microbiota. Pearson correlation analysis revealed 3, 5 and 23 positive correlations of rumen bacteria with milk yield, rumen fermentation and serum antioxidant parameters, respectively. A positive correlation of MCP was observed with three bacterial genera (Acetobacter, Enterobacter, and Klebsiella). The relative abundance of Pseudobutyrivibrio and Empedobacter also showed a positive correlation with the ruminal acetate and propionate. The present study indicated 45 g/d as an appropriate dose of MLF which modulated rumen bacteria and its functional profile in water buffalo.
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Zhou, Zhengyao, Meixia Qi, and Hongping Wang. "Achieving Partial Nitrification via Intermittent Aeration in SBR and Short-Term Effects of Different C/N Ratios on Reactor Performance and Microbial Community Structure." Water 12, no. 12 (December 11, 2020): 3485. http://dx.doi.org/10.3390/w12123485.
Abstract:
A sequencing batch reactor (SBR) with an intermittent aeration mode was established to achieve partial nitrification (PN) and the short-term effects of C/N ratios were investigated. Stable nitrite accumulation was achieved after 107 cycles, about 56d, with the average ammonia nitrogen removal efficiency (ARE) and nitrite accumulation rate (NAR) of 96.92% and 82.49%, respectively. When the C/N ratios decreased from 4.64 to 3.87 and 2.32, ARE and NAR still kept a stable and high level. However, when the C/N ratio further decreased to 0.77, nitrite accumulation became fluctuation, and ARE, total nitrogen (TN), and chemical oxygen demand (COD) removal performance declined obviously. Except for four common phyla (Proteobacteria, Bacteroidetes, Chloroflexi, and Actinobacteria) in the wastewater treatment system, Patescibacteria, the newly defined superphylum, was found and became the most dominant phylum in the PN sludge for their ultra-small cell size. The only ammonia oxidation bacteria (AOB), Nitrosomonas, and nitrite oxidation bacteria (NOB), Nitrospira, were detected. The relative abundance of NOB was low at different C/N ratios, showing the stable and effective inhibition effects of intermittent aeration on NOB growth.
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Zhang, Zhimin, Li Yang, Yang He, Xinmao Luo, Shaokang Zhao, and Xianbo Jia. "Composition of Fecal Microbiota in Grazing and Feedlot Angus Beef Cattle." Animals 11, no. 11 (November 5, 2021): 3167. http://dx.doi.org/10.3390/ani11113167.
Abstract:
This study is to investigate the difference in bovine fecal microbiota between grazing and feedlot Angus cattle. Fecal samples were collected from six Angus cattle grazed on grassland and six Angus cattle fed on a feedlot. The fecal bacterial community was analyzed by high-throughput sequencing of 16S rRNA gene. Sequencing of the V3–V4 region totally produced 1,113,170 effective tages that were computationally clustered into 775 operational taxonomic units (OTUs). These 775 OTUs were taxonomically assigned to bacterial 12 phyla, 19 classes, 25 orders, 54 families, 141 genera, and 145 species. The dominant phyla were Firmicutes and Bacteroidetes. There was similar species richness between grazing and feedlot Angus beef, while higher species diversity was observed in feedlot Angus beef. The relative abundance of Firmicutes, Cyanobacteria, Elusimicrobia and Patescibacteria was significantly different between grazing and feedlot Angus beef (p < 0.05). At a genus level, five microbiotas were significantly different between the two groups and all belonged to the Firmicutes phylum. These significant differences in microbiota composition between grazing and feedlot Angus beef may have an impact on the meat quality of Angus beef.
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Ravegnini, Gloria, Bruno Fosso, Viola Di Saverio, Giulia Sammarini, Federica Zanotti, Giulio Rossi, Monica Ricci, et al. "Gastric Adenocarcinomas and Signet-Ring Cell Carcinoma: Unraveling Gastric Cancer Complexity through Microbiome Analysis—Deepening Heterogeneity for a Personalized Therapy." International Journal of Molecular Sciences 21, no. 24 (December 20, 2020): 9735. http://dx.doi.org/10.3390/ijms21249735.
Abstract:
Gastric cancer (GC) is the fifth most prevalent cancer worldwide and the third leading cause of global cancer mortality. With the advances of the omic studies, a heterogeneous GC landscape has been revealed, with significant molecular diversity. Given the multifaceted nature of GC, identification of different patient subsets with prognostic and/or predictive outcomes is a key aspect to allow tailoring of specific treatments. Recently, the involvement of the microbiota in gastric carcinogenesis has been described. To deepen this aspect, we compared microbiota composition in signet-ring cell carcinoma (SRCC) and adenocarcinoma (ADC), two distinct GC subtypes. To this purpose, 10 ADC and 10 SRCC and their paired non-tumor (PNT) counterparts were evaluated for microbiota composition through 16S rRNA analysis. Weighted and unweighted UniFrac and Bray–Curtis dissimilarity showed significant community-level separation between ADC and SRCC. Through the LEfSe (linear discriminant analysis coupled with effect size) tool, we identified potential microbial biomarkers associated with GC subtypes. In particular, SRCCs were significantly enriched in the phyla Fusobacteria, Bacteroidetes, Patescibacteria, whereas in the ADC type, Proteobacteria and Acidobacteria phyla were found. Overall, our data add new insights into GC heterogeneity and may contribute to deepening the GC classification.
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Wieczorek, Robert, Zofia Zydlik, Agnieszka Wolna-Maruwka, Alicja Niewiadomska, and Dariusz Kayzer. "The Effect of Biofumigation on the Microbiome Composition in Replanted Soil in a Fruit Tree Nursery." Agronomy 13, no. 10 (September 28, 2023): 2507. http://dx.doi.org/10.3390/agronomy13102507.
Abstract:
The imbalance of the soil microbiome is a primary indicator of ARD (apple replant disease). Biofumigation is a treatment that enables the restoration of microbiome balance. This study involved an analysis of the taxonomic and functional diversity of bacterial communities in replanted soil (ARD), in replanted soils with forecrops of French marigold (Tagetes patula L.), white mustard (Sinapis alba), and oilseed radish (Raphanus sativus var. oleifera), and in agricultural soil. The biofumigation treatment with phytosanitary plants changed the structure and abundance of the replanted soil microbiome in a fruit tree nursery. The count of operational taxonomic units (OTU) of the Proteobacteria, Bacteroidota, Patescibacteria, Chloroflexi, and Verrucomicrobiota phyla increased, whereas the count of the Firmicutes, Acidobacteriota, and Actinobacteriota phyla decreased. Biofumigation caused an increase in the content of some dominant bacterial genera, such as Flavobacterium, Massila, Sphingomonas, Arenimonas, and Devosia, in the replanted soil. Their presence in the soil may improve the growth of plants, induce their systemic resistance, and thus improve the production properties of soil with ARD. The research results led to the conclusion that the use of phytosanitary plants in nursery production can be an effective alternative to the chemical fumigation of soil.
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Cataruci, Amalia C. S., Dione Kawamoto, Natali Shimabukuro, Karin H. Ishikawa, Ellen S. Ando-Suguimoto, Rodolfo A. Ribeiro, Gianlucca G. Nicastro, Emanuel Albuquerque-Souza, Robson F. de Souza, and Marcia P. A. Mayer. "Oral Administration of Lactobacillus acidophilus LA5 Prevents Alveolar Bone Loss and Alters Oral and Gut Microbiomes in a Murine Periodontitis Experimental Model." Microorganisms 12, no. 6 (May 24, 2024): 1057. http://dx.doi.org/10.3390/microorganisms12061057.
Abstract:
Periodontitis is a destructive inflammatory response triggered by dysbiosis. Lactobacillus acidophilus LA5 (LA5) may impair microbial colonization and alter the host. Thus, we evaluated the effect of LA5 on alveolar bone loss in a periodontitis murine model and investigated its effect on the oral and gut microbiomes. Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum, and Streptococcus gordonii were inoculated in C57BL/6 mice (P+), with LA5 (L+). SHAM infected controls (P- and/or L- groups) were also evaluated. After 45 days, alveolar bone loss in the maxilla and oral and gut microbiomes were determined. The administration of LA5 controlled the microbial consortium-induced alveolar bone loss. Periodontopathogens infection resulted in shifts in the oral and gut microbiomes consistent with dysbiosis, and LA5 reshaped these changes. The oral microbiome of P+L- group showed the increased abundance of Enterococaccea, Streptoccocaceae, Staphylococcaceae, Moraxellaceae, and Pseudomonadaceae, which were attenuated by the administration of LA5 to the infected group (P+L+). The administration of LA5 to otherwise non-infected mice resulted in the increased abundance of the superphylum Patescibacteria and the family Saccharamonadaceae in the gut. These data indicate L. acidophilus LA5 as a candidate probiotic for the control of periodontitis.
28
Fujii, Naoki, Kyohei Kuroda, Takashi Narihiro, Yoshiteru Aoi, Noriatsu Ozaki, Akiyoshi Ohashi, and Tomonori Kindaichi. "Metabolic Potential of the Superphylum <i>Patescibacteria</i> Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant." Microbes and Environments 37, no. 3 (2022): n/a. http://dx.doi.org/10.1264/jsme2.me22012.
29
Cui, Guojie, Jun Li, Zhaoming Gao, and Yong Wang. "Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep." PeerJ 7 (May 17, 2019): e6961. http://dx.doi.org/10.7717/peerj.6961.
Abstract:
Microbial communities in hadal sediments are least explored in hadal zone (>6,000 m), especially in the Challenger Deep with high pressure (∼110 M pa at the bottom). In this study, we investigated the microbial communities in the sediments of the slope and trench-axis bottom of the Challenger Deep in the Mariana Trench. Classification of the reads of the 16S rRNA gene amplicons showed vertical distribution of prokaryotic microbial inhabitants from the surface to up to 60 centimeter below surface floor (cmbsf). The most dominant phyla were Proteobacteria, Chloroflexi, Actinobacteria, Planctomycetes and candidate phyla Patescibacteria and Marinimicrobia. Distinct dominant groups in the microbial communities were observed in trench-axis sediment (water depth >8,600 m), compared to the slopes of the Challenger Deep. A sampling site at the northern slope was enriched with archaea from mesophilic Euryarchaeota Marine Group II (MGII) as a biomarker of specific geochemical setting. Among archaeal community, Thaumarchaeota represented byNitrosopumiluswere dominant in the upper layers and diminished drastically in the deeper layers. “Ca. Woesearchaeota”, however, became the dominant group in the deeper layers. Overall, our study provides a better understanding on the pattern of the microbial communities in the deepest hadal sediments on Earth, and highlights the extraordinary diversity still waiting to be discovered.
30
Zhu, Zheng, Xiaoxi Ma, Jie Wu, Zhenxu Xiao, Wanqing Wu, Saineng Ding, Li Zheng, et al. "Altered Gut Microbiota and Its Clinical Relevance in Mild Cognitive Impairment and Alzheimer’s Disease: Shanghai Aging Study and Shanghai Memory Study." Nutrients 14, no. 19 (September 23, 2022): 3959. http://dx.doi.org/10.3390/nu14193959.
Abstract:
Altered gut microbiota has been reported in individuals with mild cognitive impairment (MCI) and Alzheimer’s disease (AD). Previous research has suggested that specific bacterial species might be associated with the decline of cognitive function. However, the evidence was insufficient, and the results were inconsistent. To determine whether there is an alteration of gut microbiota in patients with MCI and AD and to investigate its correlation with clinical characteristics, the fecal samples from 94 cognitively normal controls (NC), 125 participants with MCI, and 83 patients with AD were collected and analyzed by 16S ribosomal RNA sequencing. The overall microbial compositions and specific taxa were compared. The clinical relevance was analyzed. There was no significant overall difference in the alpha and beta diversity among the three groups. Patients with AD or MCI had increased bacterial taxa including Erysipelatoclostridiaceae, Erysipelotrichales, Patescibacteria, Saccharimonadales, and Saccharimonadia, compared with NC group (p < 0.05), which were positively correlated with APOE 4 carrier status and Clinical Dementia Rating (correlation coefficient: 0.11~0.31, p < 0.05), and negatively associated with memory (correlation coefficient: −0.19~−0.16, p < 0.01). Our results supported the hypothesis that intestinal microorganisms change in MCI and AD. The alteration in specific taxa correlated closely with clinical manifestations, indicating the potential role in AD pathogenesis.
31
Ramdat, Naven, Zi-Jing Wang, Jung-Chen Huang, Yikun Wang, Azharuddin Chachar, Chuanqi Zhou, and Zhiping Wang. "Effects of Enrofloxacin on Nutrient Removal by a Floating Treatment Wetland Planted with Iris pseudacorus: Response and Resilience of Rhizosphere Microbial Communities." Sustainability 14, no. 6 (March 13, 2022): 3358. http://dx.doi.org/10.3390/su14063358.
Abstract:
Constructed wetlands (CWs), including floating treatment wetlands (FTWs), possess great potential for treating excessive nutrients in surface waters, where, however, the ubiquitous presence of antibiotics, e.g., enrofloxacin (ENR), is threatening the performance of CWs. In developing a more efficient and resilient system, we explored the responses of the FTW to ENR, using tank 1, repeatedly exposed to ENR, and tank 2 as control. Plant growth and nutrient uptake were remarkably enhanced in tank 1, and similar phosphorus removal rates (86~89% of the total added P) were obtained for both tanks over the experimental period. Contrarily, ENR apparently inhibited N removal by tank 1 (35.1%), compared to 40.4% for tank 2. As ENR rapidly decreased by an average of 71.6% within a week after each addition, tank 1 took only 4 weeks to adapt and return to a similar state compared to that of tank 2. This might be because of the recovery of microbial communities, particularly denitrifying and antibiotic-resistance genes containing bacteria, such as Actinobacteria, Patescibacteria, Acidovorax and Pseudomonas. After three ENR exposures over six weeks, no significant differences in the nutrient removal and microbial communities were found between both tanks, suggesting the great resilience of the FTW to ENR.
32
Ivanova, Anastasia A., Alexey V. Beletsky, Andrey L. Rakitin, Vitaly V. Kadnikov, Dmitriy A. Philippov, Andrey V. Mardanov, Nikolai V. Ravin, and Svetlana N. Dedysh. "Closely Located but Totally Distinct: Highly Contrasting Prokaryotic Diversity Patterns in Raised Bogs and Eutrophic Fens." Microorganisms 8, no. 4 (March 29, 2020): 484. http://dx.doi.org/10.3390/microorganisms8040484.
Abstract:
Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat layers of the neighbouring raised bogs and eutrophic fens that are located within two geographically remote mire sites in Vologda region using 16S rRNA gene sequencing. Regardless of location, the microbial communities in raised bogs were highly similar to each other but were clearly distinct from those in eutrophic fens. Bogs were dominated by the Acidobacteria (30%–40% of total 16S rRNA gene reads), which belong to the orders Acidobacteriales and Bryobacterales. Other bog-specific bacteria included the Phycisphaera-like group WD2101 and the families Isosphaeraceae and Gemmataceae of the Planctomycetes, orders Opitutales and Pedosphaerales of the Verrucomicrobia and a particular group of alphaproteobacteria within the Rhizobiales. In contrast, fens hosted Anaerolineae-affiliated Chloroflexi, Vicinamibacteria- and Blastocatellia-affiliated Acidobacteria, Rokubacteria, uncultivated group OM190 of the Planctomycetes and several groups of betaproteobacteria. The Patescibacteria were detected in both types of wetlands but their relative abundance was higher in fens. A number of key parameters that define the distribution of particular bacterial groups in mires were identified.
33
Ujvári, Gergely, Andrea K. Borsodi, Melinda Megyes, Márton Mucsi, Tibor Szili-Kovács, Attila Szabó, Zoltán Szalai, Gergely Jakab, and Károly Márialigeti. "Comparison of Soil Bacterial Communities from Juvenile Maize Plants of a Long-Term Monoculture and a Natural Grassland." Agronomy 10, no. 3 (March 2, 2020): 341. http://dx.doi.org/10.3390/agronomy10030341.
Abstract:
Nowadays, one of the most important challenges is to ensure sustainable agricultural management of crops such as maize (Zea mays L.). Long-term crop production, however, may influence the soil properties, the composition and activity of microbial communities. The aim of this study was to compare the catabolic activity and taxonomic diversity of bacterial communities inhabiting the soil of a non-fertilized maize monoculture and a natural grassland. Samples were taken from the horizons A and C in the first part of the vegetation period. MicroResp™ technique was used to explore the catabolic potential of microbial communities and next generation amplicon sequencing to reveal the bacterial diversity. Based on the catabolic activity results, higher differences were revealed among the soil horizons than the different land uses. The highest degree carbon source utilization was detected in the soil horizon A of the natural grassland. The taxonomic composition of bacterial communities was dominated by Proteobacteria. The relative abundance of other dominant phyla (Acidobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi and Patescibacteria) varied according to both the land use and soil depth. Amplicon sequences belonging to genera of r-strategist “copiotrophic” and K-strategist “oligotrophic” bacteria were identified from the soils of both maize monoculture and grassland.
34
Coelho, Catarina, Igor Tiago, and António Veríssimo. "Guts Bacterial Communities of Porcellio dilatatus: Symbionts Predominance, Functional Significance and Putative Biotechnological Potential." Microorganisms 10, no. 11 (November 11, 2022): 2230. http://dx.doi.org/10.3390/microorganisms10112230.
Abstract:
Terrestrial isopods are effective herbivorous scavengers with an important ecological role in organic matter cycling. Their guts are considered to be a natural enrichment environment for lignocellulosic biomass (LCB)-degrading bacteria. The main goal of this work was to assess the structural diversity of Porcellio dilatatus gut bacterial communities using NGS technologies, and to predict their functional potential using PICRUSt2 software. Pseudomonadota, Actinomycetota, Bacillota, Cyanobacteria, Mycoplasmatota, Bacteroidota, Candidatus Patescibacteria and Chloroflexota were the most abundant phyla found in P. dilatatus gut bacterial communities. At a family level, we identified the presence of eleven common bacterial families. Functionally, the P. dilatatus gut bacterial communities exhibited enrichment in KEGG pathways related to the functional module of metabolism. With the predicted functional profile of P. dilatatus metagenomes, it was possible to envision putative symbiotic relationships between P. dilatatus gut bacterial communities and their hosts. It was also possible to foresee the presence of a well-adapted bacterial community responsible for nutrient uptake for the host and for maintaining host homeostasis. Genes encoding LCB-degrading enzymes were also predicted in all samples. Therefore, the P. dilatatus digestive tract may be considered a potential source of LCB-degrading enzymes that is not to be neglected.
35
Yang, Liping, Mingyu Liu, Mengjuan Zhao, Shaoyang Zhi, Wenlei Zhang, Leya Qu, Jinrui Xiong, et al. "Dietary Bile Acid Supplementation Could Regulate the Glucose, Lipid Metabolism, and Microbiota of Common Carp (Cyprinus carpio L.) Fed with a High-Lipid Diet." Aquaculture Nutrition 2023 (May 24, 2023): 1–13. http://dx.doi.org/10.1155/2023/9953927.
Abstract:
This study sought to examine the role of bile acids in the regulation of glucose and lipid metabolism, intestinal flora, and growth in high-fat diet-fed common carp (Cyprinus carpio L.). Fish ( 6.34 ± 0.07 g ) were fed for 56 days with three different diets, the control diet (CO, 5.4% lipid), high-fat diet (HF, 11% lipid), and high-fat diet with 60 mg/kg bile acids (BAs, 11% lipid). The results showed that high-fat diets resulted in poor growth performance and increased triglyceride (TG) in serum and the liver. The addition of bile acids significantly alleviated the adverse effects of a high-fat diet. The mRNA expression results indicated that bile acids may improve lipid metabolism through the enhancement of the peroxisome proliferator-activated receptor (PPARa). The expression of gluconeogenesis-related phosphoenolpyruvate carboxykinase (PEPCK) mRNA was inhibited, while fibroblast growth factor 19 (FGF19) was significantly higher. Bile acids reshaped the intestinal microflora community, with the level of Bacteroidetes increasing. The correlation analysis indicated that Patescibacteria, Dependentiae, Myxococcota, and Planctomycetota in the gut are associated with genes involved in glucose and lipid metabolism. These results indicated that bile acids could ameliorate the negative effects of high-fat diets on common carp.
36
Wang, Xinlu, Lili Niu, Yaxuan Wang, Siyuan Zhan, Linjie Wang, Dinghui Dai, Jiaxue Cao, et al. "Combining 16S rRNA Sequencing and Metabolomics Data to Decipher the Interactions between Gut Microbiota, Host Immunity, and Metabolites in Diarrheic Young Small Ruminants." International Journal of Molecular Sciences 24, no. 14 (July 13, 2023): 11423. http://dx.doi.org/10.3390/ijms241411423.
Abstract:
Diarrhea is associated with gut microbiota, immunity, and metabolic alterations in goat kids and lambs. This study used 28 lambs (11 healthy and 17 diarrheic) and 20 goat kids (10 healthy and 10 diarrheic) to investigate the association between diarrhea occurrence and changes in gut microbiota, metabolism, and immunity in goat kids and lambs. The results revealed that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in goat kids and lambs. In addition, Enterobacteriaceae and Lachnospiraceae families were identified in both diarrheic goat kids and lambs. Furthermore, functional prediction of microbiota showed that it was involved in cell motility and cancer pathways. The identified differential metabolites were implicated in the bile secretion pathway. Lambs had significant differences in immunoglobulin G (IgG), immunoglobulin M (IgM), interleukin-1β (IL-1β), and tumor necrosis factor-alpha (TNF-α) compared to goat kids. IgG and IL-1β were positively correlated to Patescibacteria, Clostridiaceae, and unclassified_Muribaculaceae in both diarrheic goat kids and lambs. In addition, weighted gene co-expression network analysis (WGCNA) revealed that the MEgreen module was positively associated with IgG, IgM, IL-1β, TNF-α, and triglyceride (TG). In conclusion, our results characterized the gut microbiota, metabolism, and immune status of lambs and goat kids suffering from diarrhea.
37
Kpalari, Djifa Fidele, Abdoul Kader Mounkaila Hamani, Cao Hui, Jean Mianikpo Sogbedji, Junming Liu, Yang Le, Rakhwe Kama, and Yang Gao. "Soil Bacterial Community and Greenhouse Gas Emissions as Responded to the Coupled Application of Nitrogen Fertilizer and Microbial Decomposing Inoculants in Wheat (Triticum aestivum L.) Seedling Stage under Different Water Regimes." Agronomy 13, no. 12 (November 29, 2023): 2950. http://dx.doi.org/10.3390/agronomy13122950.
Abstract:
The soil microbial community is critically important in plant nutrition and health. However, this community is extremely sensitive to various environmental conditions. A pot experiment was conducted during the wheat seedling stage to better understand the influences of the coupled application of nitrogen (N) and microbial decomposing inoculants (MDI) on the soil bacteria community under different water regimes. There were two levels of water and six levels of fertilization. The results reveal that water stress increased the relative abundance of Acidobacteria and decreased that of Firmicutes and Proteobacteria. The application of 250 kg N ha−1 altered the diversity of the bacterial community but increased the relative abundance of nitrifying bacteria. Nitrous oxide (N2O) and carbon dioxide (CO2) emissions were negatively correlated with Myxococcota and Methylomirabilota while positively correlated with Patescibacteria. These two gases were also positively correlated with nitrifying bacteria, and the correlation was more significant under the full irrigation regime. These findings indicate that MDI does not substantially influence the soil bacterial community and its relationship with greenhouse gas emission at the wheat seedling stage and that the abundance of the soil bacterial community would mainly depend on the rational control of the amount of N and water applied.
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Abakumov, Evgeny, Aleksei Zverev, Eugenia Morgun, and Ivan Alekseev. "Microbiome of abandoned agricultural and mature tundra soils in southern Yamal region, Russian Arctic." Open Agriculture 5, no. 1 (July 14, 2020): 335–44. http://dx.doi.org/10.1515/opag-2020-0034.
Abstract:
AbstractSoil microbiome plays a significant role in the development of the soil profile and the implementation of key soil biochemical processes. Observed Arctic warming creates significant environmental risks, since permafrost soils contain a huge amount of organic matter, which is in potential risk to be released in the form of greenhouse gases. This work is aimed to investigate the microbiomes in soils of mature tundra and anthropogenically affected areas of the Yamal region using a high-throughput sequencing approach. The taxonomic analysis of the soil microbiomes revealed 33 bacterial and archaeal phyla, among which the dominant were Proteobacteria, Acidobacteria, Actinobacteria, Bacteroides, Chloroflexi, Cyanobacteria, Firmicutes, Gematimonadetes, Patescibacteria, Plantomycetes, Thaumarchaeota, Verrucomicrobia, and WPS-2. The analysis of alpha and beta diversities revealed that undisturbed soil is completely different from anthropogenically affected ones in terms of microorganism biodiversity. Soils of the urban zone of Salekhard were found to be different with regard to the number of operational taxonomic units and beta diversity. Herein the microbiome in the upper and lower layers of soil developed under strong technogenic influence (M19) was unequal both in quality and in quantity. At the same time, soils developed in the recreational zone of Salekhard showed less differentiation profile of microbiome (former crop field and former vegetable garden soils). Microbial communities in the mature tundra soil showed less differentiated microbiome composition.
39
Kadnikov, Vitaly V., Nikolai V. Ravin, Diyana S. Sokolova, Ekaterina M. Semenova, Salimat K. Bidzhieva, Alexey V. Beletsky, Alexey P. Ershov, et al. "Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential." Biology 12, no. 10 (October 2, 2023): 1300. http://dx.doi.org/10.3390/biology12101300.
Abstract:
The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis.
40
EGOROVA, D. O., P. Y. SANNIKOV, Y. V. KHOTYANOVSKAYA, and S. A. BUZMAKOV. "COMPOSITION OF BACTERIAL COMMUNITIES IN OIL-CONTAMINATED BOTTOM SEDIMENTS OF THE KAMENKA RIVER." Vestnik Moskovskogo universiteta. Seria 16. Biologia 78, no. 1, 2023 (April 30, 2023): 17–24. http://dx.doi.org/10.55959/msu0137-0952-16-78-1-3.
Abstract:
The Kamenka River ows through the territory of the Kokuyskoye gas and oil eld located in the Perm Territory. Despite the absence of oil-producing facilities in the immediate vicinity of the river, oil hydrocarbons were found in the waters and bottom sediments at a concentration of 2445-25800 mg/kg. The composition of microbial communities of bottom sediments of the Kamenka River, located at the source and along the river, was studied. Using the methods of high-performance sequencing and bioinformatic data processing, it was established that the main share of microbial communities is represented by bacteria of the phylum Proteobacteria (16.7-30.3%), as well as the phyla Actinobacteriota, Bacteroidota, Bdellovibrionota, Campilobacterota, Chloro exi, Cyanobacteria, Deferribacterota, Desulfobacterota, Firmicutes, Gemmatimonadota, Methylomirabilota, Myxococcota, Nitrospirota, Patescibacteria, Planctomycetota, Spirochaetota, Synergistota, Thermotofota and Verrucomicrobiota. The values of the Shannon index for the studied communities are directly correlated with the concentration of petroleum hydrocarbons in bottom sediments. The phylum Proteobacteria in communities is represented by the classes Alphaproteobacteria and Gammaproteobacteria, among which representatives of the families Rhodobacteriaceae and Comamonadaceae dominate. When identifying to the genus, it was found that in the Comamonadaceae family, the main share is made up of bacteria of the genus Hydrogenophaga. It should be noted that bacteria of the genus Pseudomonas (class Gammaproteobacteria) were found only in the microbiocenosis of bottom sediments, characterized by the highest concentration of petroleum hydrocarbons.
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Huang, Kexin, Jian Xiang, Yuying Ma, Jinping Cheng, Jie Gu, Meng Hu, Yuan Yang, Yanming Fang, Genmei Wang, and Huanchao Zhang. "Response of Soil Microbial Communities to Elevation Gradient in Central Subtropical Pinus taiwanensis and Pinus massoniana Forests." Forests 14, no. 4 (April 9, 2023): 772. http://dx.doi.org/10.3390/f14040772.
Abstract:
In forest ecosystems, elevation gradient is one of the most influential factors on soil characteristics, vegetation types, and soil microorganisms. However, it remains unclear how the elevation gradient and the soil environment under its influence affect soil microbial communities under two distinct vegetation types. In this study, high-throughput sequencing technology from Illumina was utilized to examine the response of soil microbial communities to elevation and their driving factors in forests of Pinus taiwanensis and Pinus massoniana in various Jiangxi Province locales. The results demonstrated that the elevation gradients of the two pines had significant effects on soil organic carbon (SOC) and total nitrogen (TN), both in unimodal mode as well as on the alpha diversity of soil microbes. The community structure of soil bacteria is more sensitive to elevation than that of soil fungus. At different elevations in the two pine forests, Acidobacteria, Proteobacteria, Chloroflexi, Verrucomicrobia, Bacteroidetes, Patescibacteria, and Thaumarchaeota are the dominant bacterial phyla, and Ascomycota, Basidiomycota, and Mucoromycota are the dominant fungal phyla. This investigation revealed that SOC and TN were the two most influential factors on the alteration of the soil microbial community in two pine forests. In summary, there were substantial changes in soil microbial diversity and community composition across the two different pine forests, with elevation and soil characteristics (SOC and TN) serving as the primary drivers.
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Veloso, Marcelo, Angie Waldisperg, Patricio Arros, Camilo Berríos-Pastén, Joaquín Acosta, Hazajem Colque, Macarena A. Varas, Miguel L. Allende, Luis H. Orellana, and Andrés E. Marcoleta. "Diversity, Taxonomic Novelty, and Encoded Functions of Salar de Ascotán Microbiota, as Revealed by Metagenome-Assembled Genomes." Microorganisms 11, no. 11 (November 20, 2023): 2819. http://dx.doi.org/10.3390/microorganisms11112819.
Abstract:
Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota’s diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán’s water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet.
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Liu, Chunxiao, Jingyue Chen, Zijiao Wang, Yueyao Li, Yuanyuan Zhang, and Guangyu Li. "Nodakenin Ameliorates Ovariectomy-Induced Bone Loss by Regulating Gut Microbiota." Molecules 29, no. 6 (March 11, 2024): 1240. http://dx.doi.org/10.3390/molecules29061240.
Abstract:
Disordered gut microbiota (GM) structure and function may contribute to osteoporosis (OP). Nodakenin has been shown to ameliorate osteoporosis; however, its anti-osteoporotic mechanism is unknown. This study aimed to further reveal the mechanism of the anti-osteoporotic action of nodakenin from the perspective of the microbiome and metabolome. An osteoporosis model was induced in mice through ovariectomy (OVX), with bone mass and microstructure assessed using μCT. Subsequently, ELISA and histologic examination were used to detect biochemical indicators of bone conversion and intestinal morphology. Using metabolomics and 16S rRNA sequencing, it was possible to determine the composition and abundance of the gut microbiota in feces. The results revealed that nodakenin treatment improved the bone microstructure and serum levels of bone turnover markers, and increased the intestinal mucosal integrity. 16S rRNA sequencing analysis revealed that nodakenin treatment decreased the relative abundance of Firmicutes and Patescibacteria, as well as the F/B ratio, and elevated the relative abundance of Bacteroidetes in OVX mice. In addition, nodakenin enhanced the relative abundance of Muribaculaceae and Allobaculum, among others, at the genus level. Moreover, metabolomics analysis revealed that nodakenin treatment significantly altered the changes in 113 metabolites, including calcitriol. A correlation analysis revealed substantial associations between various gut microbiota taxa and both the osteoporosis phenotype and metabolites. In summary, nodakenin treatment alleviated OVX-induced osteoporosis by modulating the gut microbiota and intestinal barrier.
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Zhang, Jing-Yao, Hui-Chen Lo, Feili Lo Yang, Yi-Fang Liu, Wen-Mein Wu, and Chi-Chun Chou. "Plant-Based, Antioxidant-Rich Snacks Elevate Plasma Antioxidant Ability and Alter Gut Bacterial Composition in Older Adults." Nutrients 13, no. 11 (October 29, 2021): 3872. http://dx.doi.org/10.3390/nu13113872.
Abstract:
Plant-rich diets alleviate oxidative stress and gut dysbiosis and are negatively linked to age-associated chronic disorders. This study examined the effects of consuming plant-based, antioxidant-rich smoothies and sesame seed snacks (PBASS) on antioxidant ability and gut microbial composition in older adults. Healthy and sub-healthy older adults (n = 42, 79.7 ± 8.6 years old) in two senior living facilities were given PBASS for 4 months. Blood and fecal samples were collected from these individuals at the baseline and after 2 and 4 months of PBASS consumption. After 2 months, serum levels of albumin and high-density lipoprotein-cholesterol and the ratio of reduced to oxidized glutathione (GSH/GSSG) had increased significantly and erythrocytic glutathione, GSH/GSSG and superoxide dismutase activity had decreased significantly compared with baseline levels (p < 0.05). After 4 months, red blood cells, hematocrit, serum blood urea nitrogen and erythrocyte glutathione peroxidase activity had decreased significantly, whereas plasma and erythrocyte protein-bound sulfhydryl groups had increased significantly. Furthermore, plasma glutathione and total antioxidant capacity were significantly greater after 2 months and increased further after 4 months of PBASS consumption. The results of next generation sequencing showed that PBASS consumption prompted significant decreases in observed bacterial species, their richness, and the abundance of Actinobacteria and Patescibacteria and increases in Bacteroidetes in feces. Our results suggest that texture-modified, plant-based snacks are useful nutrition support to benefit healthy ageing via the elevation of antioxidant ability and alteration of gut microbiota.
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Qiu, Qinghua, Chaoyu Gao, Muhammad Aziz ur Rahman, Binghai Cao, and Huawei Su. "Digestive Ability, Physiological Characteristics, and Rumen Bacterial Community of Holstein Finishing Steers in Response to Three Nutrient Density Diets as Fattening Phases Advanced." Microorganisms 8, no. 3 (February 27, 2020): 335. http://dx.doi.org/10.3390/microorganisms8030335.
Abstract:
The aim of this study is to track the dynamic alterations in nutrient intake and digestion, rumen fermentation and plasma metabolic characteristics, and rumen bacterial community of Holstein finishing steers in response to three nutrient density diets as fattening phases advanced. A total of eighteen Holstein steers were randomly allocated into three nutrient density groups and steers in each group were fed under a three-phase fattening strategy, with nutrient density increased in each group when fattening phase advanced. Results showed that both fattening phase and dietary nutrient density significantly influenced the nutrient digestion, most of the rumen fermentation parameters, and part of bacteria at phylum and genus levels. Individually, dietary nutrient density affected the concentrations of plasma alanine aminotransferase and urea N, bacterial richness and evenness. All determined nutrient intake and plasma biochemical parameters, except for alanine aminotransferase and triglyceride, differed among fattening phases. Spearman correlation analysis revealed strong correlations between fiber intake and bacterial richness and evenness, rumen fermentation characteristics and certain bacteria. Moreover, Patescibacteria abundance was positively correlated with ambient temperature and plasma total protein. These results indicate that rumen fermentation and nutrient digestion were influenced by both dietary nutrient density and fattening phase, and these influences were regulated by certain rumen bacterial community and ruminal bacteria may be affected simultaneously by ambient temperature. This study may provide insights into diet optimization and potentially adaptive mechanism of rumen bacterial community in response to fattening phases and gradually climatic change.
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Guan, Yu, Lei Bao, Lei Zhou, Chang Dai, Zhisai Li, Shuai Zhang, Yugang Shang, Wenhui Niu, Yizhuo Zhang, and Hongfang Wang. "Comparative analysis of the fecal microbiota of healthy and injured common kestrel (Falco tinnunculus) from the Beijing Raptor Rescue Center." PeerJ 11 (August 22, 2023): e15789. http://dx.doi.org/10.7717/peerj.15789.
Abstract:
The gut microbiota is a complex ecosystem that interacts with many other factors to affect the health and disease states of the host. The common kestrel (Falco tinnunculus) is protected at the national level in China. However, the available sequencing data of the gut microbiota from the feces of wild common kestrels, especially for being rescued individuals by professional organization, remains limited. In the present study, we characterized the fecal bacterial communities of healthy and injured common kestrels, and compared the structure of their fecal microbiota by analyzing the V3–V4 region of the 16S rRNA gene using high-throughput sequencing technology with the Illumina MiSeq platform. We found that Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla in common kestrels. Further, the beta diversity analysis showed that changes in gut microbes were associated with injuries to the common kestrel. The Bacteroides/Firmicutes ratio was significantly lower in the injured group. At the genus level, Glutamicibacter showed significant difference in the two groups. The aim of our current study was to characterize the basic bacterial composition and community structure in the feces of healthy common kestrels, and then compare the differences in the fecal microbiota between healthy and injured individuals. Patescibacteria, Spirochaetes, and Glutamicibacter may be studied as potential biomarkers for certain diseases in raptors. The results could provide the basic data for additional research on the fecal microbiota of common kestrels and contribute to the rescue of wild raptors in the future.
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Farkas, Rózsa, Tamás Mireisz, Marwene Toumi, Gorkhmaz Abbaszade, Nóra Sztráda, and Erika Tóth. "The Impact of Anti-Inflammatory Drugs on the Prokaryotic Community Composition and Selected Bacterial Strains Based on Microcosm Experiments." Microorganisms 11, no. 6 (May 30, 2023): 1447. http://dx.doi.org/10.3390/microorganisms11061447.
Abstract:
Non-steroidal anti-inflammatory drugs (NSAIDs) are increasingly recognized as potential environmental contaminants that may induce toxicity in aquatic ecosystems. This 3-week microcosm experiment explores the acute impacts of NSAIDs, including diclofenac (DCF), ibuprofen (IBU), and acetylsalicylic acid (ASA), on bacterial communities using a wide range of these substances (200–6000 ppm). The results showed that the NSAID-treated microcosms had higher cell count values than control samples, though the diversity of microbial communities decreased. The isolated heterotrophic bacteria mostly belonged to Proteobacteria, particularly Klebsiella. Next-generation sequencing (NGS) revealed that NSAIDs altered the structure of the bacterial community composition, with the proportion of Proteobacteria aligning with the selective cultivation results. Bacteria had higher resistance to IBU/ASA than to DCF. In DCF-treated microcosms, there has been a high reduction of the number of Bacteroidetes, whereas in the microcosms treated with IBU/ASA, they have remained abundant. The numbers of Patescibacteria and Actinobacteria have decreased across all NSAID-treated microcosms. Verrucomicrobia and Planctomycetes have tolerated all NSAIDs, even DCF. Cyanobacteria have also demonstrated tolerance to IBU/ASA treatment in the microcosms. The archaeal community structure was also impacted by the NSAID treatments, with Thaumarchaeota abundant in all microcosms, especially DCF-treated microcosms, while Nanoarchaeota is more typical of IBU/ASA-treated microcosms with lower NSAID concentrations. These results indicate that the presence of NSAIDs in aquatic environments could lead to changes in the composition of microbial communities.
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Hu, Huifeng, Jannie Munk Kristensen, Craig William Herbold, Petra Pjevac, Katharina Kitzinger, Bela Hausmann, Morten Kam Dahl Dueholm, Per Halkjaer Nielsen, and Michael Wagner. "Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants." Microbiome 12, no. 1 (March 16, 2024). http://dx.doi.org/10.1186/s40168-024-01769-1.
Abstract:
Abstract Background Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning. Results Here, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9 to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosphoribacter. Conclusions Our study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs.
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Vigneron, Adrien, Perrine Cruaud, Rémy Guyoneaud, and Marisol Goñi-Urriza. "Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations." Frontiers in Microbiology 13 (January 9, 2023). http://dx.doi.org/10.3389/fmicb.2022.1073483.
Abstract:
Patescibacteria form a highly diverse and widespread superphylum of uncultured microorganisms representing a third of the global microbial diversity. Most of our knowledge on Patescibacteria putative physiology relies on metagenomic mining and metagenome-assembled genomes, but the in situ activities and the ecophysiology of these microorganisms have been rarely explored, leaving the role of Patescibacteria in ecosystems elusive. Using a genome-centric metatranscriptomic approach, we analyzed the diel and seasonal gene transcription profiles of 18 Patescibacteria populations in brackish microbial mats to test whether our understanding of Patescibacteria metabolism allows the extrapolation of their in situ activities. Although our results revealed a circadian cycle in Patescibacteria activities, a strong streamlined genetic expression characterized the Patescibacteria populations. This result has a major consequence for the extrapolation of their physiology and environmental function since most transcribed genes were uncharacterized, indicating that the ecophysiology of Patescibacteria cannot be yet reliably predicted from genomic data.
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Chaudhari, Narendrakumar M., Will A. Overholt, Perla Abigail Figueroa-Gonzalez, Martin Taubert, Till L. V. Bornemann, Alexander J. Probst, Martin Hölzer, Manja Marz, and Kirsten Küsel. "The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers." Environmental Microbiome 16, no. 1 (December 2021). http://dx.doi.org/10.1186/s40793-021-00395-w.
Abstract:
Abstract Background The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges. Results Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1 µm filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 µm fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 µm fractions. On average, Patescibacteria enriched in the smaller 0.1 µm filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell–cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2 µm fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota). Conclusion Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to attach multiple hosts just long enough to loot or exchange supplies.