scholarly journals Exploring Yak (Bos grunniens) Rumen Bacterial and Fungal Communities from 5 Days after Birth to Adulthood

2022 ◽  
Author(s):  
Shuli Yang ◽  
Guangrong Zhang ◽  
Mingyue Deng ◽  
Liyuan Sun ◽  
Shichun He ◽  
...  
Keyword(s):  
Microbial Community ◽  
Anaerobic Bacteria ◽  
Age Groups ◽  
Amplicon Sequencing ◽  
Meat Production ◽  
Gradual Change ◽  
Microbial Composition ◽  
Plant Fibers ◽  
Rumen Microorganisms ◽  
Facultative Anaerobic Bacteria

Abstract The gut microbial community of mammals, especially ruminants, plays an important role at different ages of the host. Ruminants have a unique compartment in their digestive tract; the rumen, comprising microorganisms that can effectively decompose plant fibers for the host to transform into milk and for growth and development, which is important for meat production. Colonization of rumen microorganisms is closely related to host developmental stage and affects host performance production. There is little information regarding initial colonization and subsequent changes of the rumen microbial population in wild grazing animals, from birth to adulthood. This study investigated the rumen bacterial and fungal populations of grazing yaks in five experimental groups, ranging from a few days after birth to adulthood using amplicon sequencing. Results indicated that rumen microbial communities of these yaks undergo a gradual change from 5 to 180 days after birth, with the bacterial and fungal diversity stabilizing at the age of 2 years. Additionally, Ruminococcus was detected in 5-day-old yak rumens, with a high percentage of Penicillium and other microbial species are important for normal rumen function detected in the adult rumen. The changes to the yak rumen microbial community after birth were reflected in the increased anaerobic fiber degradation group, and decreased aerobic and facultative anaerobic bacteria. Microbial diversity and abundance in the yak rumen increased with age. Rumen microbial composition of 6-month and 2-year-old yaks had obvious homogeneity. There were some differences in dominant rumen microorganisms among the different age groups. Further studies are required to confirm the functions of these differential and dominant microorganisms in each age group.

scholarly journals Streptomycin-Induced Inflammation Enhances Escherichia coli Gut Colonization Through Nitrate Respiration

mBio ◽  
2013 ◽  
Vol 4 (4) ◽  
Author(s):  
Alanna M. Spees ◽  
Tamding Wangdi ◽  
Christopher A. Lopez ◽  
Dawn D. Kingsbury ◽  
Mariana N. Xavier ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Microbial Community ◽  
Intestinal Inflammation ◽  
Anaerobic Bacteria ◽  
Nitrate Respiration ◽  
Colonization Resistance ◽  
Content Type ◽  
E Coli ◽  
Gut Colonization ◽  
Facultative Anaerobic Bacteria

ABSTRACTTreatment with streptomycin enhances the growth of human commensalEscherichia coliisolates in the mouse intestine, suggesting that the resident microbial community (microbiota) can inhibit the growth of invading microbes, a phenomenon known as “colonization resistance.” However, the precise mechanisms by which streptomycin treatment lowers colonization resistance remain obscure. Here we show that streptomycin treatment rendered mice more susceptible to the development of chemically induced colitis, raising the possibility that the antibiotic might lower colonization resistance by changing mucosal immune responses rather than by preventing microbe-microbe interactions. Investigation of the underlying mechanism revealed a mild inflammatory infiltrate in the cecal mucosa of streptomycin-treated mice, which was accompanied by elevated expression ofNos2, the gene that encodes inducible nitric oxide synthase. In turn, this inflammatory response enhanced the luminal growth ofE. coliby nitrate respiration in aNos2-dependent fashion. These data identify low-level intestinal inflammation as one of the factors responsible for the loss of resistance toE. colicolonization after streptomycin treatment.IMPORTANCEOur intestine is host to a complex microbial community that confers benefits by educating the immune system and providing niche protection. Perturbation of intestinal communities by streptomycin treatment lowers “colonization resistance” through unknown mechanisms. Here we show that streptomycin increases the inflammatory tone of the intestinal mucosa, thereby making the bowel more susceptible to dextran sulfate sodium treatment and boosting theNos2-dependent growth of commensalEscherichia coliby nitrate respiration. These data point to the generation of alternative electron acceptors as a by-product of the inflammatory host response as an important factor responsible for lowering resistance to colonization by facultative anaerobic bacteria such asE. coli.

Abstract 17318: Cardioprotective Microbes and Restorative Sleep Are Reduced and Blood Pressure During Sleep is Increased When Rats Have Fragmented Sleep

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Katherine A Maki ◽  
Jennifer J Barb ◽  
Ulf G Bronas ◽  
Michael W Calik ◽  
Stefan Green ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Gut Microbiome ◽  
Slow Wave Sleep ◽  
Anaerobic Bacteria ◽  
Amplicon Sequencing ◽  
Poor Quality ◽  
Microbial Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Quality Sleep ◽  
Wistar Kyoto

Introduction: Sleep that is restless and fragmented impairs cardiovascular (CV) health. Using a rat model, we measured sleep characteristics and assessed bacterial communities in the gut microbiome. We hypothesized poor quality sleep to be associated with a reduction in cardioprotective microbiomes and adverse CV outcomes. Methods: Wistar Kyoto rats had normal sleep (n= 7, controls) or 8-hrs of fragmented sleep (n = 8) for 28 days. Implanted telemetry transmitters recorded blood pressure (BP), heart rate (HR), and cortical electroencephalogram (EEG) signals continuously. Fecal samples were collected daily; microbial composition was determined by 16S rRNA amplicon sequencing. Results: The sleep fragmented (SF) rats could not achieve deep slow-wave sleep (SWS) for 8-hrs each day—compared with controls, relative EEG delta power (a marker of the depth of sleep) was significantly lower (29±3% versus 39±3%, P = 0.04). In addition, SF was associated with a rise in BP and HR. The relative abundance of Parabacteroides (classified to genus level) and Tannerellaceae (classified to family level), both gram-negative anaerobic bacteria from the phylum Bacteroidetes, were decreased in SF rats during late-SF (intervention days 20 & 27), relative to controls. Elevated Parabacteroides levels (%) were significantly and inversely correlated with systolic (R= -0.002, P <0.001) and diastolic (R= -0.003, P <0.001) BP levels recorded during sleep in both groups of rats. Conclusions: Parabacteroides levels in the gut microbiome may contribute to changes in BP. Undesirable changes in sleep from SF are associated with reduced levels of Parabacteroides during the late-SF period in the gut microbiome, compared with controls. The Parabacteroides -BP associations and reactivity of this bacterium to disrupted sleep support Parabacteroides as an exciting cardioprotective biomarker to stratify and prevent negative CV outcomes provoked by SF.

scholarly journals Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

2015 ◽  
Vol 81 (7) ◽  
pp. 2525-2533 ◽  
Author(s):  
Daniel J. O'Sullivan ◽  
Paul D. Cotter ◽  
Orla O'Sullivan ◽  
Linda Giblin ◽  
Paul L. H. McSweeney ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Microbial Population ◽  
Amplicon Sequencing ◽  
Production Cycle ◽  
Microbial Composition ◽  
Temporal And Spatial Distribution ◽  
Content Type ◽  
Temporal And Spatial

ABSTRACTWe sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the generaThermus,Pseudoalteromonas, andBifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.

scholarly journals Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection

2019 ◽  
Vol 117 (2) ◽  
pp. 1148-1159 ◽  
Author(s):  
Norma M. Morella ◽  
Francis Cheng-Hsuan Weng ◽  
Pierre M. Joubert ◽  
C. Jessica E. Metcalf ◽  
Steven Lindow ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Amplicon Sequencing ◽  
Host Genotype ◽  
Microbial Composition ◽  
Internal Transcribed Spacer Region ◽  
Tomato Plants ◽  
16S Amplicon Sequencing ◽  
Host Evolution ◽  
Plant Microbiome

There is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across 5 plant genotypes for 4 45-d passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (internal transcribed spacer region amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment, suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted within the experimental setting. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond. In light of the consistent response of the microbiome to selection in the absence of reciprocal host evolution (coevolution) described here, future studies should address how such adaptation influences host health.

scholarly journals Microbial Diversity and Community Variation in the Intestines of Layer Chickens

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 840
Author(s):  
Sha-Sha Xiao ◽  
Jian-Dui Mi ◽  
Liang Mei ◽  
Juanboo Liang ◽  
Kun-Xian Feng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Intestinal Microbiota ◽  
Anaerobic Bacteria ◽  
Temporal Variations ◽  
Factors Affecting ◽  
Intestinal Microbes ◽  
Facultative Anaerobic ◽  
Environment Control ◽  
Layer Chickens ◽  
Facultative Anaerobic Bacteria

The intestinal microbiota is increasingly recognized as an important component of host health, metabolism and immunity. Early gut colonizers are pivotal in the establishment of microbial community structures affecting the health and growth performance of chickens. White Lohmann layer is a common commercial breed. Therefore, this breed was selected to study the pattern of changes of microbiota with age. In this study, the duodenum, caecum and colorectum contents of white Lohmann layer chickens from same environment control farm were collected and analyzed using 16S rRNA sequencing to explore the spatial and temporal variations in intestinal microbiota. The results showed that the diversity of the microbial community structure in the duodenum, caecum and colorectum increased with age and tended to be stable when the layer chickens reached 50 days of age and the distinct succession patterns of the intestinal microbiota between the duodenum and large intestine (caecum and colorectum). On day 0, the diversity of microbes in the duodenum was higher than that in the caecum and colorectum, but the compositions of intestinal microbes were relatively similar, with facultative anaerobic Proteobacteria as the main microbes. However, the relative abundance of facultative anaerobic bacteria (Escherichia) gradually decreased and was replaced by anaerobic bacteria (Bacteroides and Ruminococcaceae). By day 50, the structure of intestinal microbes had gradually become stable, and Lactobacillus was the dominant bacteria in the duodenum (41.1%). The compositions of dominant microbes in the caecum and colorectum were more complex, but there were certain similarities. Bacteroides, Odoribacter and Clostridiales vadin BB60 group were dominant. The results of this study provide evidence that time and spatial factors are important factors affecting the intestinal microbiota composition. This study provides new knowledge of the intestinal microbiota colonization pattern of layer chickens in early life to improve the intestinal health of layer chickens.

Investigating temporal microbial dynamics in the rumen of beef calves raised on two farms during early life

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Eóin O'Hara ◽  
David A Kenny ◽  
Emily McGovern ◽  
Colin J Byrne ◽  
Matthew S McCabe ◽  
...  
Keyword(s):  
Early Life ◽  
Local Environment ◽  
Archaeal Community ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Rumen Microorganisms ◽  
Beef Calves ◽  
Fundamental Information ◽  
Nutrient Utilisation

ABSTRACT Manipulation of the rumen microorganisms during early life has emerged as a promising strategy for persistent improvement of nutrient utilisation and lowering of enteric methanogenesis. However, limited understanding of the dynamics of rumen microbial colonisation has prevented the identification of the optimum timeframe for such interventions. The present study used DNA amplicon sequencing of the 16S rRNA gene to assess bacterial and archaeal dynamics in the rumen digesta of beef calves raised on two farms from birth through to post-weaning. The colonisation patterns of both communities were influenced by age (P &lt; 0.05) and farm of origin (P &lt; 0.05). The bacterial community exhibited an age-wise progression during the first month of life which appeared to be partly related to diet, and settled by day 21, indicating that this may mark the boundary of a timeframe for intervention. The archaeal community appeared less sensitive to age/diet than bacteria in the first month of life but was more sensitive to farm environment. These data show that ruminal microbial composition during early life is driven by calf age, diet and local environment, and provide important fundamental information concerning the ontogeny of the rumen microbiota from birth.

scholarly journals Effects of multi-electron acceptor coexistence system on perchlorate biodegradation and microbial community variation

2017 ◽  
Vol 18 (4) ◽  
pp. 1428-1436 ◽  
Author(s):  
Na Liu ◽  
Xueming Qin ◽  
Yonglei An ◽  
Hua Qiu ◽  
Yue Wang
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Electron Acceptor ◽  
Microbial Community Structure ◽  
Anaerobic Bacteria ◽  
Mixed Population ◽  
Electron Acceptors ◽  
Degrading Bacterium ◽  
Degrading Bacteria ◽  
Facultative Anaerobic Bacteria

Abstract Many studies have reported that a certain preference is obeyed by perchlorate-degrading bacteria to utilize different electron acceptors. This conclusion was stated considering only the removal rate of different electron acceptors, indicating a lack of adequate proof. This study investigated the selective utilization of different electron acceptors by a perchlorate-degrading bacterium. The results showed that the mixed population of microorganisms (containing perchlorate-degrading bacteria) obeyed a certain sequence to utilize different electron acceptors, which was oxygen &gt; nitrate &gt; perchlorate &gt; sulfate. The results of high-throughput sequencing showed that the mixed population of microorganisms contained anaerobic bacteria, facultative anaerobic bacteria, and aerobic bacteria. The microbial community structure actually had been changed by adding another electron acceptor to the perchlorate-medium and the microbial genera were distinguished in terms of utilizing the specific electron acceptor (e.g., oxygen, nitrate, sulfate). The result of canonical correspondence analysis demonstrated that the abundance of microorganisms appeared as a good positive correlation with the corresponding electron acceptor. Therefore, a new viewpoint was inferred that there are two main reasons at least that make the mixed microorganisms obey a certain sequence to utilize different electron acceptors. One reason is that the perchlorate-degrading bacteria in the mixed microorganisms change their own respiratory metabolism pathway. The other reason is that the mixed microorganisms actually change their microbial community structure.

scholarly journals Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection

2019 ◽  
Author(s):  
Norma M. Morella ◽  
Francis Cheng-Hsuan Weng ◽  
Pierre M. Joubert ◽  
C. Jessica E. Metcalf ◽  
Steven Lindow ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Amplicon Sequencing ◽  
Host Genotype ◽  
Microbial Composition ◽  
Plant Host ◽  
Independent Manner ◽  
16S Amplicon Sequencing ◽  
The Impact ◽  
Plant Microbiome

AbstractThere is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across five plant genotypes for four eight-week long passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (ITS amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond.Significance StatementThere is great interest in selecting for host-associated microbiomes that confer particular functions to their host, and yet it remains unknown whether selection for a robust and stable microbiome is possible. Here, we use a microbiome passaging approach to measure the impact of host-mediated selection on the tomato phyllosphere (above ground) microbiome. We find robust community selection across replicate lines that is shaped by plant host genotype in early passages, but changes in a genotype-independent manner in later passages. Work such as ours is crucial to understanding the general principles governing microbiome assembly and adaptation, and is widely applicable to both sustainable agriculture and microbiome-related medicine.

CHANGES IN SMALL INTESTINE MICROFLORA IN PATIENTS WITH ACUTE INTESTINAL OBSTRUCTION

2020 ◽  
pp. 16-18
Author(s):  
V. M. Lykhman ◽  
O. M. Shevchenko ◽  
Ye. O. Bilodid ◽  
Igor Vladimirovich Volchenko ◽  
I. A. Kulyk ◽  
...  
Keyword(s):  
Small Intestine ◽  
Gastrointestinal Tract ◽  
Species Composition ◽  
Intestinal Obstruction ◽  
Bacterial Flora ◽  
Anaerobic Bacteria ◽  
Acute Intestinal Obstruction ◽  
Gram Positive ◽  
Mechanical Intestinal Obstruction ◽  
Facultative Anaerobic Bacteria

Among urgent surgical diseases of abdominal cavity, an acute intestinal obstruction is the most difficult to be diagnosed and treated. Leading factor, determining the development of pathophysiological processes is considered to be the progressive manifestations of enteric insufficiency syndrome, resulting in intestinal barrier impairment, negative changes in ecology of intestinal flora, increased endotoxins. To identify the small intestine microflora in acute intestinal obstruction and determine the role of dysbiotic disorders in clinical manifestations of main pathological process, a study was conducted in 60 patients with mechanical intestinal obstruction. The small intestine has a relatively rare microflora, consisting mainly of gram−positive facultative aerobic microorganisms, streptococci, lactobacilli. The distal ileum in nearly 30−55 % of healthy people contains scanty microflora, and yet the flora of this area differs from the microbial population of the higher gastrointestinal tract due to higher concentration of gram−negative bacteria. Optional−anaerobic coliform bacilli, anaerobic bifidobacteria and fusobacteria, bacteroids, the number of which starts exceeding the one of gram−positive species, are presented in significant quantities. Distal to the ileocecal valve there are significant changes in the microflora quantitative and species composition. Obligatory anaerobic bacteria become the predominant part of microflora, exceeding the number of aerobic and facultative anaerobic bacteria. The bacterial flora in different parts of gastrointestinal tract has its own specifics and is quite constant, as a result of the interaction of many factors, regulating the bacterial population in small intestine. The most important among them are: acidity of gastric juice, normal peristaltic activity of the intestine, bacterial interactions and immune mechanisms. Disorders of the intestine motor and evacuation function with its obstruction lead to slow passage of the chyme and contamination of the upper gastrointestinal tract with new types of microbes. There is a syndrome of small intestine excessive colonization, which means an increased concentration of bacterial populations in it, similar in species composition to the colon microflora. Pathological intra−intestinal contents become a source of endogenous infection and re−infection of the patient, leads to internal digestive disorders, which is manifested by syndrome of malabsorption of proteins, carbohydrates and vitamins. Key words: acute intestinal obstruction, small intestinal microflora, conditionally pathogenic microorganisms, intestinal biocenosis.

scholarly journals Colonocyte metabolism shapes the gut microbiota

Science ◽  
2018 ◽  
Vol 362 (6418) ◽  
pp. eaat9076 ◽  
Author(s):  
Yael Litvak ◽  
Mariana X. Byndloss ◽  
Andreas J. Bäumler
Keyword(s):  
Gut Microbiota ◽  
Anaerobic Bacteria ◽  
Enteric Pathogens ◽  
Metabolic Reprogramming ◽  
Human Diseases ◽  
Fermentation Products ◽  
Colonic Microbiota ◽  
Obligate Anaerobic ◽  
Control Switch ◽  
Facultative Anaerobic Bacteria

An imbalance in the colonic microbiota might underlie many human diseases, but the mechanisms that maintain homeostasis remain elusive. Recent insights suggest that colonocyte metabolism functions as a control switch, mediating a shift between homeostatic and dysbiotic communities. During homeostasis, colonocyte metabolism is directed toward oxidative phosphorylation, resulting in high epithelial oxygen consumption. The consequent epithelial hypoxia helps to maintain a microbial community dominated by obligate anaerobic bacteria, which provide benefit by converting fiber into fermentation products absorbed by the host. Conditions that alter the metabolism of the colonic epithelium increase epithelial oxygenation, thereby driving an expansion of facultative anaerobic bacteria, a hallmark of dysbiosis in the colon. Enteric pathogens subvert colonocyte metabolism to escape niche protection conferred by the gut microbiota. The reverse strategy, a metabolic reprogramming to restore colonocyte hypoxia, represents a promising new therapeutic approach for rebalancing the colonic microbiota in a broad spectrum of human diseases.

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