Changes In Bacterial Diversity Research Articles

Cervical microbiota dysbiosis associated with high-risk Human Papillomavirus infection.

High-risk Human Papillomavirus (HR-HPV) genotypes, specifically HPV16 and HPV18, pose a significant risk for the development of cervical intraepithelial neoplasia and cervical cancer. In the multifaceted cervical microenvironment, consisting of immune cells and diverse microbiota, Lactobacillus emerges as a pivotal factor, wielding significant influence in both stabilizing and disrupting the microbiome of the reproductive tract. To analyze the distinction between the cervical microbiota and Lactobacillus-dominant/non-dominant status of HR-HPV and non-infected healthy women, sixty-nine cervical swab samples were analyzed, included 44 with HR-HPV infection and healthy controls. All samples were recruited from Human Papillomavirus-based cervical cancer screening program and subjected to 16s rRNA sequencing analysis. Alpha and beta diversity analyses reveal no significant differences in the cervical microbiota of HR-HPV-infected women, including 16 and 18 HPV genotypes, and those with squamous intraepithelial lesion (SIL), compared to a control group. In this study we identified significantly lower abundance of Lactobacillus mucosae in women with HR-HPV infection compared to the control group. Furthermore, changes in bacterial diversity were noted in Lactobacillus non-dominant (LND) samples compared to Lactobacillus-dominant (LD) in both HR-HPV-infected and control groups. LND samples in HR-HPV-infected women exhibited a cervical dysbiotic state, characterized by Lactobacillus deficiency. In turn, the LD HR-HPV group showed an overrepresentation of Lactobacillus helveticus. In summary, our study highlighted the distinctive roles of L. mucosae and L. helveticus in HR-HPV infections, signaling a need for further research to demonstrate potential clinical implications of cervical microbiota dysbiosis.

Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont

Host-associated microbiota are critical for eukaryotic host functioning, to the extent that hosts and their associated microbial communities are often considered “holobionts”. Most studies of holobionts have focused on descriptive approaches or have used model systems, usually in the laboratory, to understand host-microbiome interactions. To advance our understanding of host-microbiota interactions and their wider ecological impacts, we need experimental frameworks that can explore causation in non-model hosts, which often have highly diverse microbiota, and in their natural ecological setting (i.e. in the field). We used a dominant habitat-forming seaweed, Hormosira banksii, to explore these issues and to experimentally test host-microbiota interactions in a non-model holobiont. The experimental protocols were aimed at trying to disentangle microbially mediated effects on hosts from direct effects on hosts associated with the methods employed to manipulate host-microbiota. This was done by disrupting the microbiome, either through removal/disruption using a combination of antimicrobial treatments, or additions of specific taxa via inoculations, or a combination of thew two. The experiments were done in mesocosms and in the field. Three different antibiotic treatments were used to disrupt seaweed-associated microbiota to test whether disturbances of microbiota, particularly bacteria, would negatively affect host performance. Responses of bacteria to these disturbances were complex and differed substantially among treatments, with some antibacterial treatments having little discernible effect. However, the temporal sequence of responses antibiotic treatments, changes in bacterial diversity and subsequent decreases in host performance, strongly suggested an effect of the microbiota on host performance in some treatments, as opposed to direct effects of the antibiotics. To further test these effects, we used 16S-rRNA-gene sequencing to identify bacterial taxa that were either correlated, or uncorrelated, with poor host performance following antibiotic treatment. These were then isolated and used in inoculation experiments, independently or in combination with the previously used antibiotic treatments. Negative effects on host performance were strongest where specific microbial antimicrobials treatments were combined with inoculations of strains that were correlated with poor host performance. For these treatments, negative host effects persisted the entire experimental period (12 days), even though treatments were only applied at the beginning of the experiment. Host performance recovered in all other treatments. These experiments provide a framework for exploring causation and disentangling microbially mediated vs. direct effects on hosts for ecologically important, non-model holobionts in the field. This should allow for better predictions of how these systems will respond to, and potentially mitigate, environmental disturbances in their natural context.

Common commercially available parasiticides do not cause fatal changes in the microbiome of the dung beetle Onthophagus binodis–a pilot study

ABSTRACT Dung beetles perform vital ecosystem functions, but their survival is threatened by parasiticide use in veterinary practices. Currently, it's unclear if parasiticides directly harm dung beetles or cause damage via secondary effects on crucial microbiome components. We investigated the impact of three commercial parasiticides (P1–levamisole and oxfendazole; P2–abamectin, levamisole and oxfendazole; P3–moxidectin) on Onthophagus binodis dung beetle gut and exoskeleton microbiomes. Dung beetles were subjected to parasiticides mixed with fresh dung for 14 days, and we used 16S rRNA genes to detect bacterial diversity changes. The tested parasiticides didn't alter dung beetle gut communities, but slightly affected the exoskeleton microbiota composition. No mortality difference was observed. Onthophagus binodis microbiomes are mainly diet-influenced, and their exoskeleton is more adaptable than their gut. Our study suggests that adjustable dung beetle microbiomes aren't susceptible to parasiticides due to their innate resilience.

Analysis of changes in bacterial diversity in healthy and bacterial wilt mulberry samples using metagenomic sequencing and culture-dependent approaches.

Mulberry bacterial wilt is a serious destructive soil-borne disease caused by a complex and diverse group of pathogenic bacteria. Given that the bacterial wilt has been reported to cause a serious damage to the yield and quality of mulberry, therefore, elucidation of its main pathogenic groups is essential in improving our understanding of this disease and for the development of its potential control measures. In this study, combined metagenomic sequencing and culture-dependent approaches were used to investigate the microbiome of healthy and bacterial wilt mulberry samples. The results showed that the healthy samples had higher bacterial diversity compared to the diseased samples. Meanwhile, the proportion of opportunistic pathogenic and drug-resistant bacterial flora represented by Acinetobacter in the diseased samples was increased, while the proportion of beneficial bacterial flora represented by Proteobacteria was decreased. Ralstonia solanacearum species complex (RSSC), Enterobacter cloacae complex (ECC), Klebsiella pneumoniae, K. quasipneumoniae, K. michiganensis, K. oxytoca, and P. ananatis emerged as the main pathogens of the mulberry bacterial wilt. In conclusion, this study provides a valuable reference for further focused research on the bacterial wilt of mulberry and other plants.

Human oral mucosa and oral microbiome interactions following supragingival plaque reconstitution in healthy volunteers: a diet-controlled balanced design proof-of-concept model to investigate oral pathologies

ABSTRACT Changes in the oral microbiome may contribute to oral pathologies, especially in patients undergoing cancer therapy. Interactions between oral microbiome and oral mucosa may exacerbate inflammation. We determined whether probiotic-controlled plaque formation could impact proximal oral mucosa gene expression profiles in healthy volunteers. A 3-weeks balanced sample collection design from healthy volunteers (HVs) was implemented. At Week-1 plaques samples and labial mucosa brush biopsies were obtained from HVs in the morning (N = 4) and/or in the afternoon (N = 4), and groups were flipped at Week-3. A fruit yogurt and tea diet were given 2-4hrs before sample collection. mRNA gene expression analysis was completed using RNA-Seq and DESeq2. Bacterial taxa relative abundance was determined by 16S HOMINGS. Bacterial diversity changes and metabolic pathway enrichment were determined using PRIMERv7 and LEfSe programs. Alpha- and beta-diversities did not differ morning (AM) vs. afternoon (PM). The most affected KEGG pathway was Toll-like receptor signaling in oral mucosa. Eighteen human genes and nine bacterial genes were differentially expressed in plaque samples. Increased activity for ‘caries-free’ health-associated calcifying Corynebacterium matruchotii and reduced activity for Aggregatibacter aphrophilus, an opportunistic pathogen, were observed. Microbial diversity was not altered after 8 hours plaque formation in healthy individuals as opposed to gene expression.

94 Changes in Vaginal Microbiome of Beef Cows Enrolled in an Estrous Synchronization Protocol

Abstract Vaginal pH and microbiome have been reported to influence fertility in women. In cattle, estrous synchronization protocols are a great tool to overcome infertility; however, the effects of the hormones administered in the protocol on vaginal microbiome and pH are unknown. A total of 24 cows were enrolled in the 7-d Co-Synch + controlled internal drug release (CIDR) protocol and had individual vaginal flushes collected during the handling events of the protocol on days 0, 7 and on day 10 at timed-artificial insemination (TAI). Flushes were used for pH analysis and DNA extraction. Extracted DNA was submitted to analysis by whole genome shotgun sequencing. Pregnancy status was assessed by ultrasonography 35 days after TAI. Firmicutes was the most abundant phylum, followed by Proteobacteria, and Actinobacteria for all collection days. Bacteria from the Clostridia genus were the most abundant in all samples. Greater alpha Shannon diversity (within sample diversity) was observed for pregnant animals on day -10 compared with non-pregnant animals at the phylum, class, and order (P < 0.01), as well as family, and genus level (P < 0.001). Overall, Shannon diversity was decreased on day 7 compared with day 0 (P < 0.05 at class and order level; P< 0.01 at genus and family level) and was greater at TAI compared with day 7 (P < 0.01 at the phylum, class, and order level; P < 0.001 at family and genus level). No differences were observed for Shannon diversity between samples from D0 and TAI (P > 0.05). No correlations between Shannon diversity were observed in relation to vaginal pH (P > 0.1). Bray-Curtis analysis (between sample diversity) revealed clustering by day (P < 0.05 at the order, family, and genus level) and a tendency (0.1 < P < 0.05) at the phylum and class level. In conclusion, greater fertility was observed for animals with greater within sample diversity prior to protocol initiation. Furthermore, vaginal bacterial diversity changes throughout the protocol, with decreased diversity observed on day 7 of the protocol, but restored diversity on day0 at TAI.

Effect of eucalyptus saponin and sophorolipid amendment on soil and sediment microbial communities and seed germination: potential application for PAH bioremediation

PurposeThe potential toxic effects due to the application of sophorolipid and the novel saponin biosurfactant extracted from the leaves of Eucalyptus camaldulensis for the purpose of bioremediating PAH-contaminated soils and sediments were studied.MethodsThe phytotoxic effects of sophorolipid and eucalyptus saponin were determined based on the seed germination assays carried out using the seeds of Lactuca sativa L and compared with commonly used rhamnolipid and Tween 20 surfactants. Further, biosurfactant-induced changes in soil/sediment bacterial structure and diversity were investigated by conducting Miseq amplicon sequencing of the bacterial genes.ResultsGermination indices (GI) demonstrated the non-phytotoxic effects (GI > 80%) of saponin and sophorolipid biosurfactants (100–500 mg/L), while rhamnolipid demonstrated greater phytotoxicity than Tween 20 at high concentrations (500 mg/L). Saponin-amended soil resulted in greater bacterial diversity and richness compared to controls, while sophorolipid produced the opposite effect. These significant variations were not observed in sediment samples. Incubation of biosurfactants for 20 and 40 days did not result in significant changes in bacterial diversity and structure in any of the samples. Increased abundance of some of the PAH-degrading bacteria was noted at OTU level, in the presence of saponin and sophorolipid. Saponin had less impact on native soil/sediment bacteria relative to sophorolipid based on the prevalence of the significantly shifted OTUs.ConclusionAs saponin and sophorolipid were shown to have no adverse impacts on the microbiome, and non-phytotoxic effects, their sustainable applications to remediate PAH-contaminated soils and sediments can be recommended.

Different changes of bacterial diversity and soil metabolites in tea plants-legume intercropping systems.

As an essential agroforestry, intercropping legumes can improve the physical, chemical, and biological fertility of the soil in tea plantations. However, the effects of intercropping different legume species on soil properties, bacterial communities, and metabolites remain elusive. In this study, the 0-20cm and 20-40cm soils of three planting patterns (T1: tea plants/mung bean intercropping, T2: tea plants/adzuki bean intercropping, T3: tea plants/mung bean and adzuki bean intercropping) were sampled to explore the diversity of the bacterial community and soil metabolites. The findings showed that, as compared to monocropping, intercropping systems had greater concentrations of organic matter (OM) and dissolved organic carbon (DOC). Notably, pH values were significantly lower, and soil nutrients increased in intercropping systems compared with monoculture in 20-40cm soils, especially in T3. In addition, intercropping resulted in an increased relative abundance of Proteobacteria but a decreased relative abundance of Actinobacteria. 4-methyl-Tetradecane, acetamide, and diethyl carbamic acid were key metabolites mediating the root-microbe interactions, especially in tea plants/adzuki intercropping and tea plants/mung bean, adzuki bean mixed intercropping soils. Co-occurrence network analysis showed that arabinofuranose, abundant in tea plants and adzuki bean intercropping soils, showed the most remarkable correlation with the soil bacterial taxa. Our findings demonstrate that intercropping with adzuki beans is better at enhancing the diversity of soil bacteria and soil metabolites and is more weed-suppressing than other tea plants/legume intercropping systems.

Insights into whereby raw wheat Qu contributes to the flavor quality of Huangjiu during brewing

The influence of raw wheat Qu (RWQ) on the flavor quality of Huangjiu was investigated in this study. When used as a single saccharification starter, RWQ showed poor fermentation performance during Huangjiu brewing. However, as a co-fermentation starter with cooked wheat Qu (CWQ), RWQ considerably enhanced flavor quality of the resultant Huangjiu by promoting the accumulation of fatty acid ethyl esters (FAEEs) with odor activity values exceeding 1. Based on dynamic changes in bacterial diversity during Huangjiu brewing, a three-stage fermentation mode was identified for the first time. During stage III (5–15 d), the relative proportions of predominant genera Weissella and Lactococcus, which were strongly associated with the synthesis of FAEEs, were significantly adjusted by the co-fermentation of RWQ with CWQ. Moreover, co-fermentation of RWQ with CWQ reduced the bacterial diversity of Huangjiu samples, and this was strongly related to the total acidity (R2 = 0.867) and ethanol (R2 = 0.802) content. Therefore, the proportions of predominant bacteria were changed by RWQ, which affected bacterial diversity and enhanced the flavor quality of Huangjiu. Controlling environmental factors during brewing is suggested as a feasible way to regulate the proportions of bacterial genera, thereby regulating the flavor characteristic in the resultant wine.

Assessment of the human placental microbiome in early pregnancy.

Bacteria derived from the maternal circulation have been suggested to seed the human placenta during development leading to an intrinsic placental microbiome. This concept has become controversial as numerous studies suggest that the apparent placental microbiome is mostly, if not completely, comprised of contaminants. If the maternal circulation seeds the placenta then there should be an increase in abundance and diversity of detectable bacteria with onset of maternal perfusion of the placenta around 10 weeks gestational age; however, if only contaminants are present then there should be no significant evolution of the placental microbiome with increasing gestational age. This pilot study addresses whether bacterial abundance and diversity increase in human placenta and whether there is an associated shift in the immunophenotype of the decidual immune cell complement before and after initiation of placental perfusion. Human placental and decidual tissue from 5 to 19 weeks gestational age, handled aseptically to minimize contamination, is assessed by quantitative 16S polymerase chain reaction (PCR), 16S gene sequencing, and immunological flow cytometry studies. A weak positive correlation between placental bacterial abundance and gestational age is identified but is not statistically significant. No significant changes in bacterial diversity are found with increasing gestational age. The proportion of decidual activated memory T helper cells increases with gestational age but no change was observed in other lymphocyte subsets. This pilot study does not strongly support bacterial colonization of the placenta after initiation of maternal perfusion; however, the minor trends towards increases in bacterial abundance and activated memory T helper cells may represent an early stage of this process. Additional investigations in larger cohorts are warranted.

Changes in bacterial diversity, co-occurrence pattern, and potential pathogens following digestate fertilization: Extending pathogen management to field for anaerobic digestion of livestock manure

Digestate can spread pathogens into agroecosystem, posing serious threats to public health. However, the effect of digestate fertilization on digestate- or soil-borne pathogens has not been fully explored. Herein, two settings of microcosm experiment were performed with arable soil and digestate collected at two sites (Beilangzhong or Shunyi) to dissect the succession of the total and potential pathogenic bacterial communities following digestate fertilization. Each experimental setting consisted of three treatments, including digestate aerobically incubated in sterilized soil, and soil amended with sterilized or non-sterilized digestate. Digestate-borne potential pathogenic bacteria were enriched after the aerobic incubation, with Streptococcus sobrinus in the Beilangzhong setting, and Escherichia coli and Enterococcus faecium in the Shunyi setting. Potential soil-borne pathogenic bacteria, such as Acinetobacter lowffii and Pseudomonas fluorescens, were stimulated by the sterilized digestate in the Shunyi setting. Interestingly, S. sobrinus, E. coli, and Ent. faecium did not increase when digestate was amended into the non-sterilized soil, suggesting that soil microorganisms can inhibit the resurgence of these digestate-borne pathogens. A large-scale survey further revealed that organic fertilization exerted a site-dependent effect on different species of potential pathogen, but it did not enrich the total relative abundance of potential pathogenic bacteria in soils. Collectively, these results highlight that pathogen management of anaerobic digestion of livestock manure needs to be extended from anaerobic reactor to field.

尖峰岭热带天然林不同土层细菌群落多样性和组成的海拔变异规律

PDF HTML阅读 XML下载 导出引用 引用提醒 尖峰岭热带天然林不同土层细菌群落多样性和组成的海拔变异规律 DOI: 10.5846/stxb202203090570 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金项目（32171643，U1703332） The altitudinal patterns of bacterial community diversity and composition at different soil depths in Jianfengling mountain tropical forest Author: Affiliation: Fund Project: The National Natural Science Foundation of China (General Program, Key Program, Major Research Plan) 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:土壤微生物群落结构沿海拔梯度的变异是微生物生物地理学分异和群落空间分布的重要内容，然而，热带森林土壤微生物多样性及其群落特征的海拔模式尚不明确。研究海南省尖峰岭自然保护区0-20cm和20-40cm土壤细菌多样性和群落组成沿海拔梯度（400-1410m）的变化及其与环境因子的关系。结果表明：在0-20cm土壤微生物生物量碳、生物量氮和生物量磷随海拔升高（峰顶降低）而增加，20-40cm土壤微生物生物量碳、生物量氮和生物量磷随海拔升高呈先升高后降低趋势；整体上，变形菌门、放线菌门、酸杆菌门、拟杆菌门、厚壁菌门在0-20cm中占优势，丰度总和占该层细菌总量的88.17%；变形菌门、放线菌门、酸杆菌门、厚壁菌门、绿弯菌门在20-40cm中占优势，丰度总和占该层细菌总量的90.82%；随海拔增加，0-20cm细菌多样性线性减少，20-40cm细菌多样性变化不显著；沿海拔梯度，0-20cm细菌群落组成可分为低（409-1018m），中（1018-1357m）和高（1410m）三个海拔聚集群落，20-40cm细菌群落组成随海拔无显著性变化；两土层细菌多样性与土壤pH显著正相关，土壤细菌群落组成在0-20cm主要受年均温度和pH影响，20-40cm受年均温度和土壤有机碳影响；根据Bray-Curtis指数，0-20cm和20-40cm土壤细菌相似性随地理距离的增加逐渐降低，细菌群落相似性随环境距离的增大也逐渐降低。总之，尖峰岭土壤细菌多样性和群落组成的海拔格局受土壤深度影响，且驱动细菌群落组成变化的因素在土层间不同，暗示在未来气候变化背景下，热带森林0-20cm和20-40cm土壤微生物群落可能具有不同的响应机制。 Abstract:The variation of soil microbial community structure along the altitudinal gradient is an important content of microbial biogeographic differentiation and community spatial distribution. However, the altitudinal pattern of soil microbial diversity and its community characteristics in tropical forests is not clear. This paper studied the changes of bacterial diversity and community composition and their relationship with environmental factors in 0-20cm and 20-40cm soil depths along the altitudinal gradient (400-1410 m) in Jianfengling Nature Reserve, Hainan Province. The results showed that the soil microbial biomass carbon, biomass nitrogen and biomass phosphorus increased with the elevation of 0-20cm (the peak decreased), and the soil microbial biomass carbon, biomass nitrogen and biomass phosphorus increased first and then decreased with the elevation of 20-40cm. On the whole, Proteobacteria, Actinomycetes, Acidobacteria, Bacteroidetes and Firmicutes are dominant in 0-20cm, and the total abundance accounts for 88.17% of the total bacteria in this layer; Proteobacteria, Actinomycetes, Acidobacteria, Firmicutes and Chloroflexi are dominant in 20-40cm, and the total abundance accounts for 90.82% of the total bacteria in this layer. With the increase of altitude, the bacterial diversity decreased linearly in 0-20cm, and that of 20-40cm did not change significantly. The bacterial community composition of 0-20cm can be divided into three communities at low altitude (409-1018 m), medium altitude (1018-1357 m), and high altitude (1410 m) and the bacterial community composition of 20-40cm has no significant change with altitude. There was a significantly positive correlation between bacterial diversity and soil pH in the two soil depths. The composition of soil bacterial community was mainly affected by mean annual temperature and pH at 0-20cm, and by mean annual temperature and soil organic carbon at 20-40cm. According to the Bray Curtis index, the similarity of bacteria in 0-20cm and 20-40cm soil depths decreased with the increase of geographical distance, and the similarity of bacterial community also decreased with the increase of environmental distance. In a word, the altitudinal pattern of soil bacterial diversity and community composition in Jianfengling is affected by soil depth, and the factors driving the change of bacterial community composition are different among soil depths. It is suggested that the soil microbial communities in 0-20cm and 20-40cm of tropical forests may have different response mechanisms under the background of future climate change. 参考文献 相似文献 引证文献

The relationship between bacterial dynamics, phenols and antioxidant capability during compressed white tea storage

The quality and efficacy of compressed white tea (CWT) can be affected by the bacterial community during its long-term storage. However, it is not clear how bacteria affect the CWT storage process. In this study, 16S rDNA was used to identify the composition and dynamic changes of bacterial community during CWT storage, and chemometrics methods were used to evaluate the relationship between the bacterial community and phenol/antioxidant indices. A total of 31 bacterial phyla and 764 bacterial genera were identified during CWT storage, and their diversity decreased significantly at first and then increased significantly (P < 0.05). The 10th year of storage was the key period for changes in bacterial diversity and dominant phyla and genera. The prediction of phenotype and function revealed that these changes were dominated by aerobic bacteria, which could involved in 264 metabolic pathways, including flavonoids metabolism. Chemometric analysis verified that seven core functional bacteria promoted the decline of eight phenols during CWT storage, thus reducing antioxidant capability. In conclusion, this study reveals that the bacteria in CWT affect its antioxidant capability by altering the phenol content during storage. In addition, 29 biomarkers during CWT storage were screened, which accumulated uniquely in different storage years.

Parkinson’s disease and the Interaction of Photobiomodulation, the Microbiome, and Antibiotics: A Case Series A Case Series

It is apparent that there is a close association between the gut microbiome and Parkinson’s disease, with many patients having gut symptoms. Gut microbiome dysfunction may be related to instigation and progression of Parkinson’s disease in many patients. There is also evidence that disrupting the gut microbiome, such as with antibiotics, can increase the risk of developing Parkinson’s disease. Photobiomodulation has the potential to alleviate the symptoms of Parkinson’s disease in both animal models and in humans and has also been shown to alter the microbiome in a mouse model. Here we assessed the interaction between photobiomodulation and the gut microbiome in four people with Parkinson’s disease, three of whom had participated in clinical trials and two of whom were prescribed antibiotics during the photobiomodulation treatment. Patients were treated three times per week using infrared laser treatment to the abdomen and neck with or without LED treatment to the head. Gastrointestinal symptoms were assessed prior to treatment and after 4 weeks and 12 weeks of photobiomodulation therapy and microbiome status was assessed in 3 of the 4 patients. Outcome measures included motor signs and patient-reported non-motor symptoms including symptoms of constipation/diarrhea/gastric motility, and abdominal pain, as well as phylogenetic analysis of microbiome diversity. Participants in this case series were seen as good responders to photobiomodulation treatment, with improvements in motor signs and non-motor symptoms. Gastrointestinal symptoms, including irritable bowel symptoms were improved, and microbiome analysis indicated a generally positive change in bacterial diversity. Antibiotic use during the photobiomodulation treatment had a negative effect on motor and non-motor improvements, as well as disrupting the microbiome. Results of this study suggest that photobiomodulation may have a role in the improvement of the gut microbiome, which could be advantageous in the treatment of Parkinson’s disease, considering the strong microbiome-gut-brain-axis in the disease.

Changes in bacterial diversity and community structure in drinking water distribution system revealed by high throughput sequencing.

For microbiological management of water quality, it is important to identify bacteria and to understand the community structure. To analyze the community structure during water purification and distribution, we selected a distribution system in which water from other water treatment facilities was not mixed with the target water. Changes in the bacterial community structure during treatment and distribution processes in a slow filtration water treatment facility were analyzed using 16S rRNA gene amplicon sequencing with a portable sequencer MinION. The microbial diversity was reduced by chlorination. The genus level diversity increased during distribution and this diversity was maintained through to the terminal tap water. Yersinia and Aeromonas were dominant in the intake water, and Legionella was dominant in the slow sand filtered water. Chlorination greatly reduced the relative abundance of Yersinia, Aeromonas, and Legionella, and these bacteria were not detected in the terminal tap water. Sphingomonas, Starkeya and Methylobacterium became dominant in the water after chlorination. These bacteria could be used as important indicator bacteria to provide useful information for microbiological control in drinking water distribution systems.

Bovine Escherichia coli Mastitis and Effects on Milk Microbiota

Escherichia coli is a microorganism that is found in the normal intestinal microbiota of humans and warm-blooded animals, causing intestinal or extra-intestinal infections. Many pathogenic E. coli strains can cause diarrhea, septicemia, neonatal meningitis, mastitis, urogenital system infections and various intra-abdominal, lung, soft tissue and skin infections in pets. Determining the genotypic and phenotypic characteristics of Escherichia coli strains isolated from animals is very important for the prevention of infections caused by E. coli. In recent years, a new animal pathotype mammary pathogenic E. coli (MPEC), which causes mammary gland infections in animals has been included in the extraintestinal pathogenic E. coli group. The fact that approximately %25-%35 of the use of antimicrobials in the treatment of Gram-negative agents is unsuccessful indicates that the use of correct diagnostic tools should take place in routine before etiological diagnosis. Profiles in bovine milk with mastitis suggest that clinical mastitis is associated with dysbacteriosis and that the microbial community in an intact mammary gland helps prevent intramammary infection. In this review, the change in bacterial diversity of milk microbiota due to antimicrobial use in E. coli-induced mastitis cases is discussed together with current studies.

A quality improvement study on the relationship between intranasal povidone-iodine and anesthesia and the nasal microbiota of surgery patients.

The composition of the nasal microbiota in surgical patients in the context of general anesthesia and nasal povidone-iodine decolonization is unknown. The purpose of this quality improvement study was to determine: (i) if general anesthesia is associated with changes in the nasal microbiota of surgery patients and (ii) if preoperative intranasal povidone-iodine decolonization is associated with changes in the nasal microbiota of surgery patients. One hundred and fifty-one ambulatory patients presenting for surgery were enrolled in a quality improvement study by convenience sampling. Pre- and post-surgery nasal samples were collected from patients in the no intranasal decolonization group (control group, n = 54). Pre-decolonization nasal samples were collected from the preoperative intranasal povidone-iodine decolonization group (povidone-iodine group, n = 97). Intranasal povidone-iodine was administered immediately prior to surgery and continued for 20 minutes before patients proceeded for surgery. Post-nasal samples were then collected. General anesthesia was administered to both groups. DNA from the samples was extracted for 16S rRNA sequencing on an Illumina MiSeq. In the control group, there was no evidence of change in bacterial diversity between pre- and post-surgery samples. In the povidone-iodine group, nasal bacterial diversity was greater in post-surgery, relative to pre-surgery (Shannon's Diversity Index (P = 0.038), Chao's richness estimate (P = 0.02) and Inverse Simpson index (P = 0.027). Among all the genera, only the relative abundance of the genus Staphylococcus trended towards a decrease in patients after application (FDR adjusted P = 0.06). Abundant genera common to both povidone-iodine and control groups included Staphylococcus, Bradyrhizobium, Corynebacterium, Dolosigranulum, Lactobacillus, and Moraxella. We found general anesthesia was not associated with changes in the nasal microbiota. Povidone-iodine treatment was associated with nasal microbial diversity and decreased abundance of Staphylococcus. Future studies should examine the nasal microbiota structure and function longitudinally in surgical patients receiving intranasal povidone-iodine.

Phytomanagement of a Lead-Polluted Shooting Range Using an Aromatic Plant Species and Its Effects on the Rhizosphere Bacterial Diversity and Essential Oil Production.

This field study aimed to assess the baseline conditions of a long-term shooting range in Argentina polluted with 428 mg kg-1 lead (Pb) to evaluate the establishment and development of Helianthus petiolaris plants and address the efficacy of the phytomanagement strategy through: (i) element accumulation in plant tissues; (ii) rhizosphere bacterial diversity changes by Illumina Miseq™, and (iii) floral water and essential oil yield, composition, and element concentration by GC-MS and ICP. After one life cycle growing in the polluted sites, in the roots of Helianthus petiolaris plants, Pb concentration was between 195 and 304 mg kg-1 Pb. Only a limited fraction of the Pb was translocated to the aerial parts. The predominance of the genus Serratia in the rhizosphere of Helianthus petiolaris plants cultivated in the polluted sites and the decrease in the essential oil yield were some effects significantly associated with soil Pb concentration. No detectable Pb concentration was found in the floral water and essential oil obtained. Extractable Pb concentration in the soil reduced between 28% and 45% after the harvest.

Effects of different amoxicillin treatment durations on microbiome diversity and composition in the gut

Antibiotics seize an effect on bacterial composition and diversity and have been demonstrated to induce disruptions on gut microbiomes. This may have implications for human health and wellbeing, and an increasing number of studies suggest a link between the gut microbiome and several diseases. Hence, reducing antibiotic treatments may be beneficial for human health status. Further, antimicrobial resistance (AMR) is an increasing global problem that can be counteracted by limiting the usage of antibiotics. Longer antibiotic treatments have been demonstrated to increase the development of AMR. Therefore, shortening of antibiotic treatment durations, provided it is safe for patients, may be one measure to reduce AMR. In this study, the objective was to investigate effects of standard and reduced antibiotic treatment lengths on gut microbiomes using a murine model. Changes in the murine gut microbiome was assessed after using three different treatment durations of amoxicillin (3, 7 or 14 days) as well as a control group not receiving amoxicillin. Fecal samples were collected before and during the whole experiment, until three weeks past end of treatment. These were further subject for 16S rRNA Illumina MiSeq sequencing. Our results demonstrated significant changes in bacterial diversity, richness and evenness during amoxicillin treatment, followed by a reversion in terms of alpha-diversity and abundance of major phyla, after end of treatment. However, a longer restitution time was indicated for mice receiving amoxicillin for 14 days, and phylum Patescibacteria did not fully recover. In addition, an effect on the composition of Firmicutes was indicated to last for at least three weeks in mice treated with amoxicillin for 14 days. Despite an apparently reversion to a close to original state in overall bacterial diversity and richness, the results suggested more durable changes in lower taxonomical levels. We detected several families, genera and ASVs with significantly altered abundance three weeks after exposure to amoxicillin, as well as bacterial taxa that appeared significantly affected by amoxicillin treatment length. This may strengthen the argument for shorter antibiotic treatment regimens to both limit the emergence of antibiotic resistance and risk of gut microbiome disturbance.

Bacterial diversity changes in response to an altitudinal gradient in arid and semi-arid regions and their effects on crops growth

The microbiome of soil has a fundamental role in maintaining the health of soil and plants. While the diversity of microbes is one of the most important factors in the environment, little is known about the effects of elevation on the microbiome and the impact of the affected microbiome on plants. The main goal of this study is to expand our knowledge of what happens to the soil bacterial community along an altitudinal gradient and investigate their possibly different impacts on plant growth. Bacteria from soils at various altitudes have been isolated, characterized, and identified by Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) to determine the effects of an elevational gradient on the microbiome and plant growth. Furthermore, their effects have been investigated by isolates assessment on maize, wheat, and canola. Based on our results, higher altitude results in a higher diversity of the microbiome and lower bacteria biomass. Bacillus cereus is found in abundance in arid and semi-arid samples. Interestingly, enhanced diversity in higher altitudes shows similarity in response to environmental stress and tolerates these factors well. Furthermore, the inoculation of these bacteria could enhance the overall growth of plants. We prove that bacterial communities could change their biomass and diversity in response to altitude changes. These indicate evolutionary pressure as these bacteria could tolerate stress factors well and have a better relationship with plants.