The Nutritional Significance of Intestinal Fungi: Alteration of Dietary Carbohydrate Composition Triggers Colonic Fungal Community Shifts in a Pig Model

ABSTRACT Carbohydrates represent the most important energy source in the diet of humans and animals. A large number of studies have shown that dietary carbohydrates (DCHO) are related to the bacterial community in the gut, but their relationship with the composition of intestinal fungi is still unknown. Here, we report the response of the colonic fungal community to different compositions of DCHO in a pig model. Three factors, ratio (2:1, 1:1, and 1:2) of amylose to amylopectin (AM/AP), level of nonstarch polysaccharides (NSP; 1%, 2%, and 3%), and mannan-oligosaccharide (MOS; 400, 800, and 1,200 mg/kg body weight), were considered according to an L9 (34) orthogonal design to form nine diets with different carbohydrate compositions. Sequencing based on an Illumina HiSeq 2500 platform targeting the internal transcribed spacer 1 region showed that the fungal community in the colon of the pigs responded to DCHO in the order of MOS, AM/AP, and NSP. A large part of some low-abundance fungal genera correlated with the composition of DCHO, represented by Saccharomycopsis, Mrakia, Wallemia, Cantharellus, Eurotium, Solicoccozyma, and Penicillium, were also associated with the concentration of glucose and fructose, as well as the activity of β-d-glucosidase in the colonic digesta, suggesting a role of these fungi in the degradation of DCHO in the colon of pigs. Our study provides direct evidence for the relationship between the composition of DCHO and the fungal community in the colon of pigs, which is helpful to understand the function of gut microorganisms in pigs. IMPORTANCE Although fungi are a large group of microorganisms along with bacteria and archaea in the gut of monogastric animals, the nutritional significance of fungi has been ignored for a long time. Our previous studies revealed a distinct fungal community in the gut of grazing Tibetan pigs (J. Li, D. Chen, B. Yu, J. He, et al., Microb Biotechnol 13:509–521, 2020, https://doi.org/10.1111/1751-7915.13507) and a close correlation between fungal species and short-chain fatty acids, the main microbial metabolites of carbohydrates in the hindgut of pigs (J. Li, Y. Luo, D. Chen, B. Yu, et al., J Anim Physiol Anim Nutr 104:616–628, 2020, https://doi.org/10.1111/jpn.13300). These groundbreaking findings indicate a potential relationship between intestinal fungi and the utilization of DCHO. However, no evidence directly proves the response of intestinal fungi to changes in DCHO. Here, we show a clear alteration of the colonic fungal community in pigs triggered by different compositions of DCHO simulated by varied concentrations of starch, nonstarch polysaccharides (NSP), and oligosaccharides. Our results highlight the potential involvement of intestinal fungi in the utilization of nutrients in monogastric animals.

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A pilot study of possible anti-inflammatory effects of the specific carbohydrate diet in children with juvenile idiopathic arthritis

Pediatric Rheumatology ◽

10.1186/s12969-021-00577-3 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Lillemor Berntson

Keyword(s):

Juvenile Idiopathic Arthritis ◽

Health Assessment ◽

Short Chain Fatty Acids ◽

Carbohydrate Diet ◽

Positive Effects ◽

Link Type ◽

Parents And Children ◽

Inflammatory Proteins ◽

Anti Inflammatory ◽

Specific Carbohydrate Diet

Abstract Background To explore possible anti-inflammatory effects of the specific carbohydrate diet in children with juvenile idiopathic arthritis. This diet has shown anti-inflammatory effect in children with inflammatory bowel disease. Methods Twenty-two patients with juvenile idiopathic arthritis (age 6.3–17.3 years), with ≤2 inflamed joints and an erythrocyte sedimentation rate < 30 mm/h, were included in this explorative study. Fifteen children completing four weeks on the diet were evaluated. A dietician introduced parents and children to the diet, and two follow-ups were performed during the intervention. Conventional laboratory tests and multiplex analyses of 92 inflammatory proteins were used. Short-chain fatty acids in faecal samples were examined. Results The diet significantly decreased morning stiffness (p = 0.003) and pain (p = 0.048). Physical function, assessed through the child health assessment questionnaire, improved (p = 0.022). Arthritis improved in five of the seven children with arthritis; in those seven, multiplex analyses showed a significant decrease in nine inflammatory proteins, including TNF-alpha (p = 0.028), after four weeks. Faecal butyrate, analysed in all 15 participants, increased significantly (p = 0.020). Conclusion The specific carbohydrate diet may have significant positive effects on arthritis in children with juvenile idiopathic arthritis, but further studies are needed. Clinical trials identifier NCT04205500, 2019/12/17, retrospectively registered. URL: https://register.clinicaltrials.gov

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Eutypella parasitica and Other Frequently Isolated Fungi in Wood of Dead Branches of Young Sycamore Maple (Acer pseudoplatanus) in Slovenia

Forests ◽

10.3390/f11040467 ◽

2020 ◽

Vol 11 (4) ◽

pp. 467 ◽

Cited By ~ 4

Author(s):

Ana Brglez ◽

Barbara Piškur ◽

Nikica Ogris

Keyword(s):

Species Diversity ◽

Fungal Community ◽

Sampling Site ◽

Outer Part ◽

Similarity Index ◽

Asymptomatic Infection ◽

Fungal Species ◽

Acer Pseudoplatanus ◽

Pure Cultures ◽

Sycamore Maple

Eutypella parasitica R.W. Davidson and R.C. Lorenz is the causative agent of Eutypella canker of maple, a destructive disease of maples in Europe and North America. The fungus E. parasitica infects the trunk through a branch stub or bark wound. Because the fungal community may have an impact on infection and colonization by E. parasitica, the composition of fungi colonizing wood of dead branches of sycamore maple (Acer pseudoplatanus L.) was investigated in five sampling sites in Slovenia. Forty samples from each sampling site were collected between the November 2017 and March 2018 period. Isolations were made from the wood in the outer part of dead branches and from discoloured wood in the trunk that originated from a dead branch. Pure cultures were divided into morphotypes, and one representative culture per morphotype was selected for further molecular identification. From a total of 2700 cultured subsamples, 1744 fungal cultures were obtained, which were grouped into 212 morphotypes. The investigated samples were colonized by a broad spectrum of fungi. The most frequently isolated species were Eutypa maura (Fr.) Sacc., Eutypa sp. Tul. and C. Tul., Fusarium avenaceum (Fr.) Sacc., Neocucurbitaria acerina Wanas., Camporesi, E.B.G. Jones and K.D. Hyde and E. parasitica. In this study, we distinguished species diversity and the fungal community. There were no significant differences in the diversity of fungal species between the five sampling sites, and branch thickness did not prove to be a statistically significant factor in fungal species diversity. Nevertheless, relatively low Jaccard similarity index values suggested possible differences in the fungal communities from different sampling sites. This was confirmed by an analysis of similarities, which showed that the isolated fungal community distinctly differed between the five sampling sites and between the different isolation sources. Eutypella parasitica was isolated from all five investigated sampling sites, although Eutypella cankers were observed in only three sampling sites, indicating the possibility of asymptomatic infection.

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Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

10.7287/peerj.preprints.2918v1 ◽

2017 ◽

Author(s):

Jacoline Gerritsen ◽

Bastian Hornung ◽

Bernadette Renckens ◽

Sacha A.F.T. van Hijum ◽

Vitor A.P. Martins dos Santos ◽

...

Keyword(s):

Amino Acids ◽

Small Intestine ◽

Short Chain Fatty Acids ◽

Limited Capacity ◽

Illumina Hiseq ◽

Circular Chromosome ◽

Protein Coding ◽

Mate Pair ◽

Simple Carbohydrates

Background. The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. Methods. The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired end, mate pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) while growing on three different carbohydrate sources and short chain fatty acids were measured via HPLC. Results. Hence, we present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed pinpointing the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. Discussion. This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available and uncovered potential mechanisms for competition with mucus-degrading microbes.

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Detection of arbuscular mycorrhizal fungi associated with pecan (Carya illinoinensis) trees by molecular and morphological approaches

MycoKeys ◽

10.3897/mycokeys.42.26118 ◽

2018 ◽

Vol 42 ◽

pp. 73-88 ◽

Cited By ~ 1

Author(s):

L. Fernández Bidondo ◽

R. P. Colombo ◽

M. Recchi ◽

V. A. Silvani ◽

M. Pérgola ◽

...

Keyword(s):

Fungal Community ◽

Mycorrhizal Fungi ◽

Sequence Similarity ◽

Arbuscular Mycorrhizal ◽

Soil Disturbance ◽

Fungal Species ◽

Fungal Community Composition ◽

Molecular Approaches ◽

Field Samples ◽

Fungal Specificity

Arbuscular mycorrhizal (AM) fungal community associated with pecan (Caryaillinoinensis) roots and rhizospheric soils was assessed by spore isolation and morphological characterisation and by pyrosequencing of AM molecular markers. The AM fungal community associated with pecan growing in the field, was always more diverse than that associated with pecan growing in containers. This was not observed when AM richness was studied, suggesting that soil disturbance by a reduction in host plant richness leads to a less equitable distribution of AM fungal species, in contrast to natural soils. The chosen primers (AMV4.5F/AMDGR) for pyrosequencing showed high AM fungal specificity. Based on 97% sequence similarity, 49 operational taxonomic units (MOTUs) were obtained and, amongst these, 41 MOTUs corresponded to the Glomeromycotaphylum. The number of obtained AM sequences ranged from 2164, associated with field samples, to 5572 obtained from pecan trap pot culture samples, defining 30 and 29 MOTUs, respectively. Richness estimated by conventional species identification was 6 and 9 AM fungal species in soil and pot samples, respectively. Claroideoglomuslamellosum, Funneliformismosseae and Entrophosporainfrequens were the only taxa detected using both techniques. Predominant sequences in the pecan rhizosphere samples, such as Rhizoglomusirregulare and other less abundant (Dominikiairanica, Dominikiaindica, Sclerocystissinuosa, Paraglomuslaccatum), were detected only by pyrosequencing. Detection of AM fungal species based on spore morphology, in combination with molecular approaches, provides a more comprehensive estimate of fungal community composition.

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Production of short-chain fatty acids from resistant starch in a pig model

Journal of the Science of Food and Agriculture ◽

10.1002/(sici)1097-0010(199805)77:1<71::aid-jsfa3>3.0.co;2-h ◽

1998 ◽

Vol 77 (1) ◽

pp. 71-80 ◽

Cited By ~ 44

Author(s):

Lucile J M Martin ◽

Henri J W Dumon ◽

Martine M J Champ

Keyword(s):

Fatty Acids ◽

Resistant Starch ◽

Short Chain Fatty Acids ◽

Pig Model ◽

Short Chain ◽

Chain Fatty Acids

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Soil Fungal Community in Norway Spruce Forests under Bark Beetle Attack

Forests ◽

10.3390/f10020109 ◽

2019 ◽

Vol 10 (2) ◽

pp. 109 ◽

Cited By ~ 3

Author(s):

Petra Veselá ◽

Martina Vašutová ◽

Magda Edwards-Jonášová ◽

Pavel Cudlín

Keyword(s):

Bark Beetle ◽

Fungal Community ◽

Forest Ecosystems ◽

Fungal Species ◽

Thelephora Terrestris ◽

Mature Forest ◽

Soil Fungal Community ◽

Ecm Fungi ◽

Widespread Phenomenon ◽

One Year

Bark beetle infestation is a widespread phenomenon in temperate forests, which are facing significant weather fluctuations accompanying climate change. Fungi play key roles in forest ecosystems as symbionts of ectomycorrhizal trees, decomposers, or parasites, but the effect of severe disturbances on their communities is largely unknown. The responses of soil fungal communities following bark beetle attack were determined using Illumina sequencing of soil samples from 10 microsites in a mature forest not attacked by bark beetle, a forest attacked by bark beetle, a forest destroyed by bark beetle, and a stand where all trees were removed after a windstorm. The proportion of ITS2 sequences assigned to mycorrhizal fungal species decreased with increased intensity of bark beetle attack (from 70 to 15%), whereas the proportion of saprotrophs increased (from 29 to 77%). Differences in the ectomycorrhizal (ECM) fungal community was further characterized by a decrease in the sequence proportion of Elaphomyces sp. and Russula sp. and an increase in Piloderma sp., Wilcoxina sp., and Thelephora terrestris. Interestingly, the species composition of the ECM fungal community in the forest one year after removing the windstorm-damaged trees was similar to that of the mature forest, despite the sequence proportion attributed to ECM fungi decreased.

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The fungal community and its interaction with the concentration of short‐chain fatty acids in the faeces of Chenghua, Yorkshire and Tibetan pigs

Microbial Biotechnology ◽

10.1111/1751-7915.13507 ◽

2019 ◽

Vol 13 (2) ◽

pp. 509-521

Author(s):

Jiayan Li ◽

Daiwen Chen ◽

Bing Yu ◽

Jun He ◽

Zhiqing Huang ◽

...

Keyword(s):

Fatty Acids ◽

Fungal Community ◽

Short Chain Fatty Acids ◽

Short Chain ◽

Tibetan Pigs ◽

Chain Fatty Acids

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Long-Term Monoculture Negatively Regulates Fungal Community Composition and Abundance of Tea Orchards

Agronomy ◽

10.3390/agronomy9080466 ◽

2019 ◽

Vol 9 (8) ◽

pp. 466 ◽

Cited By ~ 4

Author(s):

Yasir Arafat ◽

Muhammad Tayyab ◽

Muhammad Umar Khan ◽

Ting Chen ◽

Hira Amjad ◽

...

Keyword(s):

Soil Ph ◽

Fungal Community ◽

Cropping System ◽

Alpha Diversity ◽

Fungal Species ◽

Fungal Communities ◽

Continuous Cropping ◽

Fungal Community Composition ◽

Continuous Cropping System ◽

Tea Plants

Continuous cropping frequently leads to soil acidification and major soil-borne diseases in tea plants, resulting in low tea yield. We have limited knowledge about the effects of continuous tea monoculture on soil properties and the fungal community. Here, we selected three replanted tea fields with 2, 15, and 30 years of monoculture history to assess the influence of continuous cropping on fungal communities and soil physiochemical attributes. The results showed that continuous tea monoculture significantly reduced soil pH and tea yield. Alpha diversity analysis showed that species richness declined significantly as the tea planting years increased and the results based on diversity indicated inconsistency. Principal coordinate analysis (PCoA) revealed that monoculture duration had the highest loading in structuring fungal communities. The relative abundance of Ascomycota, Glomeromycota, and Chytridiomycota decreased and Zygomycota and Basidiomycota increased with increasing cropping time. Continuous tea cropping not only decreased some beneficial fungal species such as Mortierella alpina and Mortierella elongatula, but also promoted potentially pathogenic fungal species such as Fusarium oxysporum, Fusarium solani, and Microidium phyllanthi over time. Overall, continuous tea cropping decreased soil pH and potentially beneficial microbes and increased soil pathogenic microbes, which could be the reason for reducing tea yield. Thus, developing sustainable tea farming to improve soil pH, microbial activity, and enhanced beneficial soil microbes under a continuous cropping system is vital for tea production.

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Short-Chain Fatty Acids and Human Colonic Function: Roles of Resistant Starch and Nonstarch Polysaccharides

Physiological Reviews ◽

10.1152/physrev.2001.81.3.1031 ◽

2001 ◽

Vol 81 (3) ◽

pp. 1031-1064 ◽

Cited By ~ 1689

Author(s):

David L. Topping ◽

Peter M. Clifton

Keyword(s):

Fatty Acids ◽

Resistant Starch ◽

Epidemiological Data ◽

Short Chain Fatty Acids ◽

Short Chain ◽

Indirect Measures ◽

Electrolyte Uptake ◽

Colonic Blood Flow ◽

Nonstarch Polysaccharides ◽

Chain Fatty Acids

Resistant starch (RS) is starch and products of its small intestinal digestion that enter the large bowel. It occurs for various reasons including chemical structure, cooking of food, chemical modification, and food mastication. Human colonic bacteria ferment RS and nonstarch polysaccharides (NSP; major components of dietary fiber) to short-chain fatty acids (SCFA), mainly acetate, propionate, and butyrate. SCFA stimulate colonic blood flow and fluid and electrolyte uptake. Butyrate is a preferred substrate for colonocytes and appears to promote a normal phenotype in these cells. Fermentation of some RS types favors butyrate production. Measurement of colonic fermentation in humans is difficult, and indirect measures (e.g., fecal samples) or animal models have been used. Of the latter, rodents appear to be of limited value, and pigs or dogs are preferable. RS is less effective than NSP in stool bulking, but epidemiological data suggest that it is more protective against colorectal cancer, possibly via butyrate. RS is a prebiotic, but knowledge of its other interactions with the microflora is limited. The contribution of RS to fermentation and colonic physiology seems to be greater than that of NSP. However, the lack of a generally accepted analytical procedure that accommodates the major influences on RS means this is yet to be established.

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