The impact of mixtures of xylose and glucose on the microbial diversity and fermentative metabolism of sequencing-batch or continuous enrichment cultures

ABSTRACT Efficient industrial fermentation of lignocellulosic waste containing a large part of glucose and xylose is desirable to implement a circular economy. Mixed culture biotechnologies can aid in realizing this goal. The effect of feeding equivalent substrates to a microbial community, such a xylose and glucose, is not well understood in terms of the number of dominant species and how these species compete for the substrates. We compared the metabolism and microbial community structure in a continuous-flow stirred tank reactor (CSTR) and a sequencing batch reactor (SBR) fed with a mixture of xylose and glucose, inoculated with bovine rumen at pH 8, 30°C and a hydraulic retention time of 8 h. We hypothesised that a CSTR will select for generalist species, taking up both substrates. We used 16S rRNA gene sequencing and fluorescent in situ hybridisation to accurately determine the microbial community structures. Both enrichments were stoichiometrically and kinetically characterised. The CSTR enrichment culture was dominated by Clostridium intestinale (91% ± 2%). The SBR showed an abundance of Enterobacteriaceae (75% ± 8%), dominated by Citrobacter freundii and a minor fraction of Raoultella ornithinolytica. C. freundii ferments xylose and glucose in a non-diauxic fashion. Clearly, a non-diauxic generalist outcompetes specialists and diauxic generalists in SBR environments.

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Arsenic mobilization in a high arsenic groundwater revealed by metagenomic and Geochip analyses

Scientific Reports ◽

10.1038/s41598-019-49365-w ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Zhou Jiang ◽

Ping Li ◽

Yanhong Wang ◽

Han Liu ◽

Dazhun Wei ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Arsenic Mobilization ◽

Rrna Gene Sequencing ◽

High Arsenic ◽

High Arsenic Groundwater

Abstract Microbial metabolisms of arsenic, iron, sulfur, nitrogen and organic matter play important roles in arsenic mobilization in aquifer. In this study, microbial community composition and functional potentials in a high arsenic groundwater were investigated using integrated techniques of RNA- and DNA-based 16S rRNA gene sequencing, metagenomic sequencing and functional gene arrays. 16S rRNA gene sequencing showed the sample was dominated by members of Proteobacteria (62.3–75.2%), such as genera of Simplicispira (5.7–6.7%), Pseudomonas (3.3–5.7%), Ferribacterium (1.6–4.4%), Solimonas (1.8–3.2%), Geobacter (0.8–2.2%) and Sediminibacterium (0.6–2.4%). Functional potential analyses indicated that organics degradation, assimilatory sulfate reduction, As-resistant pathway, iron reduction, ammonification, nitrogen fixation, denitrification and dissimilatory nitrate reduction to ammonia were prevalent. The composition and function of microbial community and reconstructed genome bins suggest that high level of arsenite in the groundwater may be attributed to arsenate release from iron oxides reductive dissolution by the iron-reducing bacteria, and subsequent arsenate reduction by ammonia-producing bacteria featuring ars operon. This study highlights the relationship between biogeochemical cycling of arsenic and nitrogen in groundwater, which potentially occur in other aquifers with high levels of ammonia and arsenic.

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Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys

The Journals of Gerontology Series A ◽

10.1093/gerona/glaa256 ◽

2020 ◽

Author(s):

Ravichandra Vemuri ◽

Chrissy Sherrill ◽

Matthew A Davis ◽

Kylie Kavanagh

Keyword(s):

Microbial Community ◽

Systemic Inflammation ◽

16S Rrna Gene Sequencing ◽

Microbial Interactions ◽

Rrna Gene ◽

Vervet Monkeys ◽

Fecal Samples ◽

Age Related ◽

Rrna Gene Sequencing ◽

The Stability

Abstract Age-related changes in gut microbiome impact host health. The interactive relationship between the microbiome and physiological systems in an aged body system remains to be clearly defined, particularly in the context of inflammation. Therefore, we aimed to evaluate systemic inflammation, microbial translocation (MT), and differences between fecal and mucosal microbiomes. Ascending colon mucosal biopsies, fecal samples, and blood samples from healthy young and old female vervet monkeys were collected for 16S rRNA gene sequencing, MT, and cytokine analyses, respectively. To demonstrate microbial co-occurrence patterns, we used Kendall’s tau correlation measure of interactions between microbes. We found elevated levels of plasma LBP-1, MCP-1, and CRP in old monkeys, indicative of higher MT and systemic inflammation. Microbiome analysis revealed significant differences specific to age. At the phylum level, abundances of pathobionts such as Proteobacteria were increased in the mucosa of old monkeys. At the family level, Helicobacteriaceae was highly abundant in mucosal samples (old); in contrast, Ruminococcaceae were higher in the fecal samples of old monkeys. We found significantly lower Firmicutes:Bacteroidetes ratio and lower abundance of butyrate-producing microbes in old monkeys, consistent with less healthy profiles. Microbial community co-occurrence analysis on mucosal samples revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys. Our findings provide novel insights into systemic inflammation and gut microbial interactions, highlight the importance of the mucosal niche, and facilitate further understanding of the decline in the stability of the microbial community with aging.

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Inbreeding Alters the Gut Microbiota of the Banna Minipig

Animals ◽

10.3390/ani10112125 ◽

2020 ◽

Vol 10 (11) ◽

pp. 2125

Author(s):

Limin Wei ◽

Bo Zeng ◽

Siyuan Zhang ◽

Feng Li ◽

Fanli Kong ◽

...

Keyword(s):

Gut Microbiota ◽

Gene Sequencing ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Rrna Gene Sequencing ◽

Isoleucine Metabolism ◽

Dominant Bacteria ◽

The Impact ◽

Predicted Function

The gut microbiota coevolve with the host and can be stably transmitted to the offspring. Host genetics plays a crucial role in the composition and abundance of gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity and the heterozygosity. In this study, we used 16S rRNA gene sequencing to compare the differences of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to understand the impact of inbreeding on the gut microbiota. Three dominant bacteria (Stenotrophlomonas, Streptococcus, and Lactobacillus) were steadily enriched in both the Diannan small-ear pig and Banna minipig inbred. After inbreeding, the gut microbiota alpha diversity and some potential probiotics (Bifidobacterium, Tricibacter, Ruminocaccae, Christensenellaceae, etc.) were significantly decreased, while the pathogenic Klebsiella bacteria was significantly increased. In addition, the predicted metagenomic analysis (PICRUSt2) indicated that several amino acid metabolisms (‘‘Valine, leucine, and isoleucine metabolism’’, ‘‘Phenylalanine, tyrosine, and tryptophan biosynthesis’’, ‘‘Histidine metabolism’’) were also markedly decreased after the inbreeding. Altogether our data reveal that host inbreeding altered the composition and the predicted function of the gut microbiome, which provides some data for the gut microbiota during inbreeding.

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The Gut Microbial Community of Antarctic Fish Detected by 16S rRNA Gene Sequence Analysis

BioMed Research International ◽

10.1155/2016/3241529 ◽

2016 ◽

Vol 2016 ◽

pp. 1-7 ◽

Cited By ~ 18

Author(s):

Wei Song ◽

Lingzhi Li ◽

Hongliang Huang ◽

Keji Jiang ◽

Fengying Zhang ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Communities ◽

Antarctic Fish ◽

16S Rrna Gene Sequencing ◽

Physiological Characteristics ◽

Rrna Gene ◽

Rrna Gene Sequencing ◽

Gut Microbial Community

Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and a range of fitness in fish, but little is known about the gut microbial community in Antarctic fish. In this study, the composition of intestinal microbial community in four species of Antarctic fish was detected based on 16S rRNA gene sequencing. As a result, 1 004 639 sequences were obtained from 13 samples identified into 36 phyla and 804 genera, in which Proteobacteria, Actinobacteria, Firmicutes, Thermi, and Bacteroidetes were the dominant phyla, and Rhodococcus, Thermus, Acinetobacter, Propionibacterium, Streptococcus, and Mycoplasma were the dominant genera. The number of common OTUs (operational taxonomic units) varied from 346 to 768, while unique OTUs varied from 84 to 694 in the four species of Antarctic fish. Moreover, intestinal bacterial communities in individuals of each species were not really similar, and those in the four species were not absolutely different, suggesting that bacterial communities might influence the physiological characteristics of Antarctic fish, and the common bacterial communities might contribute to the fish survival ability in extreme Antarctic environment, while the different ones were related to the living habits. All of these results could offer certain information for the future study of Antarctic fish physiological characteristics.

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Understanding host-microbiota interactions in the commercial piglet around weaning

Scientific Reports ◽

10.1038/s41598-021-02754-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Saladrigas-García ◽

M. D’Angelo ◽

H. L. Ko ◽

P. Nolis ◽

Y. Ramayo-Caldas ◽

...

Keyword(s):

Gene Expression ◽

Gut Microbiota ◽

Metabolic Response ◽

Negative Impact ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Swine Industry ◽

Weaning Stress ◽

Rrna Gene Sequencing ◽

The Impact

AbstractWeaning is a critical period in the life of pigs with repercussions on their health and welfare and on the economy of the swine industry. This study aimed to assess the effect of the commercial early weaning on gut microbiota, intestinal gene expression and serum metabolomic response via an integrated-omic approach combining 16S rRNA gene sequencing, the OpenArray gene expression technology and 1H-NMR spectroscopy. Fourteen piglets from different litters were sampled for blood, jejunum tissue and caecal content two days before (− 2d), and three days after (+ 3d) weaning. A clearly differential ordination of caecal microbiota was observed. Higher abundances of Roseburia, Ruminococcus, Coprococcus, Dorea and Lachnospira genera in weaned piglets compared to prior to weaning showed the quick microbial changes of the piglets’ gut microbiota. Downregulation of OCLN, CLDN4, MUC2, MUC13, SLC15A1 and SLC13A1 genes, also evidenced the negative impact of weaning on gut barrier and digestive functions. Metabolomic approach pinpointed significant decreases in choline, LDL, triglycerides, fatty acids, alanine and isoleucine and increases in 3-hydroxybutyrate after weaning. Moreover, the correlation between microbiota and metabolome datasets revealed the existence of metabolic clusters interrelated to different bacterial clusters. Our results demonstrate the impact of weaning stress on the piglet and give insights regarding the associations between gut microbiota and the animal gene activity and metabolic response.

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The Impact of Pre-Slaughter Fasting on the Ruminal Microbial Population of Commercial Angus Steers

Microorganisms ◽

10.3390/microorganisms9122625 ◽

2021 ◽

Vol 9 (12) ◽

pp. 2625

Author(s):

Christina Breanne Welch ◽

Jeferson M. Lourenco ◽

Darren S. Seidel ◽

Taylor Rae Krause ◽

Michael J. Rothrock ◽

...

Keyword(s):

Diversity Index ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Ecosystem Structure ◽

Opportunistic Pathogens ◽

Slaughter Cattle ◽

Before And After ◽

Ruminal Microbiota ◽

Rrna Gene Sequencing ◽

The Impact

Diet impacts the composition of the ruminal microbiota; however, prior to slaughter, cattle are fasted, which may change the ruminal microbial ecosystem structure and lead to dysbiosis. The objective of this study was to determine changes occurring in the rumen after pre-slaughter fasting, which can allow harmful pathogens an opportunity to establish in the rumen. Ruminal samples were collected before and after pre-slaughter fasting from seventeen commercial Angus steers. DNA extraction and 16S rRNA gene sequencing were performed to determine the ruminal microbiota, as well as volatile fatty acid (VFA) concentrations. Microbial richness (Chao 1 index), evenness, and Shannon diversity index all increased after fasting (p ≤ 0.040). During fasting, the two predominant families Prevotellaceae and Ruminococcaceae decreased (p ≤ 0.029), whereas the remaining minor families increased (p < 0.001). Fasting increased Blautia and Methanosphaera (p ≤ 0.003), while Campylobacter and Treponema tended to increase (p ≤ 0.086). Butyrate concentration tended to decrease (p = 0.068) after fasting. The present findings support that fasting causes ruminal nutrient depletion resulting in dysbiosis, allowing opportunistic pathogens to exploit the void in the ruminal ecological niche.

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Investigation of Oral Microbiome in Donkeys and the Effect of Dental Care on Oral Microbial Composition

Animals ◽

10.3390/ani10122245 ◽

2020 ◽

Vol 10 (12) ◽

pp. 2245

Author(s):

Yiping Zhu ◽

Wuyan Jiang ◽

Reed Holyoak ◽

Bo Liu ◽

Jing Li

Keyword(s):

Dental Treatment ◽

16S Rrna Gene Sequencing ◽

Oral Microbiome ◽

Rrna Gene ◽

Microbial Composition ◽

Dental Procedures ◽

Significant Difference ◽

Dental Diseases ◽

Rrna Gene Sequencing ◽

The Impact

The objective of this study was to investigate the oral microbial composition of the donkey and whether basic dental treatment, such as dental floating, would make a difference to the oral microbial environment in donkeys with dental diseases using high-throughput bacterial 16S rRNA gene sequencing. Oral swab samples were collected from 14 donkeys with various dental abnormalities on day 0 (before treatment) and day 20 (twenty days after treatment). It is the first report focusing on the oral microbiome in donkeys with dental diseases and the impact of common dental procedures thereon. Identified in group Day 0 and group Day 20, respectively, were 60,439.6 and 58,579.1 operational taxonomic units (OTUs). Several taxa in Day 0 differed significantly from Day 20 at the phylum and genus levels, but no statistically significant difference was observed in richness and diversity of Day 0 and Day 20. The results also indicated that a larger-scale study focusing on healthy donkey oral microbiome, as well as the correlation of dental diseases and oral microbiomes at different time frames following more specific and consistent dental treatment, are warranted.

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