Pulmonary and intestinal microbiota dynamics during Gram-negative pneumonia-derived sepsis

Abstract Background The gut microbiome plays a protective role in the host defense against pneumonia. The composition of the lung microbiota has been shown to be predictive of clinical outcome in critically ill patients. However, the dynamics of the lung and gut microbiota composition over time during severe pneumonia remains ill defined. We used a mouse model of pneumonia-derived sepsis caused by Klebsiella pneumoniae in order to follow the pathogen burden as well as the composition of the lung, tongue and fecal microbiota from local infection towards systemic spread. Results Already at 6 h post-inoculation with K. pneumoniae, marked changes in the lung microbiota were seen. The alpha diversity of the lung microbiota did not change throughout the infection, whereas the beta diversity did. A shift between the prominent lung microbiota members of Streptococcus and Klebsiella was seen from 12 h onwards and was most pronounced at 18 h post-inoculation (PI) which was also reflected in the release of pro-inflammatory cytokines indicating severe pulmonary inflammation. Around 18 h PI, K. pneumoniae bacteremia was observed together with a systemic inflammatory response. The composition of the tongue microbiota was not affected during infection, even at 18–30 h PI when K. pneumoniae had become the dominant bacterium in the lung. Moreover, we observed differences in the gut microbiota during pulmonary infection. The gut microbiota contributed to the lung microbiota at 12 h PI, however, this decreased at a later stage of the infection. Conclusions At 18 h PI, K. pneumoniae was the dominant member in the lung microbiota. The lung microbiota profiles were significantly explained by the lung K. pneumoniae bacterial counts and Klebsiella and Streptococcus were correlating with the measured cytokine levels in the lung and/or blood. The oral microbiota in mice, however, was not influenced by the severity of murine pneumonia, whereas the gut microbiota was affected. This study is of significance for future studies investigating the role of the lung microbiota during pneumonia and sepsis.

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Influence of pig gut microbiota on Mycoplasma hyopneumoniae susceptibility

Veterinary Research ◽

10.1186/s13567-019-0701-8 ◽

2019 ◽

Vol 50 (1) ◽

Cited By ~ 2

Author(s):

Meera Surendran Nair ◽

Tyson Eucker ◽

Brian Martinson ◽

Axel Neubauer ◽

Joseph Victoria ◽

...

Keyword(s):

Gut Microbiota ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Mycoplasma Hyopneumoniae ◽

Fecal Microbiota ◽

Lung Lesion ◽

Rrna Gene ◽

Post Inoculation ◽

Microbiome Composition ◽

Associated Lesions

Abstract This study investigated the influence of gut microbiome composition in modulating susceptibility to Mycoplasma hyopneumoniae in pigs. Thirty-two conventional M. hyopneumoniae free piglets were randomly selected from six different litters at 3 weeks of age and were experimentally inoculated with M. hyopneumoniae at 8 weeks of age. Lung lesion scores (LS) were recorded 4 weeks post-inoculation (12 weeks of age) from piglet lungs at necropsy. Fecal bacterial community composition of piglets at 3, 8 and 12 weeks of age were targeted by amplifying the V3–V4 region of the 16S rRNA gene. The LS ranged from 0.3 to 43% with an evident clustering of the scores observed in piglets within litters. There were significant differences in species richness and alpha diversity in fecal microbiomes among piglets within litters at different time points (p < 0.05). The dissimilarity matrices indicated that at 3 weeks of age, the fecal microbiota of piglets was more dissimilar compared to those from 8 to 12 weeks of age. Specific groups of bacteria in the gut that might predict the decreased severity of M. hyopneumoniae associated lesions were identified. The microbial shift at 3 weeks of age was observed to be driven by the increase in abundance of the indicator family, Ruminococcaceae in piglets with low LS (p < 0.05). The taxa, Ruminococcus_2 having the highest richness scores, correlated significantly between litters showing stronger associations with the lowest LS (r = −0.49, p = 0.005). These findings suggest that early life gut microbiota can be a potential determinant for M. hyopneumoniae susceptibility in pigs.

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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.

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Depletion of acetate-producing bacteria from the gut microbiota facilitates cognitive impairment through the gut-brain neural mechanism in diabetic mice

Microbiome ◽

10.1186/s40168-021-01088-9 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Hong Zheng ◽

Pengtao Xu ◽

Qiaoying Jiang ◽

Qingqing Xu ◽

Yafei Zheng ◽

...

Keyword(s):

Cognitive Impairment ◽

Gut Microbiota ◽

Cognitive Functions ◽

Neural Mechanism ◽

Fecal Microbiota ◽

Protective Role ◽

Fecal Microbiota Transplant ◽

Memory Impairments ◽

The Impact

Abstract Background Modification of the gut microbiota has been reported to reduce the incidence of type 1 diabetes mellitus (T1D). We hypothesized that the gut microbiota shifts might also have an effect on cognitive functions in T1D. Herein we used a non-absorbable antibiotic vancomycin to modify the gut microbiota in streptozotocin (STZ)-induced T1D mice and studied the impact of microbial changes on cognitive performances in T1D mice and its potential gut-brain neural mechanism. Results We found that vancomycin exposure disrupted the gut microbiome, altered host metabolic phenotypes, and facilitated cognitive impairment in T1D mice. Long-term acetate deficiency due to depletion of acetate-producing bacteria resulted in the reduction of synaptophysin (SYP) in the hippocampus as well as learning and memory impairments. Exogenous acetate supplement or fecal microbiota transplant recovered hippocampal SYP level in vancomycin-treated T1D mice, and this effect was attenuated by vagal inhibition or vagotomy. Conclusions Our results demonstrate the protective role of microbiota metabolite acetate in cognitive functions and suggest long-term acetate deficiency as a risk factor of cognitive decline.

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Fecal Microbiota Diversity in Survivors of Adolescent/Young Adult Hodgkin Lymphoma

Blood ◽

10.1182/blood.v120.21.1533.1533 ◽

2012 ◽

Vol 120 (21) ◽

pp. 1533-1533

Author(s):

Wendy Cozen ◽

Guoqin Yu ◽

Mitchell Gail ◽

Bharat N. Nathwani ◽

Amie E. Hwang ◽

...

Keyword(s):

Young Adult ◽

Gut Microbiota ◽

Hodgkin Lymphoma ◽

Relative Abundance ◽

Alpha Diversity ◽

Fecal Microbiota ◽

Shannon Index ◽

Tree Index ◽

Unique Otus ◽

Whole Tree

Abstract Abstract 1533 Survivors of adolescent/young adult Hodgkin lymphoma (AYAHL) report fewer exposures to infections during childhood compared to controls. They also have persistent genomic and functional aberrations in their lymphocytes that are partially attributable to chemotherapy or radiotherapy. Recent studies have shown that the gut microbiome can affect both the innate and adaptive immune response, and can suppress or exacerbate an inflammatory response. Given the central role of the gut microbiota in immune function, we investigated whether AYAHL survivors, who were members of 13 mono- and dizygotic twin pairs discordant for this disease, have differences in the diversity or phylogenetic configurations of their fecal microbiota compared to their unaffected co-twins. Twin pairs discordant for AYAHL are an ideal study population because they are at least partially matched on genetic and early life factors, both of which influence the composition of the gut microbiome. Pyrosequencing of bacterial 16S rRNA amplicons generated from single fecal samples obtained from each individual yielded 253,182 filtered and de-noised reads translated into species-level operational taxonomic units (OTUs). Standardized across individuals by random sampling, reads were assigned to 2513 OTUs to compare microbiome diversity and relative abundance of taxa. The number of OTU's was compared between twins using a paired student's t-test and a one-way analysis of variance was performed to determine whether such measures differed across twin pairs by comparing the measures between twins to those of randomly paired individuals. AYAHL survivors had less diverse fecal microbial communities compared to their unaffected co-twin controls by all measures of alpha diversity (Table 1). Measures that weighted the relative abundance of the bacteria were not statistically significantly different (Shannon Index, p= 0.270; Chao index, p= 0.066, PD Whole Tree Index, p= 0.051). However, when the unweighted number of unique OTUs was considered, the difference was significant (338 in cases vs. 369 in unaffected co-twin controls, p= 0.015). When the analysis was restricted to OTUs that were present at an abundance of > 0.1% in at least 2 of the 23 samples analyzed, the differences were attenuated, with only the PD Whole Tree index difference in diversity remaining marginally significant (p= 0.045). Only one bacterial taxon was associated with AYAHL, probably due to chance. Phylogenetic measurements indicated that the bacterial component of the microbiota of co-twins were more similar with respect to one another than unrelated individuals, although no differences by zygosity were observed. These results provide evidence that AYAHL survivors have reduced diversity of the gut microbiota, perhaps as a consequence the disease, its treatment, or a particularly hygienic environment. Table 1. Comparisons of alpha diversity measurements between Hodgkin lymphoma cases and co-twin controls. Measurements of Alpha Diversity Mean (Cases) Mean (Unaffected Co-twins) Mean Difference (Unaffected co-twin-case difference) P-value1 Initial analysis No. unique OTUs 338 369 31 0.015 Shannon index 5.6 5.8 0.2 0.27 Chao1 533 574 41 0.066 PD_whole tree 21.2 22.8 1.6 0.051 Conservative analysis No. unique OTUs 183 196 13 0.10 Shannon index 5.2 5.4 0.2 0.40 Chao1 230 237 7 0.47 PD_whole tree 13.7 14.6 0.9 0.045 1 P-value by paired t-tests. Disclosures: No relevant conflicts of interest to declare.

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Environmental Influences on the Human Gut Microbiota: A Longitudinal Pilot Study

Current Developments in Nutrition ◽

10.1093/cdn/nzab054_006 ◽

2021 ◽

Vol 5 (Supplement_2) ◽

pp. 1151-1151

Author(s):

Marina Brown ◽

Ginger Reeser ◽

Leila Shinn ◽

Matthew Browning ◽

Andiara Schwingel ◽

...

Keyword(s):

Gut Microbiota ◽

Dietary Habits ◽

Pilot Trial ◽

Alpha Diversity ◽

Total Sample ◽

Fecal Microbiota ◽

Healthy Eating Index ◽

Garden Soil ◽

Control Group ◽

Soil Dna

Abstract Objectives Urbanization has reduced environmental microorganism exposure, with most Americans spending over 90% of their time indoors. However, gardening remains a viable means of exposure to soil microorganisms and harvesting of edible produce. Accordingly, we aimed to determine relations between gardening, dietary habits, and gut microbiota. Methods Gardening families (N = 10) and non-gardening (control) families (N = 9) were enrolled in a longitudinal pilot trial. Families included two adults and a child (5–18 years) for a total sample size of 54 participants. Fecal samples were collected prior to and at the end of the gardening season. Garden soil samples (n = 9) were collected prior to and at the end of the season. Diet history questionnaires were collected at the beginning and end of the study to measure Healthy Eating Index (HEI) scores. Fecal and soil DNA were extracted, sequenced (V4 region of 16S rDNA gene), and analyzed using DADA2 and QIIME2. Alpha diversity measures were assessed, including Faith's phylogenetic diversity (PD) and observed operational taxonomic units (OTUs). Results Gardening families had significantly more fecal OTUs compared to control families (172.3 ± 44.2 vs. 157.0 ± 44.2, respectively; P = 0.03). Gardening families had greater (P = 0.02) Faith's PD scores and tended (P = 0.08) to have more fecal OTUs than the control group at peak gardening season. In the gardening families, fecal OTUs and Faith's PD were numerically but not statistically greater at the end of the season compared to baseline (all p’s > 0.05). Prior to the gardening season, gardening adults had greater HEI scores compared to control families (57 ± 9.1 vs. 49 ± 8.8, P = 0.03). HEI scores were not different between groups at the end of the study. Conclusions This study revealed that the fecal microbiota of families that garden differs from non-gardening families, and there are detectable changes in the fecal microbial community of gardeners and their family members over the course of the gardening season. Further research is needed to understand the role of diet in these changes and if microbes within the soil move between the soil and gastrointestinal environments. Funding Sources This research was funded by the Christopher Family Foundation Food and Family Grant Program.

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Gut Microbiota Composition and Metabolomic Profiles of Wild and Captive Chinese Monals (Lophophorus lhuysii)

10.21203/rs.3.rs-32587/v2 ◽

2020 ◽

Author(s):

Dandan Jiang ◽

Xin He ◽

Marc Valitutto ◽

Li Chen ◽

Qin Xu ◽

...

Keyword(s):

Gut Microbiota ◽

High Performance ◽

Bird Species ◽

Alpha Diversity ◽

Integrated Approach ◽

Fecal Microbiota ◽

Rrna Gene ◽

Microbiota Composition ◽

Metabolomic Profile ◽

Gut Microbiota Composition

Abstract Background：The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains of southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolome of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal RNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatography (UHPLC) based metabolomics were used to examine the fecal microbiota composition and the metabolomic profile of Chinese monals. Results: The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial taxa in the two groups showed remarkable differences at phylum, class, order, and family levels. Metabolomic profiling also revealed differences, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, strong correlations of metabolite types and bacterial genus were detected. Conclusions: There were remarkable differences in the gut microbiota composition and metabolomic profile between wild and captive Chinese monals. This study has established a baseline for a normal gut microbiota and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive organisms have an impact on their overall health and reproduction.

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Dietary Correlates of Oral and Gut Microbiota in the Water Monitor Lizard, Varanus salvator (Laurenti, 1768)

Frontiers in Microbiology ◽

10.3389/fmicb.2021.771527 ◽

2022 ◽

Vol 12 ◽

Author(s):

Yu Du ◽

Jun-Qiong Chen ◽

Qian Liu ◽

Jian-Chao Fu ◽

Chi-Xian Lin ◽

...

Keyword(s):

Gut Microbiota ◽

Water Environment ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Oral Microbiota ◽

Monitor Lizard ◽

Varanus Salvator ◽

In The Wild ◽

Monitor Lizards

Numerous studies have demonstrated that food shapes the structure and composition of the host’s oral and gut microbiota. The disorder of oral and gut microbiota may trigger various host diseases. Here, we collected oral and gut samples from wild water monitor lizards (Varanus salvator) and their captive conspecifics fed with bullfrogs, eggs, and depilated chicken, aiming to examine dietary correlates of oral and gut microbiota. We used the 16S rRNA gene sequencing technology to analyze the composition of the microbiota. Proteobacteria and Bacteroidota were the dominant phyla in the oral microbiota, and so were in the gut microbiota. The alpha diversity of microbiota was significantly higher in the gut than in the oral cavity, and the alpha diversity of oral microbiota was higher in captive lizards than in wild conspecifics. Comparing the relative abundance of oral and gut bacteria and their gene functions, differences among different animal groups presumably resulted from human contact in artificial breeding environments and complex food processing. Differences in gene function might be related to the absolute number and/or the taxonomic abundance of oral and gut microorganisms in the wild and the water environment. This study provides not only basic information about the oral and gut microbiota of captive and wild water monitor lizards, but also an inference that feeding on frogs and aquatic products and reducing human exposure help water monitor lizards maintain a microbiota similar to that in the wild environment.

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Effects of Fecal Microbiota Transplantation on Composition in Mice with CKD

Toxins ◽

10.3390/toxins12120741 ◽

2020 ◽

Vol 12 (12) ◽

pp. 741

Author(s):

Christophe Barba ◽

Christophe O. Soulage ◽

Gianvito Caggiano ◽

Griet Glorieux ◽

Denis Fouque ◽

...

Keyword(s):

Gut Microbiota ◽

Fecal Microbiota Transplantation ◽

Therapeutic Option ◽

Alpha Diversity ◽

Fecal Microbiota ◽

Uremic Toxins ◽

Uremic Toxin ◽

Renal Disorder ◽

Metabolic Complication ◽

Noticeable Improvement

Background: Chronic kidney disease (CKD) is a renal disorder characterized by the accumulation of uremic toxins with limited strategies to reduce their concentrations. A large amount of data supports the pivotal role of intestinal microbiota in CKD complications and as a major source of uremic toxins production. Here, we explored whether fecal microbiota transplantation (FMT) could be attenuated in metabolic complication and uremic toxin accumulation in mice with CKD. Methods: Kidney failure was chemically induced by a diet containing 0.25% (w/w) of adenine for four weeks. Mice were randomized into three groups: control, CKD and CKD + FMT groups. After four weeks, CKD mice underwent fecal microbiota transplantation (FMT) from healthy mice or phosphate buffered saline as control. The gut microbiota structure, uremic toxins plasmatic concentrations, and metabolic profiles were explored three weeks after transplantation. Results: Associated with the increase of alpha diversity, we observed a noticeable improvement of gut microbiota disturbance, after FMT treatment. FMT further decreased p-cresyl sulfate accumulation and improved glucose tolerance. There was no change in kidney function. Conclusions: These data indicate that FMT limited the accumulation of uremic toxins issued from intestinal cresol pathway by a beneficial effect on gut microbiota diversity. Further studies are needed to investigate the FMT efficiency, the timing and feces amount for the transplantation before, to become a therapeutic option in CKD patients.

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Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study

Nutrients ◽

10.3390/nu12072112 ◽

2020 ◽

Vol 12 (7) ◽

pp. 2112

Author(s):

Talía Sainz ◽

María José Gosalbes ◽

Alba Talavera ◽

Nuria Jimenez-Hernandez ◽

Luis Prieto ◽

...

Keyword(s):

Gut Microbiota ◽

Alpha Diversity ◽

Nutritional Intervention ◽

Fecal Microbiota ◽

Controlled Study ◽

Control Group ◽

Rrna Gene ◽

Double Blind ◽

Human Virus ◽

Intestinal Dysbiosis

Aims: The gut microbiota exerts a critical influence in the immune system. The gut microbiota of human virus immunodeficiency (HIV)-infected children remains barely explored. We aimed to characterize the fecal microbiota in vertically HIV-infected children and to explore the effects of its modulation with a symbiotic nutritional intervention. Methods: a pilot, double blind, randomized placebo-controlled study including HIV-infected children who were randomized to receive a nutritional supplementation including prebiotics and probiotics or placebo for four weeks. HIV-uninfected siblings were recruited as controls. The V3–V4 region of the 16S rRNA gene was sequenced in fecal samples. Results: 22 HIV-infected children on antiretroviral therapy (ART) and with viral load (VL) <50/mL completed the follow-up period. Mean age was 11.4 ± 3.4 years, eight (32%) were male. Their microbiota showed reduced alpha diversity compared to controls and distinct beta diversity at the genus level (Adonis p = 0.042). Patients showed decreased abundance of commensals Faecalibacterium and an increase in Prevotella, Akkermansia and Escherichia. The nutritional intervention shaped the microbiota towards the control group, without a clear directionality. Conclusions: Vertical HIV infection is characterized by changes in gut microbiota structure, distinct at the compositional level from the findings reported in adults. A short nutritional intervention attenuated bacterial dysbiosis, without clear changes at the community level. Summary: In a group of 24 vertically HIV-infected children, in comparison to 11 uninfected controls, intestinal dysbiosis was observed despite effective ART. Although not fully effective to restore the microbiota, a short intervention with pre/probiotics attenuated bacterial dysbiosis.

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High-intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.00537.2015 ◽

2016 ◽

Vol 310 (11) ◽

pp. E982-E993 ◽

Cited By ~ 87

Author(s):

Emmanuel Denou ◽

Katarina Marcinko ◽

Michael G. Surette ◽

Gregory R. Steinberg ◽

Jonathan D. Schertzer

Keyword(s):

Metabolic Disease ◽

Exercise Training ◽

Gut Microbiota ◽

High Intensity ◽

Alpha Diversity ◽

Tca Cycle ◽

Fecal Microbiota ◽

Chow Diet ◽

Tissue Mass ◽

Diet Induced Obesity

Diet and exercise underpin the risk of obesity-related metabolic disease. Diet alters the gut microbiota, which contributes to aspects of metabolic disease during obesity. Repeated exercise provides metabolic benefits during obesity. We assessed whether exercise could oppose changes in the taxonomic and predicted metagenomic characteristics of the gut microbiota during diet-induced obesity. We hypothesized that high-intensity interval training (HIIT) would counteract high-fat diet (HFD)-induced changes in the microbiota without altering obesity in mice. Compared with chow-fed mice, an obesity-causing HFD decreased the Bacteroidetes-to-Firmicutes ratio and decreased the genetic capacity in the fecal microbiota for metabolic pathways such as the tricarboxylic acid (TCA) cycle. After HFD-induced obesity was established, a subset of mice were HIIT for 6 wk, which increased host aerobic capacity but did not alter body or adipose tissue mass. The effects of exercise training on the microbiota were gut segment dependent and more extensive in the distal gut. HIIT increased the alpha diversity and Bacteroidetes/Firmicutes ratio of the distal gut and fecal microbiota during diet-induced obesity. Exercise training increased the predicted genetic capacity related to the TCA cycle among other aspects of metabolism. Strikingly, the same microbial metabolism indexes that were increased by exercise were all decreased in HFD-fed vs. chow diet-fed mice. Therefore, exercise training directly opposed some of the obesity-related changes in gut microbiota, including lower metagenomic indexes of metabolism. Some host and microbial pathways appeared similarly affected by exercise. These exercise- and diet-induced microbiota interactions can be captured in feces.

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