bacterial richness
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2021 ◽  
Vol 3 ◽  
Author(s):  
Andre Freire Cruz ◽  
R. G. S. Wijesekara ◽  
K. B. S. N. Jinadasa ◽  
Benjamin J. Gonzales ◽  
Takeshi Ohura ◽  
...  

In this study, the composition and richness of bacterial communities in treated and untreated wastewater from hospitals, commercial, and non-commercial fish farming sites, sewage effluents, and surface waters, which included seawater and fresh water in Sri Lanka and the Philippines, were investigated through 16S rRNA gene amplicon sequence analysis. Firmicutes were found predominantly in Sri Lankan hospital wastewaters, while Cyanobacteria and Acidobacteria were typically detected in fish culture sites and the waste canal in Sri Lanka, respectively. The Shannon–Weaver index (SW) and number of Operational Taxonomic Units (OTUs) were higher in the Philippines than in Sri Lanka. The bacterial richness in the university non-commercial fish pond and sewage effluent displayed greater than that in hospital wastewaters. In addition, the bacterial richness was higher in the untreated wastewater compared to that in the treated wastewater in hospitals. These results indicate the differences among water types in terms of bacterial community, especially influenced by their source.


AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shangdong Yang ◽  
Jian Xiao ◽  
Tian Liang ◽  
Weizhong He ◽  
Hongwei Tan

AbstractTo select an eco-friendly nitrogen (N) application level for sugarcane production, soil fertility and soil bacterial diversity under different nitrogen application levels were analyzed. Four levels of urea applications were high Nitrogen (H, 964 kg ha−1), medium Nitrogen (M, 482 kg ha−1), low Nitrogen (L, 96 kg ha−1) and no Nitrogen (CK, 0 kg ha−1) treatments, respectively. The results showed that the soil microbial biomass carbon and phosphorus were altered significantly by CK and L treatments. Moreover, the indexes of soil bacterial richness and diversity in the sugarcane field could be significantly improved by L. At the genus level, SC-I-84, Mycobacterium, Micropepsaceae, Saccharimonadales, Subgroup_2 and Acetobacteraceae were the unique dominant bacteria in the soil with the H treatment. JG30-KF-CM45 and Jatrophihabitans were the unique dominant genera in the M treatment. Subgroup_6, HSB_OF53-F07, Streptomyces, 67–14, SBR1031 and KD4-96 were the unique dominant genera in the L treatment. In contrast, FCPS473, Actinospica, 1921–2, Sinomonas, and Ktedonobacteraceae were the unique dominant genera in the CK treatment. The findings suggest that soil fertility all could be changed by different N application levels, but the most increasing integral effect only could be found in L. Moreover, even though soil bacterial richness could be significantly promoted by the M and H treatments, but soil bacterial diversity could not be significantly improved. On the contrary, soil bacterial diversity and richness all could be improved by L treatment. In addition, higher abundance of unique soil dominant bacteria could be only found in L treatment which compared to the CK, M and H treatments. These findings suggest that the rate of 96 kg ha−1 N application is ecofriendly for sugarcane production in Guangxi.


2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Mia M. Keady ◽  
Natalia Prado ◽  
Haw Chuan Lim ◽  
Janine Brown ◽  
Steve Paris ◽  
...  

Abstract Background The gut microbiome is important to immune health, metabolism, and hormone regulation. Understanding host–microbiome relationships in captive animals may lead to mediating long term health issues common in captive animals. For instance, zoo managed African elephants (Loxodonta africana) and Asian elephants (Elephas maximus) experience low reproductive rates, high body condition, and gastrointestinal (GI) issues. We leveraged an extensive collection of fecal samples and health records from the Elephant Welfare Study conducted across North American zoos in 2012 to examine the link between gut microbiota and clinical health issues, reproductive hormones, and metabolic hormones in captive elephants. We quantified gut microbiomes of 69 African and 48 Asian elephants from across 50 zoos using Illumina sequencing of the 16S rRNA bacterial gene. Results Elephant species differed in microbiome structure, with African elephants having lower bacterial richness and dissimilar bacterial composition from Asian elephants. In both species, bacterial composition was strongly influenced by zoo facility. Bacterial richness was lower in African elephants with recent GI issues, and richness was positively correlated with metabolic hormone total triiodothyronine (total T3) in Asian elephants. We found species-specific associations between gut microbiome composition and hormones: Asian elephant gut microbiome composition was linked to total T3 and free thyroxine (free T4), while fecal glucocorticoid metabolites (FGM) were linked to African elephant gut microbiome composition. We identified many relationships between bacterial relative abundances and hormone concentrations, including Prevotella spp., Treponema spp., and Akkermansia spp. Conclusions We present a comprehensive assessment of relationships between the gut microbiome, host species, environment, clinical health issues, and the endocrine system in captive elephants. Our results highlight the combined significance of host species-specific regulation and environmental effects on the gut microbiome between two elephant species and across 50 zoo facilities. We provide evidence of clinical health issues, reproductive hormones, and metabolic hormones associated with the gut microbiome structure of captive elephants. Our findings establish the groundwork for future studies to investigate bacterial function or develop tools (e.g., prebiotics, probiotics, dietary manipulations) suitable for conservation and zoo management.


2021 ◽  
Vol 12 ◽  
Author(s):  
Peixin Fan ◽  
Miju Kim ◽  
Grace Liu ◽  
Yuting Zhai ◽  
Ting Liu ◽  
...  

Calf diarrhea is one of the most concerning challenges facing both the dairy and beef cattle industry. Maintaining healthy gut microbiota is essential for preventing gastrointestinal disorders. Here, we observed significantly less bacterial richness in the abnormal feces with watery or hemorrhagic morphology compared to the normal solid feces. The normal solid feces showed high relative abundances of Osllospiraceae, Christensenellaceae, Barnesiella, and Lactobacillus, while the abnormal feces contained more bacterial taxa of Negativicutes, Tyzzerella, Parasutterella, Veillonella, Fusobacterium, and Campylobacter. Healthy calves had extensive bacterial-bacterial correlations, with negative correlation between Lactobacillus and potential diarrheagenic Escherichia coli-Shigella, but not in the abnormal feces. We isolated Lactobacillus species (L. reuteri, L. johnsonii, L. amylovorus, and L. animalis), with L. reuteri being the most abundant, from the healthy gut microbiota. Isolated Lactobacillus strains inhibited pathogenic strains including E. coli K88 and Salmonella Typhimurium. These findings indicate the importance of a diverse gut microbiota in newborn calf’s health and provide multiple potential probiotics that suppress pathogen colonization in the gastrointestinal tract to prevent calf diarrhea.


2021 ◽  
Vol 62 (1) ◽  
Author(s):  
Yu-Pei Chen ◽  
Chia-Fang Tsai ◽  
Asif Hameed ◽  
Yu-Jen Chang ◽  
Chiu-Chung Young

Abstract Background Agricultural management and temporal change including climate conditions and soil properties can result in the alteration of soil enzymatic activity and bacterial community, respectively. Therefore, different agricultural practices have been used globally to explore the soil quality. In this study, the temporal variations in soil property, enzymatic activity, and bacterial community at three successive trimester sampling intervals were performed in the soil samples of litchi orchards that were maintained under conventional and sustainable agricultural practices. Results Agricultural management found to significantly influence arylsulfatase, β-glucosidase, and urease activities across time as observed by repeated-measures analysis of variance. Shannon and Simpson diversity indices, and the relative abundance of predominant Acidobacteria and Proteobacteria were significantly influenced by temporal change but not agricultural management. This suggested that soil enzymatic activity was more susceptible to the interaction of temporal change and agricultural management than that of the bacterial community. Multiple regression analysis identified total nitrogen, EC, and phosphorus as the significant predictors of acid phosphatase, arylsulfatase, and β-glucosidase for explaining 29.5–39% of the variation. Moreover, the soil pH and EC were selected for the SOBS, Chao, ACE, and Shannon index to describe 33.8%, 79% of the variation, but no significant predictor was observed in the dominant bacterial phyla. Additionally, the temporal change involved in the soil properties had a greater effect on bacterial richness and diversity, and enzymatic activity than that of the dominant phyla of bacteria. Conclusions A long-term sustainable agriculture in litchi orchards would also decrease soil pH and phosphorus, resulting in low β-glucosidase and urease activity, bacterial richness, and diversity. Nevertheless, application of chemical fertilizer could facilitate the soil acidification and lead to adverse effects on soil quality. The relationship between bacterial structure and biologically-driven ecological processes can be explored by the cross-over analysis of enzymatic activity, soil properties and bacterial composition.


2021 ◽  
Author(s):  
Sydney I Glassman ◽  
James WJ Randolph ◽  
Sameer S Saroa ◽  
Joia K Capocchi ◽  
Kendra E Walters ◽  
...  

1. Prescribed fire is often used as a management tool to decrease exotic plant cover and increase native plant cover in grasslands. These changes may also be mediated by fire impacts on soil microbial communities, which drive plant productivity and function. Yet, the ecological effects of prescribed burns compared to wildfires on either plant or soil microbial composition remain unclear. 2. Here, we investigated the impacts of a spring prescribed fire versus a fall wildfire on plant cover and community composition and bacterial and fungal richness, abundance, and composition in a California grassland. We used qPCR of 16S and 18S to assess impacts on bacterial and fungal abundance and Illumina MiSeq of 16S and ITS2 to assess impacts on bacterial and fungal richness and composition. 3. Wildfire had stronger impacts than prescribed fire on microbial communities and both fires had similar impacts on plants with both prescribed and wildfire reducing exotic plant cover but neither reducing exotic plant richness. Fungal richness declined after the wildfire but not prescribed fire, but bacterial richness was unaffected by either. Yet increasing char levels in both fire types resulted in reduced bacterial and fungal biomass, and both fire types slightly altered bacterial and fungal composition. 4. Exotic and native plant diversity differentially affected soil microbial diversity, with native plant diversity leading to increased arbuscular mycorrhizal fungal richness while exotic plant diversity better predicted bacterial richness. However, the remainder of the soil microbial communities were more related to aspects of soil chemistry including cation exchange capacity, organic matter, pH and phosphorous. 5. Synthesis and applications. Understanding the different ecological effects of prescribed fires and wildfires on plant and soil communities are key to enhancing a prevalent management action and to guide potential management opportunities post wildfires. Our coupled plant and soil community sampling allowed us to capture the sensitivity of the fungal community to fire and highlights the importance of potentially incorporating management actions such as soil or fungal amendments to promote this critical community that mediates native plant performance.


Pathogens ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1225
Author(s):  
Tiphany Chrun ◽  
Joy Leng ◽  
Roberto M. La Ragione ◽  
Simon P. Graham ◽  
Elma Tchilian

Host-microbiota interactions are important in shaping immune responses that have the potential to influence the outcome of pathogen infection. However, most studies have focused on the gut microbiota and its possible association with disease outcome, while the role of the nasal microbiota and respiratory pathogen infection has been less well studied. Here we examined changes in the composition of the nasal microbiota of pigs following experimental infection with porcine reproductive and respiratory syndrome virus 2 (PRRSV-2), swine influenza A H3N2 virus (H3N2) or both viruses. DNA extracted from nasal swabs were subjected to 16S rRNA sequencing to study the composition of the nasal microbiota. Bacterial richness fluctuated in all groups, with a slight reduction in pigs singly infected with PRRSV-2 and H3N2 during the first 5 days of infection compared to uninfected controls. In contrast, nasal bacterial richness remained relatively stable after PRRSV-2/H3N2 co-infection. PRRSV-2 and H3N2, alone or in combination differentially altered the abundance and distribution of bacterial families. Single and co-infection with PRRSV-2 or H3N2 was associated with the expansion of the Neisseriaceae family. A positive correlation between H3N2 viral load and the relative abundance of the Neisseriaceae was observed. However, further mechanistic studies are required to understand the significance of the changes in specific bacterial families following these viral infections.


2021 ◽  
Author(s):  
Si-Si Li ◽  
Xiao-Yu Zhang ◽  
Xue-Jiao Zhou ◽  
Kai-Li Chen ◽  
Abolfazl Masoudi ◽  
...  

Abstract Exploring the bacterial microbiota is imperative to tick control since it has an important role in tick physiology and vector capacity. The life cycle of ticks consists of parasitic and non-parasitic stages, with a diversity of habitats and host blood meals. Whether and how these factors, such as tick developmental stages, tick organs, habitats and host blood meals affect tick bacterial microbiota is poorly elucidated. In the present study, we investigated the bacterial microbiotas of hard tick Haemaphysalis longicornis, their blood meals and habitats using 16S rRNA high-throughput sequencing. The bacterial richness and diversity in ticks varied depending on the tick developmental stage, feeding status and the tick organs. Results showed that fed ticks present a higher bacterial richness suggesting that ticks may acquire bacteria from blood meals. The significant overlap of the bacteriota of fed ticks and the host blood also support this possibility. Another possibility is that blood meals can stimulate the proliferation of certain bacteria. However, most shared bacteria cannot transmit throughout the tick life cycle, as they were not present in tick eggs. The most shared bacteria between ticks and habitats are genus of Staphylococcus, Pseudomonus, Enterobacter, Acinetobacer and Stenotrophomonas, some of them are also present in tick organ, suggesting that these environmental bacteria cannot be completely washed away and can be acquired by ticks. As tick reproductive organ, ovary showed the lowest bacterial richness and diversity compared to other organs. The predominant proportion of Coxiella in fed females and ovary further demonstrated that this genus is required for H. longicornis reproduction system. These findings further reveal that the bacterial composition of ticks is influenced by a variety of factors and will help in subsequent studies of the function of these bacteria.


Biotecnia ◽  
2021 ◽  
Vol 23 (3) ◽  
Author(s):  
Alberto Peña Rodríguez

Juvenile Litopenaeus vannamei (1.05 ± 0.1 g) were fed during 4-week with four experimental diets: control (Ctrl), inulin as prebiotic (5 g kg-1) (Pre), Bacillus subtilis and Lactobacillus sp. as probiotic (1 x 105 CFU g-1) (Pro), and a mix of inulin + B. subtilis and Lactobacillus sp. (5 g kg-1 + 1 x 105 CFU g-1) (Syn). Shrimps fed Syn diet showed significantly better feed utilization and higher growth than those in control diet (P < 0.05). The probiotic employed induced higher intestinal bacterial richness, whereas inulin in feed induced higher bacterial diversity in shrimp intestine. The most dominant bacterial phylum in the shrimp intestine among treatments was Proteobacteria with abundance ranging between 80 and 84 %. Prebiotic diet (Pre) increased relative abundance of Firmicutes in shrimp intestine (2 %) compared to the rest of the treatments (0.6 %). Nevertheless, when probiotics were included in the feed (Pro and Syn), a reduction between 3 and 13 % in the relative abundance of Vibrio sp. in shrimp intestine was observed respect to the control treatment, which represent an advantage to control potential pathogens of this genus.


Cancers ◽  
2021 ◽  
Vol 13 (17) ◽  
pp. 4439
Author(s):  
Giacomo Pietrobon ◽  
Marta Tagliabue ◽  
Luigi Marco Stringa ◽  
Rita De Berardinis ◽  
Francesco Chu ◽  
...  

We reviewed the current published literature on the impact of oral microbiota on oral cavity leukoplakia (OLK), aiming at clarifying its role in disease transformation. The analysis unveiled that bacterial richness and diversity in the oral cavity tend to be decreased in OLK compared to healthy controls, with a reduction in the prevalent commensals, such as Streptococci, and elevation of anaerobes. Moreover, Fusobacterium nucleatum, Porphyromonas gingivalis and Prevotella intermedia are recurrent findings, and they already have been linked to periodontal disease. These microbial community changes may also represent a marker for the transition from OLK to oral squamous cell carcinoma. Unfortunately, the reviewed studies present several limitations, making an objective comparison difficult. To overcome these biases, longitudinal studies are necessary.


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