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Copyright of Journal of Beijing University of Technology is the property of Journal of Beijing University of Technology, Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), is a skin disease associated with worldwide amphibian declines. Symbiotic microbes living on amphibian skin interact with Bd and may alter infection outcomes. We completed whole genome sequencing of 40 bacterial isolates cultured from the skin of four amphibian species in the Eastern US. Each isolate was tested in vitro for the ability to inhibit Bd growth. The aim of this study was to identify genomic differences among the isolates and generate hypotheses about the genomic underpinnings of Bd growth inhibition. We identified sixty-five gene families that were present in all 40 isolates. Screening for common biosynthetic gene clusters revealed that this set of isolates contained a wide variety of clusters; the two most abundant clusters with potential antifungal activity were siderophores (N=17 isolates) and Type III polyketide synthases (N=22 isolates). We then examined various subsets of the 22 isolates in the phylum Proteobacteria for genes encoding specific compounds that may inhibit fungal growth, including chitinase and violacein. We identified differences in Agrobacterium and Sphingomonas isolates in the chitinase genes that showed some association with anti-Bd activity, as well as variation in the violacein genes in the Janthinobacterium isolates. Using a comparative genomics approach, we generated several testable hypotheses about differences among bacterial isolates from amphibian skin communities that could contribute to variation in the ability to inhibit Bd growth. Further work is necessary to explore and uncover the various mechanisms utilized by amphibian skin bacterial isolates to inhibit Bd. [ABSTRACT FROM AUTHOR]

This study investigated the effects of Bacillus subtilis BC02 supplementation on broiler performance, antioxidant capacity, and cecal microbes. A total of 288 one-day-old Arbor Acres broilers were randomly divided into three groups. The control group were fed a basal diet, and experimental groups were fed a basal diet supplemented with 250 and 500 mg/kg Bacillus subtilis BC02 (BS250 and BS500), respectively. The results showed that Bacillus subtilis BC02 supplementation increased the average daily feed intake but decreased the feed to gain ratio in broilers from 0 to 14, 0 to 28, and 0 to 42 days. Meanwhile, BS500 significantly decreased triglyceride and serum urea nitrogen levels compared with the control and BS250 groups (p < 0.05). Moreover, diet supplemented with 500 mg/kg Bacillus subtilis BC02 improved the antioxidant capacity by increasing the serum and jejunum levels of superoxide dismutase and glutathione, decreasing that of malondialdehyde and increasing the jejunum mRNA expression of SOD2, CAT, GPX1, and Nrf2 (p < 0.05). Dietary Bacillus subtilis BC02 supplementation increased the villus height, velvet concealed ratio, and the mRNA expressions of IL-2, IL-4, IL-10, and IL-12 (p < 0.05). In addition, the Bacteroidota, Proteobacteria, Helicobacter, and Prevotellaceae UCG-001 were significantly increased (p < 0.05) in the BS500 group. In conclusion, dietary Bacillus subtilis BC02 supplementation can improve the growth performance, antioxidant capacity, and intestinal microflora abundances in broilers. [ABSTRACT FROM AUTHOR]

Simple Summary: Mastitis is a prevalent issue worldwide among lactating animals. It continues to be a serious problem since it has an economic impact on farmers due to direct and indirect losses. The multifactorial nature of this disease, coupled with the limitations of classical culture-based methods to identify uncultivable bacteria under normal laboratory conditions, exacerbates the situation. In the current study, milk samples from the well-known buffalo breed (Nili Ravi) were tested to explore bacterial communities associated with different udder health statuses using the 16S rRNA gene-based metagenomics technique. The bacterial communities in buffaloes with different udder health statuses, such as healthy, clinical mastitis, and subclinical mastitis, exhibited varied abundance at different taxonomic levels. Additionally, the study concluded that bacterial diversity in milk samples decreases in animals suffering from clinical mastitis compared to those with a healthy or subclinical mastitis status. These findings will contribute to our understanding of bacterial diversity's role in mastitis development. The Nili Ravi, a buffalo breed from Pakistan, significantly contributes to the dairy industry. Mastitis is one of the major challenges affecting milk production in this breed. The objective of the current study was to identify the bacterial communities and diversity in healthy and mastitic milk of this breed. Milk samples (n = 14) were collected from Nili Ravi buffaloes with different udder health statuses, i.e., healthy (5), subclinical mastitis (4), and clinical mastitis (5). The DNAs were extracted, subjected to partial amplification of 16S rDNA (V3 and V4 regions), and sequenced using the Illumina platform. The results revealed variations in the bacterial communities in the milk of animals with different udder health statuses. Proteobacteria was the predominant phylum in the healthy group, while clinical and subclinical mastitis milk had a higher abundance of Firmicutes. Dominant bacterial genera in the healthy group were Streptococcus (11.60%), Herbaspirillum (7.65%), and Staphylococcus (4.70%), whereas the clinical mastitis group was dominated by Streptococcus (33.96%), Staphylococcus (7.87%), and Corynebacterium (2.68%), and the subclinical mastitis group was dominated by Bacillus (15.70%), Corynebacterium (6.70%), and Staphylococcus (6.58%). Assignment of operational taxonomic units at the species level resulted in most species being assigned to uncultured or unknown bacteria or remaining unassigned. Alpha diversity indices indicated lower microbial diversity in the clinical mastitis group, while beta diversity indices showed a scattered pattern of sample clustering in PCA plots among different groups. It is concluded that bacterial diversity in the milk of Nili Ravi buffaloes suffering from clinical mastitis is lower compared to healthy and subclinical mastitis cases. It is concluded that the variations in the microbiota of healthy and mastitic milk may be further investigated and exploited as signature microbes associated with the udder health status of Nili Ravi buffalo. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Allergic rhinitis and asthma are two of the most common chronic respiratory diseases in developed countries and have become a major public health concern. Substantial evidence has suggested a strong link between respiratory allergy and upper airway dysbacteriosis, but the role of the oral bacteriota is still poorly understood. Here we used 16S rRNA massive parallel sequencing to characterize the oral bacteriome of 344 individuals with allergic rhinitis (AR), allergic rhinitis with asthma (ARAS), asthma (AS) and healthy controls (CT). Four of the most abundant (>2%) phyla (Actinobacteriota, Firmicutes, Fusobacteriota, and Proteobacteria) and 10 of the dominant genera (Actinomyces, Fusobacterium, Gemella, Haemophilus, Leptotrichia, Neisseria, Porphyromonas, Prevotella, Streptococcus, and Veillonella) in the oral cavity differed significantly (p = 0.03) between AR, ARAS or AS and CT groups. The oral bacteriome of ARAS patients showed the highest intra-group diversity, while CT showed the lowest. All alphadiversity indices of microbial richness and evenness varied significantly (p = 0.022) in ARAS vs. CT and ARAS vs. AR, but they were not significantly different in AR vs. CT. All beta-diversity indices of microbial structure (Unifrac, Bray-Curtis, and Jaccard distances) differed significantly (p = 0.049) between each respiratory disease group and controls. Bacteriomes of AR and ARAS patients showed 15 and 28 upregulated metabolic pathways (PICRUSt2) mainly related to degradation and biosynthesis (p < 0.05). A network analysis (SPIEC-EASI) of AR and ARAS bacteriomes depicted simpler webs of interactions among their members than those observed in the bacteriome of CT, suggesting chronic respiratory allergic diseases may disrupt bacterial connectivity in the oral cavity. This study, therefore, expands our understanding of the relationships between the oral bacteriome and allergy-related conditions. It demonstrates for the first time that the mouth harbors distinct bacteriotas during health and allergic rhinitis (with and without comorbid asthma) and identifies potential taxonomic and functional microbial biomarkers of chronic airway disease. [ABSTRACT FROM AUTHOR]

Background: Tobacco bacterial wilt (TBW) and black shank (TBS) are responsible for substantial economic losses worldwide; however, microbial interactions and metabolisms in response to TBW and TBS pathogens in the tobacco rhizosphere remain unclear. Methods: We explored and compared the response of rhizosphere microbial communities to these two plant diseases with the incidences in moderate and heavy degrees by sequencing of 16S rRNA gene amplicons and bioinformatics analysis. Results and discussions: We found that the structure of rhizosphere soil bacterial communities was significantly (p < 0.05) changed from the incidences of TBW and TBS, which also led to decreased Shannon diversity and Pielou evenness. Compared with the healthy group (CK), the OTUs with significantly (p < 0.05) decreased relative abundances were mostly affiliated with Actinobacteria (e.g., Streptomyces and Arthrobacter) in the diseased groups, and the OTUs with significantly (p < 0.05) increased relative abundances were mainly identified as Proteobacteria and Acidobacteria. Also, molecular ecological network analysis showed that the nodes (<467) and links (<641) were decreased in the diseased groups compared with the control group (572; 1056), suggesting that both TBW and TBS weakened bacterial interactions. In addition, the predictive functional analysis indicated that the relative abundance of genes related to the biosynthesis of antibiotics (e.g., ansamycins and streptomycin) was significantly (p < 0.05) decreased due to incidences of TBW and TBS, and antimicrobial tests showed that some Actinobacteria strains (e.g., Streptomyces) and their secreted antibiotics (e.g., streptomycin) could effectively inhibit the growth of these two pathogens. [ABSTRACT FROM AUTHOR]

To investigate the feasibility of livestock wastewater purification by the floating plant Pistia stratiotes L., an experimental study was conducted using P. stratiotes L. treatments of dairy wastewater to clarify the growth status and physiological responses of P. stratiotes L. in different types of wastewater and investigate the purifying effects on nitrogen, phosphorus, and organic matter. The changes in microbial communities were also analyzed using high-throughput sequencing to reveal the relationship between microbial communities and the removal of conventional pollutants. The results showed that the tolerance ranges were 0-2 000 mg·L-1 and 0-750 mg·L-1 for raw and anaerobic and oxidized pond wastewater, respectively[measured as chemical oxygen demand(CODCr)]. When P. stratiotes L. was subjected to high concentrations of wastewater, the chlorophyll content was markedly reduced, and the activities of three enzymes(catalase, peroxidase and superoxide dismutase) were significantly increased. Within the tolerance range, P. stratiotes L. showed good purification effects on the three wastewater types from dairy farms. Pistia stratiotes L. had a rapid purification speed in the first 10 days, which slowly inecreased within 10-20 days. After treatment with P. stratiotes L., the removal rates of total nitrogen, ammonia nitrogen, total phosphorus, and CODCr in raw wastewater were 84.7%-92.7%, 90.6%-96.7%, 30.0%-93.1%, and 67.3%-77.2%, respectively; however, the purification effect of P. stratiotes L. in anaerobic and oxidation ponds decreased slightly. Regarding the microbial communities, Proteobacteria, Firmicutes, and Bacteroidetes, were the main species in different dairy wastewaters. The microbial community structures in the P. stratiotes L. treatment group and non-plant control group were significantly different; in particular, the relative abundance of Cyanobacteria was distinct. The correlation between the microbial community and several indexes of wastewater was significant(P<0.05), indicating that microorganisms played an important role in the removal of pollutants. This study verified the feasibility of P. stratiotes L. in treating wastewater with high concentrations of pollutants and provides a theoretical basis and technical support for dairy farm wastewater treatment. [ABSTRACT FROM AUTHOR]

One of the main sources of bacteria that cause spoilage is microorganisms harbored on surfaces and objects in the production environment of food enterprises. This paper presents the results of the taxonomic composition of the microbiota of objects in the production environment of pork processing enterprises, with the identification of key groups of microorganisms. The microbiota in the facilities of the production environment of the meat processing enterprise was mainly represented by 12 phyla. Among these, Proteobacteria, Bacteroidota, Actinobacteria, and Firmicutes were predominant. The results of 16S rRNA amplicon sequencing were analyzed for the presence of pathogenic bacteria in the studied samples. Potentially pathogenic Shigella bacteria were found in two samples. In addition to pathogenic bacteria, bacteria detected in the samples cause spoilage of meat and meat products; these were the genera Brochothrix and Pseudomonas. Pathogenic microorganisms were studied by the molecular method with accumulation. Representatives of pathogenic microorganisms were present on the objects in the production environment. Listeria monocytogenes was found in three samples, Salmonella spp. in two samples, and Campylobacter spp. in one of the samples studied. [ABSTRACT FROM AUTHOR]

To study the effects of the probiotics on the gut microbial community of Penaeus indicus larvae, a combination of three probiotics—Bacillus subtilis, B. lichiniformis, and B. pumilus (5 × 1010 cfu/gram)—were added to the rearing environment of shrimp larvae (5,000/500 L). Altered microbial communities due to the application of probiotics were studied using 16S rRNA-based Illumina sequencing. The results suggest that the probiotics-treated group showed higher richness; the control group was even as measured by alpha diversity indices. The abundance of Proteobacteria was higher in the probiotic-treated group (94.85%) compared to the control (58.29%). At the genus level, the probiotics group was dominated by Vibrio (44.17%), Rhodobacteraceae_unclassified (25.22%), Catenococcus (12.89%), Pseudoalteromonas (4.76%), and Kordia (1.53%); Tenacibaculum (24.29%), Catenococcus (19.38%), Vibrio (7%), Gammaproteobacteria_unclassified (6.6%), Fluviicola (5.91%), and Chlamydiales_unclassified (4.61%) dominated in the control group. Results indicate that probiotic application influenced the taxonomic profile of gut microbes. This information helps us to understand the effect of probiotic application especially in penaeid shrimp hatcheries. [ABSTRACT FROM AUTHOR]

Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae) is an invasive alien pest native to the Americas, and it was introduced in the state of Karnataka, India in the year 2018. They cause severe economic damage to the maize crop, which significantly decreases the quality and quantity of the crop's yield. The microbiota of fall armyworm could play important roles in their growth, development and environmental adaptation to their host plants or animals and not much is known about the microbiota of FAW in India. Even though bacterial communities in S. frugiperda are inadequately studied, therefore, a study was undertaken on the microbial communities associated with the gut of S. frugiperda collected randomly from twelve different locations in the eastern part of India under laboratory conditions. The results revealed that the two bacterial phyla, namely, proteobacteria and firmicutes, were predominantly present in the larval gut of S. frugiperda. However, analyses at the genus level revealed that despite the high genus-level diversity between samples, there were 9 different genera observed. Interestingly, we found two bacterial genera, i.e., Kluyvera and Yokenella, which may be new findings from the eastern part of India and were not reported earlier from any other countries. On the other hand, analyses at the species level revealed that a total of thirty-three (33) species were found from the 12 samples of S. frugiperda collected from different locations. Among the 33 species, Enterococcus group genera were most abundant across the FAW gut samples collected, followed by Klebsiella sp. and Enterobacter sp. and a small proportion of Raoultella, Citrobacter, Leclercia and Pantoea. [ABSTRACT FROM AUTHOR]

Protohermes xanthodes (Megaloptera, Corydalidae, Protohermes), widespread species in China, is an important insects treated as food and medicine for aquaculture. In this study, the gut microbiota was investigated by 16S rRNA microbial profiling. A total of 600 Amplicon Sequence Variants (ASV) were identified, Proteobacteria and Firmicutes were the main dominant phyla, and 27 genera ran through the entire digestive tract, mainly Hafnia-Obesumbacterium (Proteobacteria), Lactobacillus and Lactococcus (Firmicutes). The PICRUSt2 functional prediction of gut microbiota showed that the foregut abundant pathways related to metabolism, environmental information processing, and genetic information processing. while the midgut had the most abundant metabolic and environmental information processing pathways, including the prominent phosphotransferase system (PTS), propionate metabolism, and β-lactam resistance. The hindgut had the weakest metabolic function, but its genetic information processing was more abundant than the foregut and midgut. Additionally, 26 strains of bacteria were isolated from the midgut microorganisms, with Firmicutes being the dominant bacteria, and some of the purified bacteria had potential probiotic and anti-pathogen functions. These findings suggest that there are differences in the microorganisms of the different gut floras of the larvae, and each flora has specific metabolic functions. This research could be used to further understand the function of gut microorganisms, explore the co-evolution of P. xanthodes and gut microorganisms, and promote healthy breeding based on gut microorganisms. [ABSTRACT FROM AUTHOR]

Dolphins are marine mammals with unique anatomical structures in their airways. These particular respiratory structures make dolphins very sensitive to microorganisms in the air, and the habitats of dolphins in captivity and in the wild are quite different. This causes captive dolphins to suffer from illnesses, especially respiratory diseases. Previous studies have shown that the respiratory flora plays an essential role in the health of humans and animals. Therefore, by comparative analysis of the respiratory flora of wild dolphins and dolphins in captivity, we want to find the flora related to dolphins' respiratory diseases, and try to improve dolphin health through flora homeostasis. For this purpose, we performed 16S rRNA gene sequencing and analyses. We found that Proteobacteria, Firmicutes, Actinobacteria, Campilobacterota, Paracoccus , and other flora differed between wild and healthy and sub-healthy captive dolphins. Some of them are the dominant flora for promoting health, and the others may be essential pathogenic bacteria in the sub-healthy state of dolphins in captivity. [ABSTRACT FROM AUTHOR]

This trial investigated the effects of Macleaya cordata extract (MCE) on the diversity and composition of the intestinal microbiota of European eels (Anguilla anguilla) cultured in cement tanks. After routine grading eels, six cement tanks with similar body size and fish weight (about 167 g/fish and 3620 kg/tank) were randomly divided into the control and MCE groups. The control group was fed a commercial diet, and the MCE group was fed the same commercial diet supplemented with 100 mg/kg MCE. There were three tanks in each group. This trial lasted for six weeks. Compared with the control group, the European eels in the MCE groups had a higher richness and diversity of intestinal microbiota. At the phylum level, European eels in the MCE group had higher relative abundances of Firmicutes and Proteobacteria and lower relative abundance of Spirochaetae and Fusobacteria compared to those of the control group. At the genus level, the European eels in the control group had higher relative abundances of Streptococcus and Legionella. In comparison, the relative abundances of Bacillus, Anaerobacillus, and Sphingomonas were higher in the intestine of the European eels of the MCE group. In conclusion, the dietary 100 mg/kg MCE supplementation might beneficially change the intestinal microbiota of European eels by increasing the relative abundance of certain probiotics and inhibiting some pathogenic bacteria. [ABSTRACT FROM AUTHOR]

Metabolic degeneracy describes the phenomenon that cells can use one substrate through different metabolic routes, while metabolic plasticity, refers to the ability of an organism to dynamically rewire its metabolism in response to changing physiological needs. A prime example for both phenomena is the dynamic switch between two alternative and seemingly degenerate acetyl-CoA assimilation routes in the alphaproteobacterium Paracoccus denitrificans Pd1222: the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). The EMCP and the GC each tightly control the balance between catabolism and anabolism by shifting flux away from the oxidation of acetyl- CoA in the tricarboxylic acid (TCA) cycle toward biomass formation. However, the simultaneous presence of both the EMCP and GC in P. denitrificans Pd1222 raises the question of how this apparent functional degeneracy is globally coordinated during growth. Here, we show that RamB, a transcription factor of the ScfR family, controls expression of the GC in P. denitrificans Pd1222. Combining genetic, molecular biological and biochemical approaches, we identify the binding motif of RamB and demonstrate that CoA-thioester intermediates of the EMCP directly bind to the protein. Overall, our study shows that the EMCP and the GC are metabolically and genetically linked with each other, demonstrating a thus far undescribed bacterial strategy to achieve metabolic plasticity, in which one seemingly degenerate metabolic pathway directly drives expression of the other. [ABSTRACT FROM AUTHOR]

Environmental pollution is a serious issue all around the world, especially when it is caused by metal(oid)s and pathogenic microorganisms. This study reports here for the first time on the contamination of soil and water with metal(oid)s and pathogenic bacteria directly resulting from the Soran Landfill Site. Soran landfill is a level 2 solid waste disposal site that lacks leachate collection infrastructure. The site is potentially an environmental and public hazard caused by metal(oid)s content and significantly dangerous pathogenic microorganisms through leachate release into the soil and nearby river. This study reports on the levels of the metal(oid)s content of As, Cd, Co, Cr, Cu, Mn, Mo, Pb, Zn, and Ni obtained by inductively coupled plasma mass spectrometer in soil, leachate stream mud, and leachate samples. Five pollution indices are used to assess potential environmental risks. According to the indices, Cd and Pb contamination is significant, whereas As, Cu, Mn, Mo, and Zn pollution is moderate. A total of 32 isolates of bacteria were defined from soil, leachate stream mud, and liquid leachate samples: 18, 9, and 5, respectively. Moreover, 16 s rRNA analysis suggested that the isolates belong to three enteric bacterial phyla of Proteobacteria, Actinobacteria, and Firmicutes. The closest GenBank matches of 16S rDNA sequences indicated the presence of the genera: Pseudomonas, Bacillus, Lysinibacillus, Exiguobacterium, Trichococcus, Providencia, Enterococcus, Macrococcus, Serratia, Salinicoccus, Proteus, Rhodococcus, Brevibacterium, Shigella, Micrococcus, Morganella, Corynebacterium, Escherichia, and Acinetobacter. The identity percentage was mostly between 95%–100%. The results of this study show the levels of microbiological and geochemical contamination of soils, surface and potentially ground water with harmful microorganisms and toxic metal(oid)s originating specifically from Soran landfill leachate which subsequently incorporated into the surrounding environment, creating thus a considerable health and environmental risk. [ABSTRACT FROM AUTHOR]

Naswar is a smokeless tobacco product, commonly consumed in Pashtun population of Pakistan and Afghanistan. Despite being an established risk factor for oral cancer, not much is known about microbiological constituents of Naswar. Objectives: The objective of the study was to explore bacterial diversity in Naswar using shotgun metagenomic sequencing. Methodology: DNA was extracted from twelve (n = 12) famous brands of Naswar samples using an enzymatic and mechanical lysis method followed by next generation sequencing on Illumina Miseq platform. Results: Naswar samples exhibits differential abundance profile at all taxonomic levels with Khamar brand having the highest species richness and diversity indices. Of the total 22 phyla identified, phylum Proteobacteria was the most abundant (88.4%) followed by Bacteroidetes (4.71%) and Firmicutes (3.73%). At genus level, 234 genera (range: 32 - 132) were identified. Metagenomic sequencing also revealed presence of 455 (range: 44 - 210) different bacterial species in Naswar samples. The most common species were Pesudomonas aurgenosa, Yersinia enterocolitica, Salmonella enterica, Xanthomonas campestris, and E. coli. Some of the species are of concern due their ability to cause infections in humans. Conclusions: Naswar products harbor diverse bacterial microbiota with differential abundance at phylum, genus and species level. These findings may have several implications in terms of further research to explore microbiological associated health risks and provide scientific evidence to inform potential regulations regarding manufacturing and testing of Naswar in Pakistan. [ABSTRACT FROM AUTHOR]

Plant growth-promoting (PGPR) bacteria are beneficial soil bacteria that enhance plant growth against biotic and abiotic stress. Numerous studies have been carried out over the past three decades on the isolation and characterization of rhizospheric bacteria. However, no studies have been conducted on the bacteria present in the rhizosphere of the wild legume plant Chamacytisus ruthenicus when growing in chalky soil. The purpose of this study was to evaluate the abundance of culturable bacteria, assess the morphology of the bacterial cells, profile the chalky soil bacterial community, and characterize its ability to stimulate plant growth. Three soil samples were collected in January at a temperature of 2–4 °C. The first sample was taken from the topsoil, the second sample from the soil 15 cm beneath the surface, and the third sample from the rhizosphere. The results of the study revealed that the abundances of bacteria in the first, second, and third soil samples were 4.25 × 108 cfu/g, 3.58 × 108 cfu/g, and 10.1 × 107 cfu/g, respectively. Furthermore, a total of 23 rhizospheric bacteria were isolated based on differences in their morphological characteristics. The 16S rRNA soil profiling result showed that bacteria belonging to Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria, and Bacteroidetes were the most dominant groups in the community. Six bacterial isolates (Z10, Z11, Z12, Z15, Z26, and Z44) were chosen to examine the inhibition effects on phytopathogenic microbes and their ability to promote plant growth. The bacterial isolates Z11 and Z15 showed good inhibition against all tested phytopathogenic fungi, while bacterial isolates Z10, Z12, Z15, Z26, and Z44 showed stimulatory effects on the length and fresh weight of the shoots and roots of wheat, maize, and oat seeds. In conclusion, the present study is the first report of chalky soil-associated bacteria found in the rhizosphere of the wild legume plant in the Belgorod region of Russia. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Henan Agricultural Sciences is the property of Editorial Board of Journal of Henan Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Biosolids are applied to agricultural land as a soil conditioner and source of crop nutrients. However, there is concern that bacteria from biosolids may become established in soils, particularly if that soil becomes water-logged. This study examined the microbial community of arable soils cultivated with barley under different applications of biosolids (0, 24t/ha, 48t/ha) in laboratory mesocosms which simulated a 10-day flood. Nutrients (P and N) and organic matter in the soil increased with application rate, but plant growth was not affected by biosolid application. The biosolids contained 10× more genetic material than the soil, with much lower bacterial diversity, yet application did not significantly change the taxonomy of the soil microbiome, with minor changes related to increased nutrients and SOM. Anaerobic conditions developed rapidly during flooding, causing shifts in the native soil microbiome. Some bacterial taxa that were highly abundant in biosolids had slightly increased relative abundance in amended soils during the flood. After flooding, soil bacterial populations returned to their pre-flood profiles, implying that the native microbial community is resilient to transient changes. The short-term changes in the microbiome of biosolid-amended soils during flooding do not appear to increase the environmental risk posed by biosolid application. [ABSTRACT FROM AUTHOR]

Microorganisms, occupying the largest biomass in deep sea, play essential roles in deep-sea ecosystem. It is believed that the microbes in deep-sea sediments are more representative of deep-sea microbial communities, the microbial composition of which is seldom affected by ocean currents. However, the community of benthic microbes on a global scale has not been adequately explored. Herein, we build a comprehensive global dataset determined by 16S rRNA gene sequencing to characterize the biodiversity of microorganisms in benthic sediment. The dataset comprised 212 records from 106 sites, included sequencing of bacteria and archaea for each site and yielded 4,766,502 and 1,562,989 reads, respectively. Through annotation, a total of 110,073 and 15,795 OTUs of bacteria and archaea were obtained, and 61 bacterial phyla and 15 archaeal phyla were identified, of which the dominant phyla were Proteobacteria and Thaumarchaeota in deep-sea sediment. Therefore, our findings provided a biodiversity data of microbial communities in deep-sea sediment at global-scale and laid a foundation to further reveal the structures of microorganism communities in deep sea. [ABSTRACT FROM AUTHOR]

In this study, we evaluated the intestinal contents of Pacific whiteleg shrimp (Litopenaeus vannamei), the visceral mass of razor clams (Sinonovacula constricta) and the water columns and the substrate sediments in different culture-density groups in a L. vannamei–S. constricta tandem-culture model by high-throughput sequencing of the 16S rRNA gene. The results show that the culture density affected the bacterial floral structure of the water columns, substrate sediment and razor-clam gut masses without making significant differences in the bacterial flora structure of the shrimp gut; the Shannon diversity indexes of the bacterial communities in the substrate sediment, shrimp gut and razor-clam gut masses were not significantly different among the density groups, and the Shannon diversity index of the bacterial communities in the water column was higher in the group with higher culture densities; at the phylum level, the dominant bacteria common to the shrimp guts, razor-clam visceral mass, water columns and substrate sediment were Proteobacteria and Bacteroidetes; Chloroflexi was the dominant bacterium specific to the substrate sediment; and Firmicutes was the dominant bacterium specific to the shrimp gut and razor-clam gut mass. We used national standards (GB 17378.4-2007, China) to evaluate the content of water-quality factors through the environmental factors and the genus-level correlation analysis of bacterial flora that follow: the dominant bacterium in the water column, uncultured_bacterium_f_Rhodobacteraceae, was negatively correlated with PO43−-P; the dominant bacteria in the substrate sediments, uncultured_bacterium_f_Anaerolineaceae and Woeseia, were significantly and negatively correlated with DO; and the dominant bacteria Lactococcus spp. in the razor-clam gut mass and the shrimp intestines were positively correlated with DO. These results show that culture density directly affects water-quality factors, which in turn affect the culture environment and the composition structure of the bacterial flora in a cultured organism. [ABSTRACT FROM AUTHOR]

Microbiological properties of podzolic soils (Retisols) of old-aged spruce forests in the middle taiga of the Krasnoyarsk Krai and Komi Republic are described. Despite the geographical distance, the soils of these regions are similar in their morphological and physicochemical characteristics. Any statistically significant difference in the accumulation of microbial biomass and microbial respiration rate in the soils under spruce forests of the European North (Komi Republic) and Central Siberia (Krasnoyarsk Krai) is unobservable. However, the contents of carbon, nitrogen, and microbial biomass in soil have a significant effect on the composition of microbiomes in pyrogenic and nonpyrogenic soil horizons. In addition, the pyrogenic factor considerably influences the α-diversity of bacteria and fungi. As is shown, representatives of the dominant phyla of bacteria (Proteobacteria, Actinobacteria, and Planctomycetes) and fungi (Ascomycota, Basidiomycota and Mucoromycota) are actively involved in the assimilation of organic matter containing pyrogenic carbon. The microbiomes of the upper pyrogenic subhorizons include the groups of carbotrophic bacteria (Thermomonosporaceae, Isosphaeraceae, Bacillaceae, and Xanthobacteraceae) and fungi from the Dothideomycetes (Cenococcum), Eurotiomycetes (Penicillium), Sordariomycetes (Trichoderma), Leotiomycetes (Oidiodendron), and Umbelopsidomycetes (Umbelopsis) classes, which are capable of converting pyrolysis products into available and nontoxic substrates for other organisms. [ABSTRACT FROM AUTHOR]

The determination of the last common ancestor (LCA) of a group of species plays a vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of a fully resolved species tree. From a theoretical perspective, however, inference of the LCA amounts to the reconstruction of just one branch—the root branch—of the true species tree and should therefore be a much easier task than the full resolution of the species tree. Discarding the reliance on a hypothesized species tree and its rooting leads us to reevaluate what phylogenetic signal is directly relevant to LCA inference and to recast the task as that of sampling the total evidence from all gene families at the genomic scope. Here, we reformulate LCA and root inference in the framework of statistical hypothesis testing and outline an analytical procedure to formally test competing a priori LCA hypotheses and to infer confidence sets for the earliest speciation events in the history of a group of species. Applying our methods to two demonstrative data sets, we show that our inference of the opisthokonta LCA is well in agreement with the common knowledge. Inference of the proteobacteria LCA shows that it is most closely related to modern Epsilonproteobacteria, raising the possibility that it may have been characterized by a chemolithoautotrophic and anaerobic life style. Our inference is based on data comprising between 43% (opisthokonta) and 86% (proteobacteria) of all gene families. Approaching LCA inference within a statistical framework renders the phylogenomic inference powerful and robust. [ABSTRACT FROM AUTHOR]

Potato cultivation in the middle land is an alternative solution to avoid pathogens. Although it reduces potato quantity and requires more chemical fertilizers to increase production that potentially damages the environment. Therefore, this study aims to characterize contaminations and indigenous microbes from semi-organic potato cultivation centers in Central Java. Soil samples from the semi-organic potato cultivation center of Kledung, Central, were analyzed for metal contamination using the atomic absorption spectrophotometry method and metagenomic soil bacterial diversity profiles. Specifically targeted genes of distinct regions 16SV3-V5. OTUs were identified using Uparse v7.0.1001, while Beta diversity analysis used UniFrac. All these indices in our samples were calculated with QIIME (Version 1.7.0) and displayed with R software (Version 2.15.3). The results showed that semi-organic cultivations had been polluted with Pb > Cd > Cr > As, and carbamate residue was detected in the rhizosphere and surface soil. Manure and compost application alongside NPK fertilizer increases N input, decreasing surface soil bacteria. The surface soil (with a depth of = 5 cm) has a lower index of species richness, diversity, and relative abundance than the rhizosphere layer (depth > 5 cm). Firmicutes, Proteobacteria, and Actinobacterium dominate soillevel bacteria. In comparison, the rhizosphere soil has a higher bacteria diversity dominated by N-tethering rhizobia from the phylum Proteobacteria. The potato root attracts rhizobacteria consortium that support plant growth. A further study should be conducted to describe how the bacterial consortium formed, rhizobia migration from surface to rhizosphere soil, and its interaction with the potato plants. [ABSTRACT FROM AUTHOR]

Biogeochemical reduction and mobilization of sediment-bound arsenic (As) is the major concern for widespread groundwater As contamination in the middle Gangetic plains. The present work examines a microcosm based bio-stimulation study and substrate amendments over 45 days to analyze the bacterial community structure and distribution to indicate the possible in-situ bioremediation strategy in the area. Initially, Bacterial phyla Proteobacteria was predominantly present in all the samples, followed by Actinobacteria, Bacteroidetes, and Firmicutes whereas Cyanobacteria was noted as the minor group. In genus level, Delftia, Acinetobacter, Lysobacter, Bacillus, and Pseudomonas were the major groups of bacteria in the As-rich aquifer system, while Planctomycetes dominated the bio-stimulated samples, followed by a minute portion of Proteobacteria. Alpha diversity and Chaol curve further determined the species richness in the samples with an As tolerant capacity of 152.28 ppb. The presence of γ-Proteobacteria as the dominating member in high As-content water indicated their predominant role in As mobilization, whereas, dominance of α-Proteobacterial members in low As-content water indicated their involvement in As detoxification. The complete change in microbial community structure within the bio-stimulated conditions indicated the extensive role of arsenite-oxidizing microbial communities within different levels of As-contaminated areas in Bihar that will enlighten the significant role of these communities in As-biogeochemical cycle. [ABSTRACT FROM AUTHOR]

The residential kitchen is often heavily colonized by microbes originating from different sources, including food and human contact. Although a few studies have reported the bacterial composition in cleaning utensils and surface samples there is limited knowledge of the bacterial diversity across different sample types, households, and countries. As part of a large European study, we have identified the microbiota of 302 samples from cleaning utensils (sponges and cloths), kitchen surfaces (sinks, cutting boards, countertops, tap handles, and a pooled sample of other handles) in 74 households across 5 countries (France, Hungary, Norway, Portugal, and Romania). In total, 31 bacterial phyla were identified, with Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteria being the most abundant. Despite large variations in households with respect to kitchen standards, kitchen practices, cleaning regimes, and diet and considerable differences in bacterial diversity between samples, eight bacterial genera/families commonly associated with environmental sources were identified in most samples and defined as a core microbiota: Acinetobacter, Pseudomonas, Enhydrobacter, Enterobacteriaceae, Psychrobacter, Chryseobacterium, Bacillus, and Staphylococcus. These genera/families were also among the bacteria with the highest relative abundance across all samples, in addition to Yersiniaceae, Kocuria, Pantoea, and Streptococcus. Taxa associated with potential pathogens and fecal indicators were low in abundance but broadly distributed throughout the households. The microbial composition of surface samples indicated that the microbial composition on kitchen surfaces is more characteristic for the particular country than the object type, while the microbiota of cleaning utensils was similar across countries but differed between types (sponge or cloth). IMPORTANCE There is limited knowledge of the characteristics, differences, and similarities of the bacterial composition in residential kitchens. Here, we report the microbiota of cleaning utensils (sponges and cloths) and five different surface samples in 74 households across five European countries. In addition to increasing the knowledge of the kitchen microbiota from many geographical areas, this study identified a core microbiota in European residential kitchens despite large variations in kitchen practices and kitchen design and standards across countries and households. [ABSTRACT FROM AUTHOR]

Heavy metal pollution is a severe concern worldwide, owing to its harmful effects on ecosystems. Phytoremediation has been applied to remove heavy metals from water, soils, and sediments by using plants and associated microorganisms to restore contaminated sites. The Typha genus is one of the most important genera used in phytoremediation strategies because of its rapid growth rate, high biomass production, and the accumulation of heavy metals in its roots. Plant growth-promoting rhizobacteria have attracted much attention because they exert biochemical activities that improve plant growth, tolerance, and the accumulation of heavy metals in plant tissues. Because of their beneficial effects on plants, some studies have identified bacterial communities associated with the roots of Typha species growing in the presence of heavy metals. This review describes in detail the phytoremediation process and highlights the application of Typha species. Then, it describes bacterial communities associated with roots of Typha growing in natural ecosystems and wetlands contaminated with heavy metals. Data indicated that bacteria from the phylum Proteobacteria are the primary colonizers of the rhizosphere and root-endosphere of Typha species growing in contaminated and non-contaminated environments. Proteobacteria include bacteria that can grow in different environments due to their ability to use various carbon sources. Some bacterial species exert biochemical activities that contribute to plant growth and tolerance to heavy metals and enhance phytoremediation. [ABSTRACT FROM AUTHOR]

Houseflies are alleged reservoirs as well as vectors of human and animal pathogens, including bacteria, because they frequently have contact with animal excreta and decaying organic substances. The rapid adaptation process of ingested microbes in the insect gut may involve gene transfer, including antibiotic resistance determinants among different bacterial strains. Six hundred and fifty-seven (n = 657) houseflies were collected from hospices and were identified morphologically and genetically using the 16S rRNA, CO1, and ITS2 barcoding genes. This study also characterized the bacterial communities harboured by the captured houseflies using 16S rRNA metabarcoding on the next-generation sequencing (NGS) platform and further sought to detect antibiotic resistance traits by using gene-specific PCR assays. Generated sequences for the targeted gene fragments matched with Musca domestica and all the sequences were deposited to the GenBank database. The 16S rRNA metabarcoding analysis revealed that the most abundant phyla detected with variable abundance observed among all the houseflies were Proteobacteria, followed by Firmicutes, and Bacteroidetes. Furthermore, the NGS data revealed the presence of multiple bacterial genera, including Providencia, Enterobacter, Dysgonomonas, Escherichia-Shigella, Klebsiella, Pseudomonas, and Streptococcus, which are known to harbour potentially pathogenic species of animals and humans. Antibiotic resistance genes detected from the housefly DNA in this study included ermB, tetA, blaSHV, and blaTEM. Moreover, these genes are associated with resistance to erythromycin, tetracycline, and beta-lactams antibiotics, respectively. The presence of bacterial pathogens and the detection of antibiotic resistance genes from the houseflies collected from the hospices indicates the possible health risk to patients in hospices and the surrounding community. Therefore, it is imperative to keep high standards of hygiene, food preparation, safety, and control of houseflies in hospices. [ABSTRACT FROM AUTHOR]

The priming effect (PE) is important for understanding the decomposition of soil organic matter (SOM) and forecasting C-climate feedback. However, there are limited studies on microbial community-level properties and the keystone taxa involved in the process. In this study, we collected soil from a subtropical Phyllostachys edulis forest undergoing long-term N-addition and conducted an incubation experiment to evaluate the effects of single and repeated addition of 13C-labeled glucose. Our results demonstrated that previously N-fertilized soil had a smaller cumulative PE compared with that of the control (11% average decrease). This could be primarily explained (26%) by the lower abundance of bacterial r-strategy group members (B_mod#2, constituting Proteobacteria, Firmicutes, and Actinobacteria phyla) under N-addition treatments. A single C-addition induced a greater PE than that of repeated C-additions (2.66- to 3.11-fold). Single C addition led to greater C to N ratios of microbial biomass and fungi to bacteria, positively impacting cumulative PE, indicating that the shifts in fungal/bacterial dominance play an important role in regulating PE. Moreover, a saprophytic taxa group (F_Mod#3, primarily composed of the phyla Ascomycota) explained 62% of the differences in cumulative PE between single and repeated C-additions. Compared with repeated C-additions, a greater abundance of B_Mod#2 and F_Mod#3, as well as C-related hydrolase activity, was observed under single C-addition, inducing greater cumulative PE. Therefore, sufficient C may facilitate the proliferation of r-strategy bacterial taxa and saprophytic fungal taxa, thereby increasing SOM decomposition. Our findings provide novel insights into the relationship between microbial community-level properties and PE. [ABSTRACT FROM AUTHOR]

Pulque is a traditional Mexican fermented beverage associated with numerous health benefits. Over time, there has been considerable interest in studying the bacterial diversity of pulque, and microbial characterization has been carried out using traditional microbiological and molecular methods. Therefore, the objective of this research was to characterize the microbiota of artisanal pulque obtained from the Zacatlán region in Puebla, México, by the means of Illumina sequencing, and to compare it with the microbial diversity of aguamiel (sap before fermentation), commercial pulque (supplemented with additives to increase its yield), and its seed (batch of pulque previously fermented). An analysis of the Shannon index showed medium diversity for both aguamiel and pulque samples (score > 2), while the Chao 1 index exhibited a non-significant difference between them. On the other hand, a principal components analysis confirmed the role of the seed as an essential inoculum to define the microbial diversity of pulque, emphasizing the importance of its preservation as a quality standard during the elaboration process. In addition, results showed that the dominant phyla in artisanal and commercial pulque were Firmicutes and Bacteroidetes. As the fermentation process progressed, it was possible to observe an increase in the population of lactic acid bacteria (LAB) in both types of pulque compared to those detected in aguamiel. Of these, the species Lactobacillus, Leuconostoc, and Lactococcus represented almost 95% of the total LAB. Finally, even though the safety of pulque has been in question due to its non-aseptic manufacturing process, the present study confirmed that less than 1% of its microbiota corresponds to the genera with a pathogenic potential such as γ-proteobacteria (Enterobacter and Hafnia), which decreases as the fermentation process advances. [ABSTRACT FROM AUTHOR]

Microbial activity increases after rewetting dry soil, resulting in a pulse of carbon mineralization and nutrient availability. The biogeochemical responses to wet-up are reasonably well understood and known to be microbially mediated. Yet, the population level dynamics, and the resulting changes in microbial community patterns, are not well understood as ecological phenomena. Here, we used sequencing of 16S rRNA genes coupled with heavy water (H218O) DNA quantitative stable isotope probing to estimate population-specific rates of growth and mortality in response to a simulated wet-up event in a California annual grassland soil. Bacterial growth and mortality responded rapidly to wet-up, within 3 h, and continued throughout the 168 h incubation, with patterns of sequential growth observed at the phylum level. Of the 37 phyla detected in the prewet community, growth was found in 18 phyla while mortality was measured in 26 phyla. Rapid growth and mortality rates were measurable within 3 h of wet-up but had contrasting characteristics; growth at 3 h was dominated by select taxa within the Proteobacteria and Firmicutes, whereas mortality was taxonomically widespread. Furthermore, across the community, mortality exhibited density-independence, consistent with the indiscriminate shock resulting from dry-down and wet-up, whereas growth was density-dependent, consistent with control by competition or predation. Total aggregated growth across the community was highly correlated with total soil CO2 production. Together, these results illustrate how previously "invisible" population responses can translate quantitatively to emergent observations of ecosystem-scale biogeochemistry.

BackgroundMultiple factors contribute to the etiology of addiction, including genetics, sex, and a number of addiction-related behavioral traits. One behavioral trait where individuals assign incentive salience to food stimuli ("sign-trackers", ST) are more impulsive compared to those that do not ("goal-trackers", GT), as well as more sensitive to drugs and drug stimuli. Furthermore, this GT/ST phenotype predicts differences in other behavioral measures. Recent studies have implicated the gut microbiota as a key regulator of brain and behavior, and have shown that many microbiota-associated changes occur in a sex-dependent manner. However, few studies have examined how the microbiome might influence addiction-related behaviors. To this end, we sought to determine if gut microbiome composition was correlated with addiction-related behaviors determined by the GT/ST phenotype.MethodsOutbred male (N=101) and female (N=101) heterogeneous stock rats underwent a series of behavioral tests measuring impulsivity, attention, reward-learning, incentive salience, and locomotor response. Cecal microbiome composition was estimated using 16S rRNA gene amplicon sequencing. Behavior and microbiome were characterized and correlated with behavioral phenotypes. Robust sex differences were observed in both behavior and microbiome; further analyses were conducted within sex using the pre-established goal/sign-tracking (GT/ST) phenotype and partial least squares differential analysis (PLS-DA) clustered behavioral phenotype.ResultsOverall microbiome composition was not associated to the GT/ST phenotype. However, microbial alpha diversity was significantly decreased in female STs. On the other hand, a measure of impulsivity had many significant correlations to microbiome in both males and females. Several measures of impulsivity were correlated with the genus Barnesiella in females. Female STs had notable correlations between microbiome and attentional deficient. In both males and females, many measures were correlated with the bacterial families Ruminocococcaceae and Lachnospiraceae.ConclusionsThese data demonstrate correlations between several addiction-related behaviors and the microbiome specific to sex.

Modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzymatic assembly lines are large and dynamic protein machines that generally effect a linear sequence of catalytic cycles. Here, we report the heterologous reconstitution and comprehensive characterization of two hybrid NRPS-PKS assembly lines that defy many standard rules of assembly line biosynthesis to generate a large combinatorial library of cyclic lipodepsipeptide protease inhibitors called thalassospiramides. We generate a series of precise domain-inactivating mutations in thalassospiramide assembly lines, and present evidence for an unprecedented biosynthetic model that invokes intermodule substrate activation and tailoring, module skipping and pass-back chain extension, whereby the ability to pass the growing chain back to a preceding module is flexible and substrate driven. Expanding bidirectional intermodule domain interactions could represent a viable mechanism for generating chemical diversity without increasing the size of biosynthetic assembly lines and challenges our understanding of the potential elasticity of multimodular megaenzymes.

Plant-associated microbial communities have diverse phenotypic effects on their hosts that are only beginning to be revealed. We hypothesized that morpho-physiological variations in the tropical tree Tabebuia heterophylla, observed on different geological substrates, arise in part due to microbial processes in the rhizosphere. We characterized the microbiota of the rhizosphere and soil communities associated with T. heterophylla trees in high and low altitude sites (with varying temperature and precipitation) of volcanic, karst and serpentine geologies across Puerto Rico. We sampled 6 areas across the island in three geological materials including volcanic, serpentine and karst soils. Collection was done in 2 elevations (>450m and 0-300m high), that included 3 trees for each site and 4 replicate soil samples per tree of both bulk and rhizosphere. Genomic DNA was extracted from 144 samples, and 16S rRNA V4 sequencing was performed on the Illumina MiSeq platform. Proteobacteria, Actinobacteria, and Verrucomicrobia were the most dominant phyla, and microbiomes clustered by geological substrate and elevation. Volcanic samples were enriched in Verrucomicrobia; karst was dominated by nitrogen-fixing Proteobacteria, and serpentine sites harbored the most diverse communities, with dominant Cyanobacteria. Sites with similar climates but differing geologies showed significant differences on rhizobiota diversity and composition demonstrating the importance of geology in shaping the rhizosphere microbiota, with implications for the plant's phenotype. Our study sheds light on the combined role of geology and climate in the rhizosphere microbial consortia, likely contributing to the phenotypic plasticity of the trees.

The efflux pumps from the Resistance-Nodulation-Division family, RND, are main contributors to intrinsic antibiotic resistance in Gram-negative bacteria. Among this family, the MdtABC pump is unusual by having two inner membrane components. The two components, MdtB and MdtC are homologs, therefore it is evident that the two components arose by gene duplication. In this paper, we describe the results obtained from a phylogenetic analysis of the MdtBC pumps in the context of other RNDs. We show that the individual inner membrane components (MdtB and MdtC) are conserved throughout the Proteobacterial species and that their existence is a result of a single gene duplication. We argue that this gene duplication was an ancient event which occurred before the split of Proteobacteria into Alpha-, Beta- and Gamma- classes. Moreover, we find that the MdtABC pumps and the MexMN pump from Pseudomonas aeruginosa share a close common ancestor, suggesting the MexMN pump arose by another gene duplication event of the original Mdt ancestor. Taken together, these results shed light on the evolution of the RND efflux pumps and demonstrate the ancient origin of the Mdt pumps and suggest that the core bacterial efflux pump repertoires have been generally stable throughout the course of evolution.

Introduction: Osteoarthritis (OA) is a kind of chronic, degenerative disorder with unknown causes. In this study, we aimed to improve our understanding of the gut microbiota profile in patients with knee OA. Methods: 16S rDNA gene sequencing was performed to detect the gut microbiota in fecal samples collected from the patients with OA (n = 32) and normal control (NC, n = 57). Then the metagenomic sequencing was used to identify the genes or functions linked with gut microbial changes at the species level in the fecal samples from patients with OA and NC groups. Results: The Proteobacteria was identified as dominant bacteria in OA group. We identified 81 genera resulted significantly different in abundance between OA and NC. The abundance of Agathobacter, Ruminococcus, Roseburia, Subdoligranulum, and Lactobacillus showed significant decrease in the OA compared to the NC. The abundance of genera Prevotella_7, Clostridium, Flavonifractor and Klebsiella were increasing in the OA group, and the families Lactobacillaceae, Christensenellaceae, Clostridiaceae_1 and Acidaminococcaceae were increasing in the NC. The metagenomic sequencing showed that the abundance of Bacteroides stercoris, Bacteroides vulgatus and Bacteroides uniformis at the species level were significantly decreasing in the OA, and the abundance of Escherichia coli, Klebsiella pneumoniae, Shigella flexneri and Streptococcus salivarius were significantly increased in OA. Discussion: The results of our study interpret a comprehensive profile of the gut microbiota in patients with knee OA and offer the evidence that the cartilagegut-microbiome axis could play a crucial role in underlying the mechanisms and pathogenesis of OA. [ABSTRACT FROM AUTHOR]

Background: American foulbrood (AFB) disease caused by Paenibacillus larvae is dangerous, and threatens beekeeping. The eco-friendly treatment method using probiotics is expected to be the prospective method for controlling this pathogen in honey bees. Therefore, this study investigated the bacterial species that have antimicrobial activity against P. larvae. Results: Overall, 67 strains of the gut microbiome were isolated and identified in three phyla; the isolates had the following prevalence rates: Firmicutes 41/67 (61.19%), Actinobacteria 24/67 (35.82%), and Proteobacteria 2/67 (2.99%). Antimicrobial properties against P. larvae on agar plates were seen in 20 isolates of the genus Lactobacillus, Firmicutes phylum. Six representative strains from each species (L. apis HSY8_B25, L. panisapium PKH2_L3, L. melliventris HSY3_B5, L. kimbladii AHS3_B36, L. kullabergensis OMG2_B25, and L. mellis OMG2_B33) with the largest inhibition zones on agar plates were selected for in vitro larvae rearing challenges. The results showed that three isolates (L. apis HSY8_B25, L. panisapium PKH2_L3, and L. melliventris HSY3_B5) had the potential to be probiotic candidates with the properties of safety to larvae, inhibition against P. larvae in infected larvae, and high adhesion ability. Conclusions: Overall, 20 strains of the genus Lactobacillus with antimicrobial properties against P. larvae were identified in this study. Three representative strains from different species (L. apis HSY8_B25, L. panisapium PKH2_L3, and L. melliventris HSY3_B5) were evaluated to be potential probiotic candidates and were selected for probiotic development for the prevention of AFB. Importantly, the species L. panisapium isolated from larvae was identified with antimicrobial activity for the first time in this study. [ABSTRACT FROM AUTHOR]

Simple Summary: One of the greatest challenges to achieving a sustainable aquaculture is finding alternatives to fishmeal as a primary protein source in aquafeeds. Insects represent one of the most promising alternatives being explored and produced as replacements for this ingredient. This review addresses the use of two insect species (black soldier fly, Hermetia illucens, and yellow mealworm, Tenebrio molitor) in freshwater and marine fish diet formulations and the effect of insect meal on fish gut microbiota. Furthermore, the effects of a probiotic, namely, Lactococcus lactis subsp. lactis, are considered. The study of fish gut microbiota is very important for aquaculture practice as gut microbiota plays a significant role in nutrition metabolism, also affecting a number of other physiological functions, including fish growth and development, immune response, and pathogen resistance. Along with recent and promising results in this field, new insights and future directions on fish gut microbiota research are highlighted. Aquaculture is the fastest-growing agricultural industry in the world. Fishmeal is an essential component of commercial fish diets, but its long-term sustainability is a concern. Therefore, it is important to find alternatives to fishmeal that have a similar nutritional value and, at the same time, are affordable and readily available. The search for high-quality alternatives to fishmeal and fish oil has interested researchers worldwide. Over the past 20 years, different insect meals have been studied as a potential alternate source of fishmeal in aquafeeds. On the other hand, probiotics—live microbial strains—are being used as dietary supplements and showing beneficial effects on fish growth and health status. Fish gut microbiota plays a significant role in nutrition metabolism, which affects a number of other physiological functions, including fish growth and development, immune regulation, and pathogen resistance. One of the key reasons for studying fish gut microbiota is the possibility to modify microbial communities that inhabit the intestine to benefit host growth and health. The development of DNA sequencing technologies and advanced bioinformatics tools has made metagenomic analysis a feasible method for researching gut microbes. In this review, we analyze and summarize the current knowledge provided by studies of our research group on using insect meal and probiotic supplements in aquafeed formulations and their effects on different fish gut microbiota. We also highlight future research directions to make insect meals a key source of proteins for sustainable aquaculture and explore the challenges associated with the use of probiotics. Insect meals and probiotics will undoubtedly have a positive effect on the long-term sustainability and profitability of aquaculture. [ABSTRACT FROM AUTHOR]

Background: The study evaluated the effects of bacteriophage cocktail (BP) and ZnO administered during weaning time for piglets exposed to a non-sanitary environment. The bacteriophages were designed to eliminate Escherichia coli (K88, K99 and F41), Salmonella (typhimurium and enteritidis), and Clostridium perfreingens (types A and C). Forty 21-day-old crossbreed piglets were assigned to four treatments, including the PC (sanitary environment), NC (non-sanitary environment), BP (NC plus 108 pfu/kg BP), and ZO (NC plus 2,500 mg/kg ZnO). Piglets in the NC, BP and ZO were kept in a non-sanitary environment for 14 d, which was contaminated with the feces of infected pigs. Results: Pigs in the BP and ZO treatments had a higher final body weight compared with the NC. The NC treatment showed the highest concentration of inflammatory cytokines including interleukin (IL)-1β, IL-6 and tumor necrosis factor-α in the plasma. The administration of BP and ZO showed lower myeloperoxidase concentrations compared with the NC. The NC treatment showed a lower concentration of superoxide dismutase in serum compared with the PC. Among the treatments in non-sanitary environment, the NC treatment showed a higher concentration of malondialdehyde compared with the ZO. The PC treatment showed a lower concentration of butyric acid in the feces compared with the BP treatment. Among non-sanitary treatments, the villus height in the duodenum was greater in the BP and ZO compared with the NC. The lower abundance of Proteobacteria phylum was observed in the BP and PC treatments compared with the NC. The highest relative abundance of Eubacterium was recorded in the BP treatment. The abundance of Megasphaera and Schwartzia was higher in the NC pigs compared with the BP piglets. The abundance of Desulfovibrio was lower in the supplemented treatments (BP and ZO) compared with non-supplemented (NC and PC). The abundance of Cellulosilyticum genera was higher in the BP and ZO treatments rather than in the NC. The piglets in the NC treatment had the highest abundance of Escherichia-Shigella, followed by the PC and ZO treatments. Conclusion: In conclusion, these results suggest that the supplementation of bacteriophage cocktail could effectively control Proteobacteria phylum, Clostridium spp. and coliforms population and mitigated the adverse influences of weaning stress in piglets. [ABSTRACT FROM AUTHOR]

The excessive input of nutrients into rivers can lead to contamination and eutrophication, which poses a threat to the health of aquatic ecosystems. It is crucial to identify the sources of contaminants to develop effective management plans for eutrophication. However, traditional methods for identifying pollution sources have been insufficient, making it difficult to manage river health effectively. High-throughput sequencing offers a novel method for microbial community source tracking, which can help identify dominant pollution sources in rivers. The Wanggang River was selected for study, as it has suffered accelerated eutrophication due to considerable nutrient input from riparian pollutants. The present study identified the dominant microbial communities in the Wanggang River basin, including Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia, and Firmicutes. The Source Tracker machine-learning classification system was used to create source-specific microbial community fingerprints to determine the primary sources of contaminants in the basin, with agricultural fertilizer being identified as the main pollutant source. By identifying the microbial communities of potential pollution sources, the study determined the contributing pollutant sources in several major sections of the Wanggang River, including industry, urban land, pond culture, and livestock land. These findings can be used to improve the identification of pollution sources in specific environments and develop effective pollution management plans for polluted river water. [ABSTRACT FROM AUTHOR]

Objective: To investigate the distribution differences in the respiratory tract microbiota of AECOPD patients in different BMI groups and explore its guiding value for treatment. Methods: Sputum samples of thirty-eight AECOPD patients were collected. The patients were divided into low, normal and high BMI group. The sputum microbiota was sequenced by 16S rRNA detection technology, and the distribution of sputum microbiota was compared. Rarefaction curve, α-diversity, principal coordinate analysis (PCoA) and measurement of sputum microbiota abundance in each group were performed and analyzed by bioinformatics methods. Results: 1. The rarefaction curve in each BMI group reached a plateau. No significant differences were observed in the OTU total number or α-diversity index of microbiota in each group. PCoA showed significant differences in the distance matrix of sputum microbiota between the three groups, which was calculated by the Binary Jaccard and the Bray Curtis algorithm. 2. At the phylum level, most of the microbiota were Proteobacteria, Bacteroidetes Firmicutes, Actinobacteria, and Fusobacteria. At the genus level, most were Streptococcus, Prevotella, Haemophilus, Neisseria and Bacteroides. 3. At the phylum level, the abundance of Proteobacteria in the low group was significantly higher than that in normal and high BMI groups, the abundances of Firmicutes in the low and normal groups were significantly lower than that in high BMI groups. At the genus level, the abundance of Haemophilus in the low group was significantly higher than that in high BMI group, and the abundances of Streptococcus in the low and normal BMI groups were significantly lower than that in the high BMI group. Conclusions: 1. The sputum microbiota of AECOPD patients in different BMI groups covered almost all microbiota, and BMI had no significant association with total number of respiratory tract microbiota or α-diversity in AECOPD patients. However, there was a significant difference in the PCoA between different BMI groups. 2. The microbiota structure of AECOPD patients differed in different BMI groups. Gram-negative bacteria (G- ) in the respiratory tract of patients predominated in the low BMI group, while gram-positive bacteria (G+) predominated in the high BMI group. [ABSTRACT FROM AUTHOR]

Understanding how microbial communities adapt to environmental stresses is critical for interpreting ecological patterns and microbial diversity. In the case of the Gobi Desert, little is known on the environmental factors that explain hypolithic colonization under quartz stones. By analyzing nine hypolithic communities across an arid gradient and the effects of the season of the year in the Hexi Corridor of this desert, we found a significant decrease in hypolithic colonization rates (from 47.24 to 15.73%) with the increasing drought gradient and found two distinct communities in Hot and Cold samples, which survived or proliferated after a hot or a cold period. While Cold communities showed a greater species diversity and a predominance of Cyanobacteria, Hot communities showed a predominance of members of the Proteobacteria and the Firmicutes. In comparison, Cold communities also possessed stronger functions in the photosynthesis and carbon metabolism. Based on the findings of this study, we proposed that the hypolithic communities of the Hexi Corridor of the Gobi Desert might follow a seasonal developmental cycle in which temperature play an important role. Thus after a critical thermal threshold is crossed, heterotrophic microorganisms predominate in the hot period, while Cyanobacteria predominate in the cold period. [ABSTRACT FROM AUTHOR]

Microbes contribute to the organic matter decomposition (OMD) in river ecosystems. This study considers two aspects of OMD in river ecosystems which have not been examined in scientific studies previously, and these are the microbial interactions in OMD and the influence of environmental factors on microbial interactions. Cotton strip (CS), as a substitute for organic matter, was introduced to Luanhe River Basin in China. The results of CS assay, microbial sequencing, and redundancy analysis (RDA) showed that CS selectively enriched bacterial and fungal groups related to cellulose decomposition, achieving cotton strip decomposition (CSD). Bacterial phylum Proteobacteria and fungal phyla Rozellomycota and Ascomycota were the dominant groups associated with CSD. Network analysis and Mantel test results indicated that bacteria and fungi on CS cooperatively formed an interaction network to achieve the CSD. In the network, modules 2 and 4 were significantly positively associated with CSD, which were considered as the key modules in this study. The key modules were mainly composed of phyla Proteobacteria and Ascomycota, indicating that microbes in key modules were the effective decomposers of CS. Although keystone taxa were not directly associated with CSD, they may regulate the genera in key modules to achieve the CSD, since some keystone taxa were linked with the microbial genera associated with CSD in the key modules. Total nitrogen (TN) and temperature in water were the dominant environmental factors positively influenced CSD. The key modules 2 and 4 were positively influenced by water temperature and TN in water, respectively, and two keystone taxa were positively associated with TN. This profoundly revealed that water temperature and TN influenced the OMD through acting on the keystone taxa and key modules in microbial interactions. The research findings help us to understand the microbial interactions influenced by environmental factors in OMD in river ecosystems. [ABSTRACT FROM AUTHOR]

Bentonite clays are characterized by a large specific surface area and a large pore space volume, which determines their high sorption capacity and allows them to be used as a barrier in the construction of deep geological repositories (DGR) for radioactive waste. DGRs are expected to operate for thousands of years, so it appears acute to predict possible changes in them during this time. In the course of repository operation, bentonites can change their properties under the impact of microorganisms. This study analyzes the structure of microbial community in bentonites sampled from two deposits, i.e., the 10th Khutor (Russia) and Taganskoe (Kazakhstan) at different incubation temperatures (25 and 60°C). Bentonite from the 10th Khutor deposit reveals 10 phyla and 92 genera of bacteria upon incubation at 60°C, and 12 phyla and 94 genera, upon incubation at 25°C. In the Taganskoe deposit bentonite, 14 phyla and 87 genera were identified at the incubation temperature of 60°C, and 15 phyla and 123 genera at 25°C. Bacteria of the Proteobacteria and Firmicutes phyla predominated in the samples. It is concluded that temperature rather than chemical and mineral composition of samples is the main factor influencing the microbial community formation in the studied bentonites. [ABSTRACT FROM AUTHOR]

Aim Ocular health greatly impacts the quality of life, and diabetes mellitus (DM) is a major cause of several visual diseases. Likewise, microbiomes have a pivotal role in eye health. The aim was to study the effect of DM, both type-1 (T1DM) and type-2 (T2DM) on the ocular microbiome. Methods and results A total of 70 subjects were recruited for this study and divided into two main groups healthy nondiabetic (n  = 18) and diabetic (28 T1DM and 24 T2DM). The ocular surface (OS) microbiome was more diverse in the healthy group than in the diabetic one. Taxonomic analysis revealed Proteobacteria as the main phylum (healthy nondiabetic 41.8%, T1DM 50.6%, and T2DM 52.5%), besides Streptococcus (healthy nondiabetic 16%, T1DM 26.75%, and T2DM 29.20%) and Paracoccus (healthy nondiabetic 17%, T1DM 34.85%, and T2DM 37.47%) as the main genera. No significant diversity was found between T1DM and T2DM on both phylum and genus levels; yet genera Brevundimonas and Leptotrichia were more significantly predominant in T1DM. Conclusion Two pathogenic genera, Streptococcus and Paracoccus , were more predominant in the DM group than in the healthy one. [ABSTRACT FROM AUTHOR]

Background and aims: Plants continuously interact with soil microbiota. These plant-soil feedbacks (PSFs) are considered a driving force in plant community dynamics. However, most PSF information comes from inter-family studies, with limited information on possible causes. We studied the variation of PSFs between and within grass species and identified the soil microbes that are associated with the observed PSFs effects. Methods: We grew monocultures of ten cultivars of three grass species (Lolium perenne, Poa pratensis, Schedonorus arundinaceus) using a two-phase PSF experiment. We measured plant total biomass to determine PSFs between and within species and correlated it with sequenced rhizosphere bacteria and fungi. Results: In the soil conditioning phase, grass species developed microbial legacies that affected the performance of other grass species in the feedback phase. We detected overall negative interspecific PSFs. While we show that L. perenne and P. pratensis increased their performance respectively in conspecific and heterospecific soils, S. arundinaceus was not strongly affected by the legacies of the previous plant species. Contrary to our expectation, we found no evidence for intraspecific variation in PSFs. Bacterial taxa associated with PSFs included members of Proteobacteria, Firmicutes, Verrucomicrobia and Planctomycetes whereas fungal taxa included members of Ascomycota. Conclusion: Our results suggest differences in PSF effects between grass species, but not between cultivars within species. Thus, in the studied grass species, there might be limited potential for breeding on plant traits mediated by PSFs. Furthermore, we point out potential microbial candidates that might be driving the observed PSF effects that could be further explored. [ABSTRACT FROM AUTHOR]

The intracellular endosymbiotic proteobacteria Wolbachia have evolved across the phyla nematoda and arthropoda. In Wolbachia phylogeny, supergroup F is the only clade known so far with members from both arthropod and filarial nematode hosts and therefore can provide unique insights into their evolution and biology. In this study, four new supergroup F Wolbachia genomes have been assembled using a metagenomic assembly and binning approach, w Moz and w Mpe from the human filarial parasites Mansonella ozzardi and M. perstans , and w Ocae and w MoviF from the blue mason bee Osmia caerulescens and the sheep ked Melophagus ovinus , respectively. A comprehensive phylogenomic analysis revealed two distinct lineages of filarial Wolbachia in supergroup F, indicating multiple horizontal transfer events between arthropod and nematode hosts. The analysis also reveals that the evolution of Wolbachia -filaria symbioses is accompanied by a convergent pseudogenization and loss of the bacterioferritin gene, a phenomenon found to be shared by all filarial Wolbachia , even those outside supergroup F. These observations indicate that differences in heme metabolism might be a key feature distinguishing filarial and arthropod Wolbachia. The new genomes provide a valuable resource for further studies on symbiosis, evolution, and the discovery of new antibiotics to treat mansonellosis. [ABSTRACT FROM AUTHOR]