Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages

Seven Italian Simmental cows were monitored during three different physiological stages, namely late lactation (LL), dry period (DP), and postpartum (PP), to evaluate modifications in their metabolically-active rumen bacterial and protozoal communities using the RNA-based amplicon sequencing method. The bacterial community was dominated by seven phyla: Proteobacteria, Bacteroidetes, Firmicutes, Spirochaetes, Fibrobacteres, Verrucomicrobia, and Tenericutes. The relative abundance of the phylum Proteobacteria decreased from 47.60 to 28.15% from LL to DP and then increased to 33.24% in PP. An opposite pattern in LL, DP, and PP stages was observed for phyla Verrucomicrobia (from 0.96 to 4.30 to 1.69%), Elusimicrobia (from 0.32 to 2.84 to 0.25%), and SR1 (from 0.50 to 2.08 to 0.79%). The relative abundance of families Succinivibrionaceae and Prevotellaceae decreased in the DP, while Ruminococcaceae increased. Bacterial genera Prevotella and Treponema were least abundant in the DP as compared to LL and PP, while Ruminobacter and Succinimonas were most abundant in the DP. The rumen eukaryotic community was dominated by protozoal phylum Ciliophora, which showed a significant decrease in relative abundance from 97.6 to 93.9 to 92.6 in LL, DP, and PP, respectively. In conclusion, the physiological stage-dependent dietary changes resulted in a clear shift in metabolically-active rumen microbial communities.

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The total and active bacterial community of the chlorolichen Cetraria islandica and its response to long-term warming in sub-Arctic tundra

10.1101/2020.03.04.976944 ◽

2020 ◽

Author(s):

Ingeborg J. Klarenberg ◽

Christoph Keuschnig ◽

Denis Warshan ◽

Ingibjörg Svala Jónsdóttir ◽

Oddur Vilhelmsson

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Relative Abundance ◽

Environmental Conditions ◽

Bacterial Community Composition ◽

Arctic Tundra ◽

Amplicon Sequencing ◽

Total Community ◽

First Time

AbstractLichens are traditionally defined as a symbiosis between a fungus and a green alga and or a cyanobacterium. This idea has been challenged by the discovery of bacterial communities inhabiting the lichen thalli. These bacteria are thought to contribute to the survival of lichens under extreme and changing environmental conditions. How these changing environmental conditions affect the lichen-associated bacterial community composition remains unclear.We describe the total (rDNA-based) and potentially metabolically active (rRNA-based) bacterial community of the lichen Cetaria islandica and its response to long-term warming using a 20-year warming experiment in an Icelandic sub-Arctic tundra. 16S rRNA and rDNA amplicon sequencing showed that the orders Acetobacterales (of the class Alphaproteobacteria) and Acidobacteriales (of the phylum Acidobacteria) dominated the bacterial community. Numerous ASVs (amplicon sequence variants) taxa could only be detected in the potentially active community but not in the total community. Long-term warming led to increases in relative abundance on class, order and ASV level. Warming altered the relative abundance of ASVs of the most common bacterial genera, such as Granulicella and Endobacter. The potentially metabolically active bacterial community was also more responsive to warming than the total community.Our results suggest that the bacterial community of the lichen C. islandica is dominated by acidophilic taxa and harbors disproportionally active rare taxa. We also show for the first time that climate warming can lead to shifts in lichen-associated bacterial community composition.

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The Total and Active Bacterial Community of the Chlorolichen Cetraria islandica and Its Response to Long-Term Warming in Sub-Arctic Tundra

Frontiers in Microbiology ◽

10.3389/fmicb.2020.540404 ◽

2020 ◽

Vol 11 ◽

Author(s):

Ingeborg J. Klarenberg ◽

Christoph Keuschnig ◽

Denis Warshan ◽

Ingibjörg Svala Jónsdóttir ◽

Oddur Vilhelmsson

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Relative Abundance ◽

Environmental Conditions ◽

Bacterial Community Composition ◽

Arctic Tundra ◽

Amplicon Sequencing ◽

Total Community ◽

First Time

Lichens are traditionally defined as a symbiosis between a fungus and a green alga and or a cyanobacterium. This idea has been challenged by the discovery of bacterial communities inhabiting the lichen thalli. These bacteria are thought to contribute to the survival of lichens under extreme and changing environmental conditions. How these changing environmental conditions affect the lichen-associated bacterial community composition remains unclear. We describe the total (rDNA-based) and potentially metabolically active (rRNA-based) bacterial community of the lichen Cetaria islandica and its response to long-term warming using a 20-year warming experiment in an Icelandic sub-Arctic tundra. 16S rRNA and rDNA amplicon sequencing showed that the orders Acetobacterales (of the class Alphaproteobacteria) and Acidobacteriales (of the phylum Acidobacteria) dominated the bacterial community. Numerous amplicon sequence variants (ASVs) could only be detected in the potentially active community but not in the total community. Long-term warming led to increases in relative abundance of bacterial taxa on class, order and ASV level. Warming altered the relative abundance of ASVs of the most common bacterial genera, such as Granulicella and Endobacter. The potentially metabolically active bacterial community was also more responsive to warming than the total community. Our results suggest that the bacterial community of the lichen C. islandica is dominated by acidophilic taxa and harbors disproportionally active rare taxa. We also show for the first time that climate warming can lead to shifts in lichen-associated bacterial community composition.

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Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Biology ◽

10.3390/biology10070569 ◽

2021 ◽

Vol 10 (7) ◽

pp. 569

Author(s):

Chakriya Sansupa ◽

Sara Fareed Mohamed Wahdan ◽

Terd Disayathanoowat ◽

Witoon Purahong

Keyword(s):

Bacterial Community ◽

Forest Soil ◽

Culture Media ◽

Enrichment Culture ◽

Sequence Similarity ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Soil Samples ◽

Enrichment Cultures ◽

Total Community

This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

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Effects of dry period length on milk yield and content and metabolic status of high-producing dairy cows under heat stress

Tropical Animal Health and Production ◽

10.1007/s11250-021-02634-1 ◽

2021 ◽

Vol 53 (2) ◽

Author(s):

A. Boustan ◽

V. Vahedi ◽

M. Abdi Farab ◽

H. Karami ◽

R. Seyedsharifi ◽

...

Keyword(s):

Heat Stress ◽

Dairy Cows ◽

Milk Yield ◽

Period Length ◽

Metabolic Status ◽

Dry Period

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Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome

BMC Cancer ◽

10.1186/s12885-021-08296-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lito E. Papanicolas ◽

Sarah K. Sims ◽

Steven L. Taylor ◽

Sophie J. Miller ◽

Christos S. Karapetis ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Haematological Malignancy ◽

Amplicon Sequencing ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Conventional Chemotherapy ◽

Myelosuppressive Chemotherapy ◽

Gram Positive Bacteria ◽

Faecal Samples

Abstract Background The gut microbiota influences many aspects of host physiology, including immune regulation, and is predictive of outcomes in cancer patients. However, whether conventional myelosuppressive chemotherapy affects the gut microbiota in humans with non-haematological malignancy, independent of antibiotic exposure, is unknown. Methods Faecal samples from 19 participants with non-haematological malignancy, who were receiving conventional chemotherapy regimens but not antibiotics, were examined prior to chemotherapy, 7–12 days after chemotherapy, and at the end of the first cycle of treatment. Gut microbiota diversity and composition was determined by 16S rRNA gene amplicon sequencing. Results Compared to pre-chemotherapy samples, samples collected 7–12 days following chemotherapy exhibited increased richness (mean 120 observed species ± SD 38 vs 134 ± 40; p = 0.007) and diversity (Shannon diversity: mean 6.4 ± 0.43 vs 6.6 ± 0.41; p = 0.02). Composition was significantly altered, with a significant decrease in the relative abundance of gram-positive bacteria in the phylum Firmicutes (pre-chemotherapy median relative abundance [IQR] 0.78 [0.11] vs 0.75 [0.11]; p = 0.003), and an increase in the relative abundance of gram-negative bacteria (Bacteroidetes: median [IQR] 0.16 [0.13] vs 0.21 [0.13]; p = 0.01 and Proteobacteria: 0.015 [0.018] vs 0.03 [0.03]; p = 0.02). Differences in microbiota characteristics from baseline were no longer significant at the end of the chemotherapy cycle. Conclusions Conventional chemotherapy results in significant changes in gut microbiota characteristics during the period of predicted myelosuppression post-chemotherapy. Further study is indicated to link microbiome changes during chemotherapy to clinical outcomes.

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Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

Metabolites ◽

10.3390/metabo11080482 ◽

2021 ◽

Vol 11 (8) ◽

pp. 482

Author(s):

Jae-Kwon Jo ◽

Seung-Ho Seo ◽

Seong-Eun Park ◽

Hyun-Woo Kim ◽

Eun-Ju Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

High Fat Diet ◽

Amplicon Sequencing ◽

Gas Chromatography Mass Spectrometry ◽

Control Group ◽

Rrna Gene ◽

High Fat ◽

Underlying Mechanisms ◽

Insight Into

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

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Lactulose significantly increased the relative abundance of Bifidobacterium and Blautia in mice feces as revealed by 16S rRNA amplicon sequencing

Journal of the Science of Food and Agriculture ◽

10.1002/jsfa.11181 ◽

2021 ◽

Author(s):

Shumao Cui ◽

Jiayu Gu ◽

Xuemei Liu ◽

Dongyao Li ◽

Bingyong Mao ◽

...

Keyword(s):

16S Rrna ◽

Relative Abundance ◽

Amplicon Sequencing ◽

16S Rrna Amplicon Sequencing

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ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle

Anaerobe ◽

10.1016/j.anaerobe.2009.07.002 ◽

2010 ◽

Vol 16 (2) ◽

pp. 94-100 ◽

Cited By ~ 77

Author(s):

David G. Welkie ◽

David M. Stevenson ◽

Paul J. Weimer

Keyword(s):

Bacterial Community ◽

Dairy Cows ◽

Community Dynamics ◽

Lactating Dairy Cows ◽

Bacterial Community Dynamics ◽

Feeding Cycle

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Effect of increasing digestible undegraded protein supply to dairy cows in late gestation on the yield and composition of milk during the subsequent lactation

Animal Science ◽

10.1017/s1357729800014752 ◽

1996 ◽

Vol 63 (2) ◽

pp. 201-213 ◽

Cited By ~ 36

Author(s):

J. M. Moorby ◽

R. J. Dewhurst ◽

S. Marsden

Keyword(s):

Dairy Cows ◽

Milk Protein ◽

Barley Straw ◽

Protein Supplement ◽

Dry Period ◽

Body Protein ◽

Grass Silage ◽

Management Regime ◽

Protein Pool ◽

Ad Libitum

AbstractEffects of feeding a protein supplement to dairy cows during the dry period on performance during the following lactation were investigated in two experiments. Holstein-Friesian cows were paired towards the end of lactation, and, after drying off, one of each pair received a typical dry cow management regime of ad libitum grass silage (experiment 1), or a mix of grass silage and distillers' grains or pressed beet pulp (experiment 2). The other cows were offered restricted access to the same basal diet, together with ad libitum access to barley straw and 0·5 kg/day high protein maize gluten meal. During the following lactation, animals from both groups were treated without reference to dry period treatment, and were offered equal access to the same lactation diet. Data were analysed by analysis of variance of experiment means and by parallel curve analysis using sample means. In experiment 1, milk yields were similar (27·2 v. 27·9 (s.e.d. 2·12) kg/day for control and supplemented animals respectively) but milk protein yields, and hence concentrations, were significantly higher (P < 0·001) from supplemented animals (28·9 v. 31·8 (s.e.d. 0·58) g/kg). In experiment 2, milk yields were significantly higher (P < 0·001) from supplemented animals (mean 33·3 v. 35·4 (s.e.d. 1·66) kg/day; however, milk protein yields were also significantly increased (P < 0·001) and the change in milk protein concentration was small. No difference in dry-matter intake was recorded in a subset of animals during early lactation in experiment 2. It is hypothesized that the maternal labile body protein pool was maintained or replenished during the dry period by the provision of the protein supplement, and that this had a significant effect on subsequent lactation performance.

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