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Frontiers in Microbiology 2020Intestinal microbiota plays an important role in the health of animals. However, little is known about the gut microbiota in Ningxiang pigs. Thus, we investigated how...
Intestinal microbiota plays an important role in the health of animals. However, little is known about the gut microbiota in Ningxiang pigs. Thus, we investigated how dietary supplementation with different ε-polylysine concentrations (0, 20, 40, 80, and 160 ppm) affected the ileal microbiota in Ningxiang pigs using a replicated 5 × 5 Latin square method. Each experimental period included 10 days for diet adaptation, 3 days for feces collection and 2 days for digesta collection. The ileal contents were collected and used for sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The results revealed that ε-polylysine significantly decreased the digestibility of crude protein and crude fiber, as well as the utilization of metabolizable energy ( < 0.05). The relative abundances of 19 bacterial genera significantly increased, while those of 26 genera significantly decreased ( < 0.05). In addition, ε-polylysine increased the abundance of some bacteria (e.g., , , and lactic acid bacteria) and inhibited some other bacteria (e.g., , , , , , , , and ). Furthermore, based on the 16S rRNA gene data and data from the precalculated GreenGenes database, bacterial communities in the ileal contents exhibited enhanced functional maturation, including changes in the metabolism of carbohydrates, amino acids (e.g., alanine, lysine, tryptophan, cysteine, and methionine), cofactors, and vitamins (e.g., biotin, thiamine, and folate), as well as in the activity of the insulin signaling pathway. This study suggests that ε-polylysine may influence the utilization of feed nutrients by Ningxiang pigs, including proteins, lipids, metabolizable energy, and fiber, by regulating the gut microbiota.
PubMed: 33312165
DOI: 10.3389/fmicb.2020.544097 -
Frontiers in Microbiology 2020Osimertinib contributes to the higher efficacy and few intestinal side effects in non-small cell lung cancer (NSCLC) patients with T790M mutation. Previous studies has...
Osimertinib contributes to the higher efficacy and few intestinal side effects in non-small cell lung cancer (NSCLC) patients with T790M mutation. Previous studies has reported that intestinal microbiota play important roles in drug efficacy and toxicity. However, we have known less about the changes of intestinal microbiota in response to osimertinib therapy. In this pilot study, we used longitudinal sampling with 6 weeks sampling collection intervals for about 1 year to model intestinal microbial changes based on the 16S rRNA genes sequencing in fecal samples from NSCLC patients in response to osimertinib therapy. The results showed that there was no significantly different on the intestinal microbial composition at the phylum, family, and genus level among NSCLC patients with different treatment cycles ( > 0.05). There were no significant differences in alpha diversity characterized by the richness, Shannon diversity, and phylogenetic diversity based on the Welch's -test among NSCLC patients in response to osimertinib therapy ( > 0.05). However, the dissimilarity test and principal coordination analysis showed a few differences among NSCLC patients. The intestinal microbial markers were changed in post-therapy (, , and ) compared to that in pre-therapy (). Furthermore, the phylogenetic molecular ecological networks (MENs) were influenced by osimertinib therapy based on the module number, link number, and module taxa composition of the first six groups. Overall, it indicated that osimertinib therapy changed the intestinal microbiota to some extent, though not completely. In all, this pilot study provides an understanding of changes of intestinal microbiota from NSCLC patients in response to osimertinib therapy. No complete changes in intestinal microbiota seem to be closely linked with the few intestinal side effects and higher efficacy in response to osimertinib therapy.
PubMed: 33240237
DOI: 10.3389/fmicb.2020.583525 -
New Microbes and New Infections Sep 2020gen. nov., sp. nov. strain Marseille-P3926 is a new species from the phylum and the family that was isolated from a human faeces sample. Genome was 1 978 908 bp...
gen. nov., sp. nov. strain Marseille-P3926 is a new species from the phylum and the family that was isolated from a human faeces sample. Genome was 1 978 908 bp long with a 41.1 G + C content. The closest species based on 16S ribosomal RNA was DSM 10022 with 90.8% sequence similarity. Considering phenotypic features, 16S rRNA sequence and comparative genome studies, we proposed Marseille- P3926 as the strain type of gen. nov., sp. nov.
PubMed: 32944256
DOI: 10.1016/j.nmni.2020.100720 -
Mikrobiyoloji Bulteni Jul 2020Gram-positive anaerobic cocci (GPAC), a large group of anaerobic bacteria, are the members of the normal microbiota that colonizes the skin and mucosal surfaces of the...
Gram-positive anaerobic cocci (GPAC), a large group of anaerobic bacteria, are the members of the normal microbiota that colonizes the skin and mucosal surfaces of the human body. However, in case of a wound or when the host becomes immunocompromised, GPAC can cause invasive and most frequently mixed infections. GPAC are the second most frequently isolated bacteria in anaerobic infections. Although the studies are limited, GPAC have been reported to develop resistance to antimicrobial drugs. The resistance of the pathogens to the antimicrobials and improper therapy can cause poor clinical outcomes. Therefore, monitoring of the resistance trends of regional clinically important anaerobic bacteria periodically is recommended. In our study, we aimed to determine the antimicrobial susceptibility profiles of clinically important GPAC. A total of 100 non-duplicated pathogenic GPAC isolates were collected from Marmara University Hospital between 2013 and 2015. The isolates were identified by using conventional methods, "matrix-assisted laser desorption ionization-time of flight mass spectrometry system (MALDI-TOF MS)" (VITEK MS; v3.0, bioMerieux, France) and 16S rRNA gene sequencing. Antimicrobial susceptibility test was carried out by the agar dilution method according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. The following antimicrobials were tested: penicillin, amoxicillin/ clavulanic acid (AMC), cefoxitin, meropenem, clindamycin, erythromycin, tetracycline, tigecycline, chloramphenicol, moxifloxacin and metronidazole. The minimum inhibitory concentration (MIC) results were interpreted according to the breakpoints described by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Breakpoints recommended by CLSI for cefoxitin, tetracycline and moxifloxacin, and breakpoint recommended by Food and Drug Administration (FDA) for tigecycline were used since there were no EUCAST breakpoints for these antimicrobials. MIC50 and MIC90 values were determined for erythromycin since the breakpoint was not described by EUCAST, CLSI or FDA guidelines. The identification results showed that the strains (n= 100) consisted of five different GPAC genus; Parvomonas (40%), Finegoldia (34%), Peptoniphilus (14%), Peptostreptococcus (10%) and Anaerococcus (1%). All of the organisms were susceptible to meropenem, tigecycline and metronidazole. The isolates were highly susceptible to penicillin, AMC, cefoxitin, and chloramphenicol, since the resistance rates against these antimicrobials were 5% or less. The resistance rates against clindamycin, tetracycline and moxifloxacin were 14%, 31% and 24%, respectively. In total, 11% of the isolates were multidrug resistant. Metronidazole and tigecycline displayed high in vitro activity against GPAC and both are appropriate antimicrobials for the selection of empiric therapy. The effectiveness of meropenem was also found high, but it was observed that this antimicrobial would be more appropriate to use in the treatment of severe mixed infections accompanied by other microorganisms with the resistance potential. Detection of penicillin and AMC resistant isolates, which are frequently used in the treatment of GPAC infection, requires periodic monitoring of the antimicrobial susceptibility patterns of GPAC. The high rates of resistance against clindamycin, tetracycline and moksifloxacin indicated that these antimicrobials should not be used for empirical treatment of infections without prior antimicrobial susceptibility testing. This study is one of the largest susceptibility studies specifically carried out on GPAC to date in Turkey. We believe that our results will provide good surveillance data both for our hospital and our country.
Topics: Anaerobiosis; Anti-Bacterial Agents; Drug Resistance, Bacterial; Gram-Positive Cocci; Humans; Microbial Sensitivity Tests; RNA, Ribosomal, 16S; Turkey
PubMed: 32755517
DOI: 10.5578/mb.69556 -
Scientific Reports Jul 2020The vaginal microbiota of healthy women typically has low diversity, which increases after perturbations. Among these, lifestyle associated with certain sexual and...
The vaginal microbiota of healthy women typically has low diversity, which increases after perturbations. Among these, lifestyle associated with certain sexual and antimicrobial practices may be associated with higher diversity. To test this hypothesis, we characterized the vaginal microbiota in the cervicovaginal and introital sites in sexually active Amerindians (N = 82) spanning urbanization, and in urban mestizos (N = 29), in the Venezuelan Amazonas. HPV status was also considered. Sampling was performed in an urban gradient from remote villages to a town, and women were individually classified by the degree of urbanization (low, medium, and high). Amerindian cervicovaginal and introital microbiota diversity were not associated with major changes in urbanization or ethnicity. There was a non-significant trend of increased diversity with urbanization, with a few taxa found overrepresented in urban Amerindians (Brevibacterium linens and Peptoniphilus lacrimalis) or mestizos (Mobiluncus mulieris and Prevotella sp.). Among all women, cervicovaginal and introital samples clustered, respectively, in four and two community state types (CSTs), where most profiles were dominated by Lactobacillus iners, Gardnerella vaginalis or were highly diverse profiles. HPV status did not associate with microbial diversity. In conclusion, no association was found between urban level and the vaginal microbiome in Amerindian women, and little difference was found between ethnicities. L. iners and high diversity profiles, associated with vaginal health outcomes, prevail in these populations.
Topics: Biodiversity; Cervix Uteri; Cluster Analysis; Female; Geography; Humans; Microbiota; Papillomavirus Infections; Urbanization; Vagina; Venezuela; American Indian or Alaska Native
PubMed: 32719372
DOI: 10.1038/s41598-020-69111-x -
The Journals of Gerontology. Series A,... Jun 2020Emerging links between gut microbiota and diseases of aging point to possible shared immune, metabolic, and cellular damage mechanisms, operating long before diseases...
Emerging links between gut microbiota and diseases of aging point to possible shared immune, metabolic, and cellular damage mechanisms, operating long before diseases manifest. We conducted 16S rRNA sequencing of fecal samples collected from a subsample (n = 668) of Add Health Wave V, a nationally representative longitudinal study of adults aged 32-42. An overlapping subsample (n = 345) included whole-blood RNA-seq. We examined associations between fecal taxonomic abundances and dried blood spot-based markers of lipid and glucose homeostasis and C-reactive protein (measured in Wave IV), as well as gene expression markers of inflammation, cellular damage, immune cell composition, and transcriptomic age (measured in Wave V), using Bayesian hierarchical models adjusted for potential confounders. We additionally estimated a co-abundance network between inflammation-related genes and bacterial taxa using penalized Gaussian graphical models. Strong and consistent microbiota associations emerged for HbA1c, glucose, C-reactive protein, and principal components of genes upregulated in inflammation, DNA repair, and reactive oxygen species, with Streptococcus infantis, Pseudomonas spp., and Peptoniphilus as major players for each. This pattern was largely echoed (though attenuated) for immunological cell composition gene sets, and only Serratia varied meaningfully by transcriptomic age. Network co-abundance indicated relationships between Prevotella sp., Bacteroides sp., and Ruminococcus sp. and gut immune/metabolic regulatory activity, and Ruminococcus sp, Dialister, and Butyrivibrio crossotus with balance between Th1 and Th2 inflammation. In conclusion, many common associations between microbiota and major physiologic aging mechanisms are evident in early-mid adulthood and suggest avenues for early detection and prevention of accelerated aging.
Topics: Adolescent; Adult; Age Factors; Aging; Bayes Theorem; Biomarkers; Feces; Female; Gastrointestinal Microbiome; Humans; Inflammation; Longitudinal Studies; Male; Young Adult
PubMed: 32421783
DOI: 10.1093/gerona/glaa122 -
Cancer Medicine Jun 2020While the importance of commensal microbes in vaginal health is well appreciated, little is known about the effects of gynecological cancer (GynCa) and radiation therapy...
BACKGROUND
While the importance of commensal microbes in vaginal health is well appreciated, little is known about the effects of gynecological cancer (GynCa) and radiation therapy (RT) on the vaginal microbiome (VM) of postmenopausal women.
METHODS
We studied women with GynCa, pre- (N = 65) and post-RT (N = 25) and a group of healthy controls (N = 67) by sequencing the V4 region of the 16S rRNA gene from vaginal swabs and compared the diversity and composition of VMs between the three groups accounting for potential confounding factors in multivariate analysis of variance.
RESULTS
Comparisons of cancer vs healthy groups revealed that Lactobacillus and Bifidobacterium have significantly higher relative abundance in the healthy group, while the cancer group was enriched in 16 phylogroups associated with bacterial vaginosis (BV) and inflammation, including Sneathia, Prevotella, Peptoniphilus, Fusobacterium, Anaerococcus, Dialister, Moryella, and Peptostreptococcus. In our sample, RT affected the α-diversity and correlated with higher abundance of typically rare VM species, including several members of the Lacnospiraceae family, a taxon previously linked to vaginal dysbiosis. In addition to cancer and treatment modalities, age and vaginal pH were identified as significant parameters that structure the VM.
CONCLUSIONS
This is among the first reports identifying VM changes among postmenopausal women with cancer. RT alone seems to affect several phylogroups (12 bacterial genera), while gynecological cancer and its treatment modalities are associated with even greater significant shifts in the vaginal microbiota including the enrichment of opportunistic bacterial pathogens, which warrants further attention.
Topics: Bacteria; Case-Control Studies; Female; Follow-Up Studies; Genital Neoplasms, Female; Humans; Middle Aged; Prognosis; RNA, Ribosomal, 16S; Radiotherapy; Vagina
PubMed: 32237205
DOI: 10.1002/cam4.3027 -
Cureus Feb 2020Abscess of the corpus cavernosum is a condition that occurs most commonly as a result of penile injection, priapism, sexually transmitted infections, and trauma. The...
Abscess of the corpus cavernosum is a condition that occurs most commonly as a result of penile injection, priapism, sexually transmitted infections, and trauma. The diagnosis of corpus cavernosum abscess is made through imaging, typically computed tomography (CT) or ultrasound. The preferred method of treatment for corpus cavernosum abscess is incision, drainage, and antibiotic therapy. Urethral diverticulum (UD) is defined as a saccular outpouching of the urethral lumen. We present a unique case of corpus cavernosum abscess secondary to perforation of a UD requiring extensive surgical intervention and resulting in long-term complications.
PubMed: 32211265
DOI: 10.7759/cureus.7032 -
PloS One 2020Diabetic foot ulcers (DFUs) lead to nearly 100,000 lower limb amputations annually in the United States. DFUs are colonized by complex microbial communities, and...
Diabetic foot ulcers (DFUs) lead to nearly 100,000 lower limb amputations annually in the United States. DFUs are colonized by complex microbial communities, and infection is one of the most common reasons for diabetes-related hospitalizations and amputations. In this study, we examined how DFU microbiomes respond to initial sharp debridement and offloading and how the initial composition associates with 4 week healing outcomes. We employed 16S rRNA next generation sequencing to perform microbial profiling on 50 samples collected from 10 patients with vascularized neuropathic DFUs. Debrided wound samples were obtained at initial visit and after one week from two DFU locations, wound bed and wound edge. Samples of the foot skin outside of the wounds were also collected for comparison. We showed that DFU wound beds are colonized by a greater number of distinct bacterial phylotypes compared to the wound edge or skin outside the wound. However, no significant microbiome diversity changes occurred at the wound sites after one week of standard care. Finally, increased initial abundance of Gram-positive anaerobic cocci (GPAC), especially Peptoniphilus (p < 0.05; n = 5 subjects), was associated with impaired healing; thus, GPAC's abundance could be a predictor of the wound-healing outcome.
Topics: Aged; Bacteria, Anaerobic; Debridement; Diabetic Foot; Female; Foot Ulcer; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Humans; Male; Microbiota; Middle Aged; Predictive Value of Tests; Treatment Outcome; Wound Healing
PubMed: 31978071
DOI: 10.1371/journal.pone.0227006 -
PloS One 2019Bacteria and other types of microbes interact with their hosts in several ways, including metabolic pathways, development, and complex behavioral processes such as mate...
Bacteria and other types of microbes interact with their hosts in several ways, including metabolic pathways, development, and complex behavioral processes such as mate recognition. During the mating season, adult males of the lesser long-nosed agave pollinator bat Leptonycteris yerbabuenae (Phyllostomidae: Glossophaginae) develop a structure called the dorsal patch, which is located in the interscapular region and may play a role in kin recognition and mate selection. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, we identified a total of 2,847 microbial phylotypes in the dorsal patches of eleven specimens. Twenty-six phylotypes were shared among all the patches, accounting for 30 to 75% of their relative abundance. These shared bacteria are distributed among 13 families, 10 orders, 6 classes and 3 phyla. Two of these common bacterial components of the dorsal patch are Lactococcus and Streptococcus. Some of them-Helcococcus, Aggregatibacter, Enterococcus, and Corynebacteriaceae-include bacteria with pathogenic potential. Half of the shared phylotypes belong to Gallicola, Anaerococcus, Peptoniphilus, Proteus, Staphylococcus, Clostridium, and Peptostreptococcus and specialize in fatty acid production through fermentative processes. This work lays the basis for future symbiotic microbe studies focused on communication and reproduction strategies in wildlife.
Topics: Animals; Back; Bacteria; Biodiversity; Chiroptera; DNA, Bacterial; High-Throughput Nucleotide Sequencing; Male; Mexico; Microbiota; RNA, Ribosomal, 16S; Reproduction; Sexual Behavior, Animal
PubMed: 31841551
DOI: 10.1371/journal.pone.0226239