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PeerJ 2021There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and...
BACKGROUND
There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans.
METHODS
Fifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3-V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b () gene followed by Sanger sequencing. CLC workbench was used to assemble the gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database.
RESULTS
gene sequences were generated for 49/54 mammalian samples: 38 rodents ( and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, was the most abundant (45.6%), followed by (8.0%), (3.5%), (3.8%), (2.6%), (1.6%) and (1.1%). Other less abundant (<1%) and potentially pathogenic included , , , , , and . By Shannon diversity index, spleens carried more diverse bacteria (mean Shannon diversity index of 2.86, = 0.008) compared to 1.77 for , 1.44 for , 1.40 for and 0.60 for .
CONCLUSION
This study examined systemic bacteria that are filtered by the spleen and the findings underscore the utility of 16S rRNA deep sequencing in characterizing complex microbiota that are potentially relevant to one health issues. An inherent problem with the V3-V4 region of 16S rRNA is the inability to classify bacteria reliably beyond the genera. Future studies should utilize the newer long read methods of 16S rRNA analysis that can delimit the species composition.
PubMed: 34557350
DOI: 10.7717/peerj.12067 -
Frontiers in Microbiology 2021Plasmids carrying metal resistance genes (MRGs) have been suggested to be key ecological players in the adaptation of metal-impacted microbial communities, making them...
Plasmids carrying metal resistance genes (MRGs) have been suggested to be key ecological players in the adaptation of metal-impacted microbial communities, making them promising drivers of bio-remediation processes. However, the impact of metals on plasmid-mediated spread of MRGs through selection, plasmid loss, and transfer is far from being fully understood. In the present study, we used two-member bacterial communities to test the impact of lead on the dispersal of the IncP plasmid pKJK5 from a KT2440 plasmid donor and two distinct recipients, B4 or SPH-1 after 4 and 10 days of mating. Two versions of the plasmid were used, carrying or not carrying the lead resistance TRABCD operon, to assess the importance of fitness benefit and conjugative potential for the dispersal of the plasmid. The spread dynamics of metal resistance conveyed by the conjugative plasmid were dependent on the recipient and the lead concentration: For , the operon did not facilitate neither lead resistance nor variation in plasmid spread. The growth gain brought by the operon to SPH-1 and KT2440 at 1 mM Pb enhanced the spread of the plasmid. At 1.5 mM Pb after 4 days, the proteomics results revealed an oxidative stress response and an increased abundance of pKJK5-encoded conjugation and partitioning proteins, which most likely increased the transfer of the control plasmid to SPH-1 and ensured plasmid maintenance. As a consequence, we observed an increased spread of pKJK5-. Conversely, the operon reduced the oxidative stress response and impeded the rise of conjugation- and partitioning-associated proteins, which slowed down the spread of the carrying plasmid. Ultimately, when a fitness gain was recorded in the recipient strain, the spread of MRG-carrying plasmids was facilitated through positive selection at an intermediate metal concentration, while a high lead concentration induced oxidative stress with positive impacts on proteins encoding plasmid conjugation and partitioning.
PubMed: 34122370
DOI: 10.3389/fmicb.2021.655903 -
International Journal of Medical... 2021The prevalence of drug-resistant (Mtb) strains makes disease control more complicated, which is the main cause of death in tuberculosis (TB) patients. Early detection... (Observational Study)
Observational Study
The prevalence of drug-resistant (Mtb) strains makes disease control more complicated, which is the main cause of death in tuberculosis (TB) patients. Early detection and timely standard treatment are the key to current prevention and control of drug-resistant TB. In recent years, despite the continuous advancement in drug-resistant TB diagnostic technology, the needs for clinical rapid and accurate diagnosis are still not fully met. With the development of sequencing technology, the research of human microecology has been intensified. This study aims to use 16 rRNA sequencing technology to detect and analyze upper respiratory flora of TB patients with anti-TB drug sensitivity (DS, n = 55), monoresistance isoniazide (MR-INH, n = 33), monoresistance rifampin (MR-RFP, n = 12), multidrug resistance (MDR, n = 26) and polyresistance (PR, n = 39) in southern China. Potential microbial diagnostic markers for different types of TB drug resistance are searched by screening differential flora, which provides certain guiding significance for drug resistance diagnosis and clinical drug use of TB. The results showed that the pulmonary microenvironment of TB patients was more susceptible to infection by external pathogens, and the infection of different drug-resistant Mtb leads to changes in different flora. Importantly, seven novel microorganisms (Leptotrichia, Granulicatella, Campylobacter, Delfitia, Kingella, Chlamydophila, Bordetella) were identified by 16S rRNA sequencing as diagnostic markers for different drug resistance types of TB. Leptotrichia, Granulicatella, Campylobacter were potential diagnostic marker for TB patients with INH single-resistance. Delftia was a potential diagnostic marker for TB patients with RFP single drug-resistance. Kingella and Chlamydophila can be used as diagnostic markers for TB patients with PR. Bordetella can be used as a potential diagnostic marker for identification of TB patients with MDR.
Topics: Adolescent; Adult; Aged; Antitubercular Agents; DNA, Bacterial; Female; Humans; Isoniazid; Male; Microbial Sensitivity Tests; Microbiota; Middle Aged; Mycobacterium tuberculosis; RNA, Ribosomal, 16S; Rifampin; Sensitivity and Specificity; Sputum; Tuberculosis, Multidrug-Resistant; Tuberculosis, Pulmonary; Young Adult
PubMed: 33850462
DOI: 10.7150/ijms.53492 -
Frontiers in Microbiology 2023The aim of our study was to investigate the impact of long-term exposure to heavy metals on the microbiome of the buccal mucosa, to unveil the link between environmental...
OBJECTIVES
The aim of our study was to investigate the impact of long-term exposure to heavy metals on the microbiome of the buccal mucosa, to unveil the link between environmental contamination and the oral microbial ecosystem, and to comprehend its potential health implications.
METHODS
Subjects were divided into two groups: the exposure group and the control group. We collected samples of buccal mucosa, soil, and blood, and conducted microbial diversity analysis on both groups of oral samples using 16S rRNA gene sequencing. The concentrations of heavy metals in blood and soil samples were also determined. Additionally, microbial networks were constructed for the purpose of topological analysis.
RESULTS
Due to long-term exposure to heavy metals, the relative abundance of , , , and increased, while the abundance of , , , , and decreased. The concentrations of heavy metals in the blood (Pb, Cd, Hg, and Mo) were associated with the growth of , , , and . In addition, the relative abundances of some pathogenic bacteria, such as , , and , were found to be enriched in the exposure group. Compared to the exposure group network, the control group network had a greater number of nodes, modules, interactive species, and keystone taxa. Module hubs and connectors in the control group converted into peripherals in the exposure group, indicating that keystone taxa changed. Metals in the blood (Pb, Cd, Hg, and Mo) were drivers of the microbial network of the buccal mucosa, which can have adverse effects on the network, thus providing conditions for the occurrence of certain diseases.
CONCLUSION
Long-term exposure to multiple metals perturbs normal bacterial communities in the buccal mucosa of residents in contaminated areas. This exposure reduces the complexity and stability of the microbial network and increases the risk of developing various diseases.
PubMed: 37928665
DOI: 10.3389/fmicb.2023.1264619 -
PloS One 2019Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to...
Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.
Topics: Animals; Bacteria; Birds; Metagenome; Microbiota
PubMed: 31825977
DOI: 10.1371/journal.pone.0225858 -
Journal of Animal Science Jan 2023Cat obesity has become a serious problem that affects cats' lives and welfare. Knowing how to control obesity in pet cats and its mechanism is urgently needed. Here, by...
Cat obesity has become a serious problem that affects cats' lives and welfare. Knowing how to control obesity in pet cats and its mechanism is urgently needed. Here, by feeding 30 cats different diets for 28 d, we explored the effects of 5 cat foods with potato, sweet potato, cassava, rice, and wheat as the main carbohydrate sources on the glycolipid metabolism of pet cats. The results showed that dietary carbohydrate sources did not affect the normal growth performance and stool scores of cats. Notably, we found that the starch gelatinization degree of sweet potato and cassava cat food were higher than those of other groups, while the rice diets had the highest digestibility, but the difference was not significant (P > 0.05). Furthermore, cats fed cassava diets had lower postprandial glucose responses. The mean glucose value, maximum glucose value, AUC0-360 min, AUC≤30 min, and AUC≥30 min in the cassava group were lower than those in other dietary groups (P > 0.05). In addition, we found that the carbohydrate source had a minimal effect on serum biochemical immune indices, but the blood lipid indices, such as TG, TC, HDL, and LDL of cats fed the cassava diet were maintained at a low level compared with other groups (P > 0.05). In addition, diets with different carbohydrate sources affect the gut microbial composition, and sweet potato and cassava diets tend to increase the diversity of gut microbiota with a higher Shannon index and Simpson index. The abundance of Fusobacterium, Veillonella, and Actinobacillus was significantly higher in sweet potato diet-fed cats (P < 0.05), while the abundance of Delftia, Shinella, Rothia, and Hydrogenophage was highest in cassava diet-fed cats (P < 0.05). Collectively, this study revealed that cassava and sweet potato diets have a better effect on feeding value, controlling blood glucose and blood lipids, and improving the intestinal flora of pet cats, which is worth developing dietary formulations to alleviate pet obesity.
Topics: Cats; Animals; Glucose; Insulin; Gastrointestinal Microbiome; Animal Feed; Diet; Obesity; Blood Glucose; Dietary Carbohydrates; Digestion; Cat Diseases
PubMed: 36789882
DOI: 10.1093/jas/skad049 -
Frontiers in Medicine 2023Sepsis-associated liver dysfunction (SALD) has high incidence and mortality in patients with intra-abdominal infection (IAI). The associations between acute...
Acute gastrointestinal injury and altered gut microbiota are related to sepsis-induced cholestasis in patients with intra-abdominal infection: a retrospective and prospective observational study.
BACKGROUND
Sepsis-associated liver dysfunction (SALD) has high incidence and mortality in patients with intra-abdominal infection (IAI). The associations between acute gastrointestinal injury (AGI), gut microbiota, and SALD were evaluated in patients with IAI.
METHODS
A retrospective study was conducted to assess the relationship between AGI and SALD in patients with IAI. Patients were divided into non-SALD and sepsis-induced cholestasis () groups, which is a subtype of SALD. was defined as total bilirubin >2 mg/dL. AGI incidences between the two groups were compared using Chi-square test. Subsequently, a prospective study was conducted to investigate the gut microbiota differences between patients without SALD and those with . Fecal samples were collected on days 1, 3, and 7 after admission to analyze changes in gut microbiota using 16S ribosomal ribonucleic acid sequencing.
RESULTS
One hundred thirty-four patients with IAI were included retrospectively, with 77 SALD and 57 non-SALD cases. Among patients with SALD, 71 were diagnosed with . Patients with had a higher incidence of AGI compared to those without SALD (28.07% vs. 56.34%, < 0.05), and a severity-dependent relationship was found between AGI grade and occurrence. Subsequently, 20 patients with IAI were recruited prospectively, with 10 patients each assigned to the non-SALD and groups. Patients with had a more severe gut microbiota disorder on day 7 than those without SALD, including lower microbiota diversities, decreased abundance of and and increased abundance of and at the phylum level. Furthermore, and the two most abundant genera, were significantly higher in the group than in the non-SALD group. Functional prediction analysis showed that the top three KEGG pathways were ribosome, pyrimidine metabolism, and the two-component system. During the first week, the abundance of decreased significantly, whereas increased in the non-SALD group; however, the phyla taxa did not change significantly in the group.
CONCLUSION
There exists a severity-dependent relationship between AGI grade and occurrence in adult patients with IAI. A severe gut microbiota disorder was discovered in during the first week of the intensive care unit stay.
PubMed: 37575984
DOI: 10.3389/fmed.2023.1144786 -
Brazilian Journal of Microbiology :... Jun 2023Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries...
Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries has become a common approach for the discovery of new antibiotics from uncultured microorganisms. This study focuses on capturing nonribosomal peptide synthase (NRPS) gene clusters implicated in the synthesis of many natural compounds of industrial relevance. A NRPS PCR assay was used to screen 2976 Escherichia coli clones in a soil metagenomic library to target NRPS genes. DNA extracts from 4 clones were sequenced and subjected to bioinformatic analysis to identify NRPS domains, their phylogeny, and substrate specificity.Successfully, 17 NRPS-positive hits with a biosynthetic potential were identified. DNA sequencing and BLAST analysis confirmed that NRPS protein sequences shared similarities with members of the genus Delftia in the Proteobacteria taxonomic position. Multiple alignment and phylogenetic analysis demonstrated that clones no. 15cd35 and 15cd37 shared low bootstrap values (54%) and were distantly far from close phylogenetic neighbors. Additionally, NRPS domain substrate specificity has no hits with the known ones; hence, they are more likely to use different substrates to produce new diverse antimicrobials. Further analysis confirmed that the NRPS hits resemble several transposon elements from other bacterial taxa, confirming its diversity. We confirmed that the analyses of the soil metagenomic library revealed a diverse set of NRPS related to the genus Delftia. An in-depth understanding of those positive NRPS hits is a crucial step for genetic manipulation of NRPS, shedding light on alternative novel antimicrobial compounds that can be used in drug discovery and hence supports the pharmaceutical sector.
Topics: Metagenome; Phylogeny; Microbiota; Anti-Bacterial Agents; Soil
PubMed: 36977970
DOI: 10.1007/s42770-023-00953-z -
Indian Journal of Microbiology Jun 2020Respiratory bacterial microbiota plays a key role in human health. Lung cancer microbiome is a significant yet an understudied area while bronchiectasis microbiome is...
Respiratory bacterial microbiota plays a key role in human health. Lung cancer microbiome is a significant yet an understudied area while bronchiectasis microbiome is often studied. We assessed the bacterial microbiota in the upper and lower respiratory tract of the patients with lung cancer and bronchiectasis against a healthy group and their variations in individuality. 16S rRNA gene based metagenomic sequencing was used to detect entire bacterial community along with conventional aerobic bacterial culturing. In comparison to healthy, increased bacterial diversity was observed in diseased population. Abundance of more than 1% was considered and bacteria were identified in 97% similarity. Only lung cancer patients exhibited bacteria specific to the disease: and . However, and were also observed limited to lung cancer and bronchiectasis respectively, in less than 1% but supported with bacterial culturing. In conclusion the disease condition and intra-group variability should be considered in future with larger cohorts to understand individual patient variability highlighting the social habits and gender of the individual.
PubMed: 32255852
DOI: 10.1007/s12088-019-00850-w -
Frontiers in Medicine 2022Qin-Qiao-Xiao-Du (QQXD), a traditional Chinese medicine (TCM) formula, has been used in the clinical treatment of influenza virus pneumonia. However, the effects and...
Qin-Qiao-Xiao-Du (QQXD), a traditional Chinese medicine (TCM) formula, has been used in the clinical treatment of influenza virus pneumonia. However, the effects and mechanisms of QQXD on influenza virus pneumonia remain unknown. Therefore, this study explores the mechanisms of QQXD in the treatment of influenza virus pneumonia from the point of view of intestinal flora and metabolism. The results showed that QQXD was able to reduce mortality, weight loss, lung viral load, lung index, and lung injury in influenza virus mice. A cytokine array found that the QQXD attenuated the expression of serum IL-1α, IL-4, IL-12(P70), and TNF-α. Subsequently, 16s rRNA gene sequencing showed that QQXD could increase the relative abundances of Gemmiger, Anaerofustis, Adlercreutzia, and Streptococcus and decrease those of Dehalobacteriu, Burkholderia, Prevotella, Butyrimimonas, Delftia, and others. Meanwhile, targeted metabolic profiling analysis showed that QQXD could regulate nitrogen metabolism, phenylalanine metabolism, valine, leucine, and isoleucine biosynthesis. Correlation analysis demonstrated that the regulatory effect of QQXD on the cyanoamino acid metabolism pathway was associated with changes in the abundance of Parabacteroides, Pediococcus, and Clostridium in influenza mice. In conclusion, our study revealed that QQXD can inhibit influenza virus replication, suppress cytokine storms, and protect mice from influenza virus infection pneumonia. The mechanisms are likely to be related to improved gut microbiota dysbiosis, increased intestinal carbohydrate metabolism, and up-regulated cyanoamino acid metabolism pathways.
PubMed: 36313993
DOI: 10.3389/fmed.2022.1032127