Bacterial Diversity in the Intestinal Mucosa of Dysbiosis Diarrhea Mice Treated with Qiweibaizhu Powder

The current research tried to explore the effect of Qiweibaizhu powder (QWBZP) on the bacterial diversity and community structure of the intestinal mucosa of dysbiosis diarrhea mice and provide a scientific basis for the efficacy of QWBZP on antibiotic-induced diarrhea. A dysbiosis diarrhea mouse model was constructed with broad-spectrum antibiotics through a mixture of cephradine capsules and gentamicin sulfate (23.33 mL·kg-1·d-1). Intestinal mucosa was collected, and DNA was extracted from each group. The bacterial characteristics in intestinal mucosa were analyzed by MiSeq sequencing based on the 16S rRNA sequencing platform. There were no significant differences in alpha diversity indices among the three groups. The sample distributions in both the normal and QWBZP groups were relatively concentrated, and the distance among individuals was close. However, an opposite result was obtained in the model group. Furthermore, the composition and abundance of species were similar between the normal group and the QWBZP group at both the phylum and genus levels. After treatment with QWBZP, the abundance of Lactobacillus increased, and Proteobacteria decreased, and the Firmicutes/Bacteroidetes ratio decreased to a normal level. Our results indicate that QWBZP can help repair mucosal bacterial structure and recover mucosal microbiota. Specifically, QWBZP increased the abundance of Lactobacillus and Bacteroidales S24-7 group norank.

Download Full-text

Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome

Viruses ◽

10.3390/v13102093 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2093

Author(s):

Shen-Yuan Hsieh ◽

Mohammad A. Tariq ◽

Andrea Telatin ◽

Rebecca Ansorge ◽

Evelien M. Adriaenssens ◽

...

Keyword(s):

Alpha Diversity ◽

Diversity Indices ◽

P Value ◽

Library Preparation ◽

High Genetic Diversity ◽

Sequencing Platform ◽

Viral Genomes ◽

Healthy Donors ◽

Faecal Samples ◽

Sequencing Platforms

The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as “viral dark matter”. However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating “rare” members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.

Download Full-text

The Gut Microbiome in Polycystic Ovary Syndrome and Its Association with Metabolic Traits

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/clinem/dgaa848 ◽

2020 ◽

Author(s):

Kreete Lüll ◽

Riikka K Arffman ◽

Alberto Sola-Leyva ◽

Nerea M Molina ◽

Oliver Aasmets ◽

...

Keyword(s):

Polycystic Ovary Syndrome ◽

Bacterial Diversity ◽

Gut Microbiome ◽

Metabolic Diseases ◽

Polycystic Ovary ◽

Alpha Diversity ◽

Diversity Indices ◽

Normal Glucose Tolerance ◽

Ovary Syndrome ◽

Shannon Diversity

Abstract Context Despite the gut microbiome being widely studied in metabolic diseases, its role in polycystic ovary syndrome (PCOS) has been scarcely investigated. Objective Compare the gut microbiome in late fertile age women with and without PCOS and investigate whether changes in the gut microbiome correlate with PCOS-related metabolic parameters. Design Prospective, case–control study using the Northern Finland Birth Cohort 1966. Setting General community. Participants A total of 102 PCOS women and 201 age- and body mass index (BMI)-matched non-PCOS control women. Clinical and biochemical characteristics of the participants were assessed at ages 31 and 46 and analyzed in the context of gut microbiome data at the age of 46. Intervention (s): None Main outcome measure(s) Bacterial diversity, relative abundance, and correlations with PCOS-related metabolic measures. Results Bacterial diversity indices did not differ significantly between PCOS and controls (Shannon diversity P = .979, unweighted UniFrac P = .175). Four genera whose balance helps to differentiate between PCOS and non-PCOS were identified. In the whole cohort, the abundance of 2 genera from Clostridiales, Ruminococcaceae UCG-002, and Clostridiales Family XIII AD3011 group, were correlated with several PCOS-related markers. Prediabetic PCOS women had significantly lower alpha diversity (Shannon diversity P = .018) and markedly increased abundance of genus Dorea (false discovery rate = 0.03) compared with women with normal glucose tolerance. Conclusion PCOS and non-PCOS women at late fertile age with similar BMI do not significantly differ in their gut microbial profiles. However, there are significant microbial changes in PCOS individuals depending on their metabolic health.

Download Full-text

Exposure to traffic-related air pollution and bacterial diversity in the lower respiratory tract of children

PLoS ONE ◽

10.1371/journal.pone.0244341 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0244341

Author(s):

Christine Niemeier-Walsh ◽

Patrick H. Ryan ◽

Jaroslaw Meller ◽

Nicholas J. Ollberding ◽

Atin Adhikari ◽

...

Keyword(s):

Air Pollution ◽

Respiratory Tract ◽

Bacterial Diversity ◽

Lower Respiratory Tract ◽

Alpha Diversity ◽

Diversity Indices ◽

Rrna Genes ◽

Exposure Group ◽

Asthma Status ◽

The Impact

Background Exposure to particulate matter has been shown to increase the adhesion of bacteria to human airway epithelial cells. However, the impact of traffic-related air pollution (TRAP) on the respiratory microbiome is unknown. Methods Forty children were recruited through the Cincinnati Childhood Allergy and Air Pollution Study, a longitudinal cohort followed from birth through early adolescence. Saliva and induced sputum were collected at age 14 years. Exposure to TRAP was characterized from birth through the time of sample collection using a previously validated land-use regression model. Sequencing of the bacterial 16S and ITS fungal rRNA genes was performed on sputum and saliva samples. The relative abundance of bacterial taxa and diversity indices were compared in children with exposure to high and low TRAP. We also used multiple linear regression to assess the effect of TRAP exposure, gender, asthma status, and socioeconomic status on the alpha diversity of bacteria in sputum. Results We observed higher bacterial alpha diversity indices in sputum than in saliva. The diversity indices for bacteria were greater in the high TRAP exposure group than the low exposure group. These differences remained after adjusting for asthma status, gender, and mother’s education. No differences were observed in the fungal microbiome between TRAP exposure groups. Conclusion Our findings indicate that exposure to TRAP in early childhood and adolescence may be associated with greater bacterial diversity in the lower respiratory tract. Asthma status does not appear to confound the observed differences in diversity. These results demonstrate that there may be a TRAP-exposure related change in the lower respiratory microbiota that is independent of asthma status.

Download Full-text

Biofilm Microbiome in Extracorporeal Membrane Oxygenator Catheters

10.21203/rs.3.rs-86235/v1 ◽

2020 ◽

Author(s):

Yeuni Yu ◽

Yun Hak Kim ◽

Woo Hyun Cho ◽

HYE JU YEO

Keyword(s):

Alpha Diversity ◽

Illumina Miseq ◽

16S Rrna Genes ◽

Rrna Genes ◽

Miseq Sequencing ◽

Membrane Oxygenator ◽

Significant Elevation ◽

Sequencing Platform ◽

Extracorporeal Membrane Oxygenator ◽

The Relationship

Abstract Background : To assess the relationship between bacteremia and biofilms in extracorporeal membrane oxygenation (ECMO) catheters.Methods: We evaluated the biofilm microbiome of ECMO catheters from adults with (n = 6) and without bacteremia (n = 15). Microbiomes of the catheter biofilms were evaluated by profiling the V3 and V4 regions of bacterial 16s rRNA genes using the Illumina Miseq sequencing platform.Results: In total, 2,548,172 reads, with an average of 121,341 reads per sample, were generated. Although alpha diversity was slightly higher in the non-bacteremic group, it was not statistically significant. Also, there was no difference in beta diversity between the two groups. At the genus level, Delftia was more abundant in the non-bacteremic group, but Bacillus, Flavobacterium, CL0-1, Candidatus, and Xiphinematobacter were more abundant in the bacteremic group. In particular, Arthrobacter, SMB53, Neisseria, Candidatus, Ortrobactrum, Candidatus, Rhabdochlamydia, Deefgae, Dyella, Paracoccus, and Pedobacter were more abundant in the bacteremic group. In a network analysis, compared to the non-bacteremic group, the microbiome of the bacteremic group was very complex. Notably, there was a significant elevation in the secretion system of the non-bacteremic group.Conclusions: Biofilm characteristics in ECMO catheters varied according to the presence or absence of bacteremia.

Download Full-text

Temporal and Spatial Changes in Phyllosphere Microbiome of Acacia Trees Growing in Arid Environments

Frontiers in Microbiology ◽

10.3389/fmicb.2021.656269 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ashraf Al Ashhab ◽

Shiri Meshner ◽

Rivka Alexander-Shani ◽

Hana Dimerets ◽

Michael Brandwein ◽

...

Keyword(s):

Bacterial Diversity ◽

Air Temperature ◽

Bacterial Communities ◽

Abiotic Factors ◽

Keystone Species ◽

Illumina Miseq ◽

Diversity Indices ◽

Arid Environments ◽

Sequencing Platform ◽

Acacia Species

Background: The evolutionary relationships between plants and their microbiomes are of high importance to the survival of plants in general and even more in extreme conditions. Changes in the plant's microbiome can affect plant development, growth, fitness, and health. Along the arid Arava, southern Israel, acacia trees (Acacia raddiana and Acacia tortilis) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate, phenology, and seasonality on the epiphytic and endophytic microbiome of acacia trees. One hundred thirty-nine leaf samples were collected throughout the sampling year and were assessed using 16S rDNA gene amplified with five different primers (targeting different gene regions) and sequenced (150 bp paired-end) on an Illumina MiSeq sequencing platform.Results: Epiphytic bacterial diversity indices (Shannon–Wiener, Chao1, Simpson, and observed number of operational taxonomic units) were found to be nearly double compared to endophyte counterparts. Epiphyte and endophyte communities were significantly different from each other in terms of the composition of the microbial associations. Interestingly, the epiphytic bacterial diversity was similar in the two acacia species, but the canopy sides and sample months exhibited different diversity, whereas the endophytic bacterial communities were different in the two acacia species but similar throughout the year. Abiotic factors, such as air temperature and precipitation, were shown to significantly affect both epiphyte and endophytes communities. Bacterial community compositions showed that Firmicutes dominate A. raddiana, and Proteobacteria dominate A. tortilis; these bacterial communities consisted of only a small number of bacterial families, mainly Bacillaceae and Comamonadaceae in the endophyte for A. raddiana and A. tortilis, respectively, and Geodematophilaceae and Micrococcaceae for epiphyte bacterial communities, respectively. Interestingly, ~60% of the obtained bacterial classifications were unclassified below family level (i.e., “new”).Conclusions: These results shed light on the unique desert phyllosphere microbiome highlighting the importance of multiple genotypic and abiotic factors in shaping the epiphytic and endophytic microbial communities. This study also shows that only a few bacterial families dominate both epiphyte and endophyte communities, highlighting the importance of climate change (precipitation, air temperature, and humidity) in affecting arid land ecosystems where acacia trees are considered keystone species.

Download Full-text

PSXII-24 Effects of supplementing ruminally protected and non-protected active dried yeast on fecal bacterial community of finishing beef steers

Journal of Animal Science ◽

10.1093/jas/skz258.844 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 425-426

Author(s):

Tao Ran ◽

Peixin Jiao ◽

Ousama AlZahal ◽

Xiaolai Xie ◽

Karen A Beauchemin ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Relative Abundance ◽

Alpha Diversity ◽

Diversity Indices ◽

Fecal Bacteria ◽

Beef Steers ◽

Fecal Bacterial Community ◽

Barley Silage ◽

And Control

Abstract The objective of this study was to evaluate the effects of supplementing ruminally protected and non-protected active dried yeast (ADY; AB Vista, UK) on fecal bacterial diversity of finishing beef steers. Seventy-five Angus steers (initial BW 448 kg) were randomly assigned to one of five treatments: control, antibiotics (ANT, 330 mg monensin + 110 mg tylosin/d), ADY (1.5 g/d), encapsulated ADY (EDY; 3 g/d), and mixture of ADY and EDY (MDY). The ADY (1.7×1010 cfu/g) was encapsulated with equal amount of ADY and capsule material. Steers were fed a diet containing 10% barley silage and 90% barley concentrate (DM basis), ANT, ADY, EDY and MDY were top-dressed at feeding. Fecal samples were rectally collected from 10 steers of each treatment on d 56 to determine fecal bacterial diversity using high throughput MiSeq sequencing. Alpha diversity indices were not different among treatments. Principal coordinate analysis revealed that samples were not clustered by treatments. Bacteroidetes and Firmicutes were dominant phyla in the fecal bacterial community for all treatments, with a tendency (P < 0.10) of ANT, EDY and MDY to have greater relative abundance of Bacteroidetes (averaged 51.3 vs 46.8%) but lesser Firmicutes (averaged 39.5 vs 47.9%) than control steers. About 50 to 61% of sequences remained unclassified and identified 32 genus, with Prevotella ranging from 15.8 to 25.5% as the dominant genus in all treatments. Notably, steers with ANT, EDY, MDY vs. control had greater (P < 0.05) relative abundance of Prevotella (averaged 23.5 vs 16.8%) but lesser (P < 0.03) Oscillospira (averaged 1.7 vs 2.8%). No differences between ADY and control were observed for aforementioned variables. The results indicate that supplementing ruminally protected or non-protected ADY have limited effect on diversity of fecal bacteria, whereas feeding protected ADY and ANT to finishing beef steers altered dominant fecal bacteria at phylum and genus level.

Download Full-text

Exposure to Traffic-Related Air Pollution is Associated with Greater Bacterial Diversity in the Lower Respiratory Tract of Children

10.1101/2020.12.09.417501 ◽

2020 ◽

Author(s):

Christine Niemeier-Walsh ◽

Patrick H Ryan ◽

Jaroslaw Meller ◽

Nicholas J. Ollberding ◽

Atin Adhikari ◽

...

Keyword(s):

Air Pollution ◽

Respiratory Tract ◽

Bacterial Diversity ◽

Lower Respiratory Tract ◽

Alpha Diversity ◽

Diversity Indices ◽

Rrna Genes ◽

Exposure Group ◽

Asthma Status ◽

The Impact

AbstractBackgroundExposure to particulate matter has been shown to increase the adhesion of bacteria to human airway epithelial cells. However, the impact of traffic-related air pollution (TRAP) on the respiratory microbiome is unknown.MethodsForty children were recruited through the Cincinnati Childhood Allergy and Air Pollution Study, a longitudinal cohort followed from birth through early adolescence. Saliva and induced sputum were collected at age 14 years. Exposure to TRAP was characterized from birth through the time of sample collection using a previously validated land-use regression model. Sequencing of the bacterial 16S and ITS fungal rRNA genes was performed on sputum and saliva samples. The relative abundance of bacterial taxa and diversity indices were compared in children with exposure to high and low TRAP. We also used multiple linear regression to assess the effect of TRAP exposure, gender, asthma status, and socioeconomic status on the alpha diversity of bacteria in sputum.ResultsWe observed higher bacterial alpha diversity indices in sputum than in saliva. The diversity indices for bacteria were greater in the high TRAP exposure group than the low exposure group. These differences remained after adjusting for asthma status, gender, and mother’s education. No differences were observed in the fungal microbiome between TRAP exposure groups.ConclusionOur findings indicate that exposure to TRAP in early childhood and adolescence may be associated with greater bacterial diversity in the lower respiratory tract. Asthma status does not appear to confound the observed differences in diversity. It is still unknown whether the development of asthma changes the lower respiratory tract microbiome or if an altered microbiome mediates a change in disease status. However, these results demonstrate that there may be a TRAP-exposure related change in the lower respiratory microbiota that is independent of asthma status.

Download Full-text

Biofilm microbiome in extracorporeal membrane oxygenator catheters

PLoS ONE ◽

10.1371/journal.pone.0257449 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257449

Author(s):

Yeuni Yu ◽

Yun Hak Kim ◽

Woo Hyun Cho ◽

Bong Soo Son ◽

Hye Ju Yeo

Keyword(s):

Alpha Diversity ◽

Illumina Miseq ◽

16S Rrna Genes ◽

Rrna Genes ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Membrane Oxygenator ◽

Sequencing Platform ◽

Extracorporeal Membrane Oxygenator ◽

The Difference

Despite the formation of biofilms on catheters for extracorporeal membrane oxygenation (ECMO), some patients do not show bacteremia. To elucidate the specific linkage between biofilms and bacteremia in patients with ECMO, an improved understanding of the microbial community within catheter biofilms is necessary. Hence, we aimed to evaluate the biofilm microbiome of ECMO catheters from adults with (n = 6) and without (n = 15) bacteremia. The microbiomes of the catheter biofilms were evaluated by profiling the V3 and V4 regions of bacterial 16s rRNA genes using the Illumina MiSeq sequencing platform. In total, 2,548,172 reads, with an average of 121,341 reads per sample, were generated. Although alpha diversity was slightly higher in the non-bacteremic group, the difference was not statistically significant. In addition, there was no difference in beta diversity between the two groups. We found 367 different genera, of which 8 were present in all samples regardless of group; Limnohabitans, Flavobacterium, Delftia, Massilia, Bacillus, Candidatus, Xiphinematobacter, and CL0-1 showed an abundance of more than 1% in the sample. In particular, Arthrobacter, SMB53, Neisseria, Ortrobactrum, Candidatus Rhabdochlamydia, Deefgae, Dyella, Paracoccus, and Pedobacter were highly abundant in the bacteremic group. Network analysis indicated that the microbiome of the bacteremic group was more complex than that of the non-bacteremic group. Flavobacterium and CL0.1, which were abundant in the bacteremic group, were considered important genera because they connected different subnetworks. Biofilm characteristics in ECMO catheters varied according to the presence or absence of bacteremia. There were no significant differences in diversity between the two groups, but there were significant differences in the community composition of the biofilms. The biofilm-associated community was dynamic, with the bacteremic group showing very complex network connections within the microbiome.

Download Full-text

Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China

Animals ◽

10.3390/ani11071938 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1938

Author(s):

Han Aricha ◽

Huasai Simujide ◽

Chunjie Wang ◽

Jian Zhang ◽

Wenting Lv ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Gut Microbiota ◽

Inner Mongolia ◽

Alpha Diversity ◽

Fecal Microbiota ◽

Composition Analysis ◽

Geographical Factors ◽

Rrna Sequencing ◽

Xilingol Grassland

Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.

Download Full-text

Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

Scientific Reports ◽

10.1038/s41598-021-81507-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hua Zha ◽

Fengping Liu ◽

Zongxin Ling ◽

Kevin Chang ◽

Jiezuan Yang ◽

...

Keyword(s):

Diabetes Mellitus ◽

Type 2 Diabetes ◽

Type 2 Diabetes Mellitus ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Diversity Indices ◽

Vital Role ◽

Rrna Gene ◽

Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

Download Full-text