Consequences of Biofilm and Sessile Growth in the Large Intestine

1997 ◽  
Vol 11 (1) ◽  
pp. 59-68 ◽  
Author(s):  
S. Macfarlane ◽  
A.J. McBain ◽  
G.T. Macfarlane
Keyword(s):  
Particulate Matter ◽  
Gut Microbiota ◽  
Product Formation ◽  
Complex Environment ◽  
Short Term ◽  
Fermentation Products ◽  
Degrading Bacteria ◽  
Food Particles ◽  
Different Strains

The human colonic ecosystem is an extremely complex environment comprised of several hundred different strains of bacteria. Studies were undertaken to determine whether these organisms formed metabolic or genotypically distinct assemblages in the gut microbiota in relation to polysaccharide fermentation. Measurements of depolymerizing enzymes (4 polysac-charidases, 6 glycosidases) showed that specific amylase and pectinase activities were comparable in bacteria desorbed from the surfaces of food particles and in non-particulate organisms. However, xylanase, β-xylosidase, arabinogalac-tanase, a-arabinofuranosidase, and β-galacturonidase activities were always significantly greater in particulate bacteria. Short-term in vitro fermentations with both groups of bacteria showed marked differences in relative rates of starch, arabinogalactan, and mucin metabolism, while rates of fermentation product formation with pectin and xylan were broadly comparable. Significant differences were observed with respect to formation of individual fermentation products, especially when mucin or pectin were substrates, where particulate bacteria produced proportionally higher amounts of acetate. Bacteriological studies showed that communities of polymer-degrading bacteria and other groups of intestinal anaerobes growing on particulate matter were essentially similar to those occurring elsewhere in the gut lumen, at genus and species levels. In vitro colonization experiments demonstrated that a variety of polysaccharide-fermenting bifidobacteria and bacteroides-together with other cross-feeding organisms such as peptostreptococci, fusobacteria, and coliforms-rapidly attached to particulate intestinal materials.

scholarly journals Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome

2021 ◽  
Vol 22 (21) ◽  
pp. 12050
Author(s):  
Cynthia B. Silveira ◽  
Ana G. Cobián-Güemes ◽  
Carla Uranga ◽  
Jonathon L. Baker ◽  
Anna Edlund ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Lung Function ◽  
Sequence Data ◽  
Anaerobic Bacteria ◽  
Keystone Species ◽  
Clinical Diagnostics ◽  
Epifluorescence Microscopy ◽  
Fermentation Products ◽  
Degrading Bacteria

Ecological networking and in vitro studies predict that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes. The metabolic byproducts from these bacteria facilitate the colonization and growth of CF pathogens like Pseudomonas aeruginosa. Here, a multi-omics study informed the control of putative anaerobic keystone species during a transition in antibiotic therapy of a CF patient. A quantitative metagenomics approach combining sequence data with epifluorescence microscopy showed that during periods of rapid lung function loss, the patient’s lung microbiome was dominated by the anaerobic, mucus-degrading bacteria belonging to Streptococcus, Veillonella, and Prevotella genera. Untargeted metabolomics and community cultures identified high rates of fermentation in these sputa, with the accumulation of lactic acid, citric acid, and acetic acid. P. aeruginosa utilized these fermentation products for growth, as indicated by quantitative transcriptomics data. Transcription levels of P. aeruginosa genes for the utilization of fermentation products were proportional to the abundance of anaerobic bacteria. Clindamycin therapy targeting Gram-positive anaerobes rapidly suppressed anaerobic bacteria and the accumulation of fermentation products. Clindamycin also lowered the abundance and transcription of P. aeruginosa, even though this patient’s strain was resistant to this antibiotic. The treatment stabilized the patient’s lung function and improved respiratory health for two months, lengthening by a factor of four the between-hospitalization time for this patient. Killing anaerobes indirectly limited the growth of P. aeruginosa by disrupting the cross-feeding of fermentation products. This case study supports the hypothesis that facultative anaerobes operated as keystone species in this CF microbiome. Personalized multi-omics may become a viable approach for routine clinical diagnostics in the future, providing critical information to inform treatment decisions.

scholarly journals Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon

2015 ◽  
Vol 112 (32) ◽  
pp. 10038-10043 ◽  
Author(s):  
Noortje Ijssennagger ◽  
Clara Belzer ◽  
Guido J. Hooiveld ◽  
Jan Dekker ◽  
Saskia W. C. van Mil ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Tumor Suppressors ◽  
Disulfide Bonds ◽  
Red Meat ◽  
Cell Turnover ◽  
Degrading Bacteria ◽  
Mucus Barrier

Colorectal cancer risk is associated with diets high in red meat. Heme, the pigment of red meat, induces cytotoxicity of colonic contents and elicits epithelial damage and compensatory hyperproliferation, leading to hyperplasia. Here we explore the possible causal role of the gut microbiota in heme-induced hyperproliferation. To this end, mice were fed a purified control or heme diet (0.5 μmol/g heme) with or without broad-spectrum antibiotics for 14 d. Heme-induced hyperproliferation was shown to depend on the presence of the gut microbiota, because hyperproliferation was completely eliminated by antibiotics, although heme-induced luminal cytotoxicity was sustained in these mice. Colon mucosa transcriptomics revealed that antibiotics block heme-induced differential expression of oncogenes, tumor suppressors, and cell turnover genes, implying that antibiotic treatment prevented the heme-dependent cytotoxic micelles to reach the epithelium. Our results indicate that this occurs because antibiotics reinforce the mucus barrier by eliminating sulfide-producing bacteria and mucin-degrading bacteria (e.g., Akkermansia). Sulfide potently reduces disulfide bonds and can drive mucin denaturation and microbial access to the mucus layer. This reduction results in formation of trisulfides that can be detected in vitro and in vivo. Therefore, trisulfides can serve as a novel marker of colonic mucolysis and thus as a proxy for mucus barrier reduction. In feces, antibiotics drastically decreased trisulfides but increased mucin polymers that can be lysed by sulfide. We conclude that the gut microbiota is required for heme-induced epithelial hyperproliferation and hyperplasia because of the capacity to reduce mucus barrier function.

In vitro fermentation and isolation of heparin-degrading bacteria from human gut microbiota

Anaerobe ◽  
2020 ◽  
pp. 102289
Author(s):  
Lin Pan ◽  
Weixia Sun ◽  
Qingsen Shang ◽  
Qingfeng Niu ◽  
Chanjuan Liu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
In Vitro Fermentation ◽  
Human Gut Microbiota ◽  
Degrading Bacteria

Carrageenan oligosaccharides and their degrading bacteria induce intestinal inflammation in germ-free mouse

2020 ◽  
Author(s):  
Yeshi Yin ◽  
Miaomiao Li ◽  
Weizhong Gu ◽  
Benhua Zeng ◽  
Wei Liu ◽  
...  
Keyword(s):  
Inflammatory Response ◽  
Gut Microbiota ◽  
Fecal Microbiota ◽  
Rna Seq ◽  
Human Gut ◽  
Germ Free ◽  
Esi Ms ◽  
Human Gut Microbiota ◽  
Degrading Bacteria

Abstract Background: Carrageenans (CGNs) are widely used in food and pharmaceutical industries. However, the safety of CGNs is still under debate, because degraded CGNs have been reported to promote an intestinal inflammatory response in animal models. Here, we studied the relationship among CGNs, human gut microbiota, and the host inflammatory response.Methods: TLC was selected for detecting the degradation of KCPs by human gut microbiota in vitro batch fermentation system. PCR-DGGE and real time PCR were used for studying bacterial community. ESI-MS was used for KCPs structure analysis. Hematoxylin-eosin staining (HE), immunohistochemistry (IHC) and RNA-seq were used to evaluated the KCPs on host inflammation response in germ-free mice.Results: Thin-layer chromatography (TLC) data showed that CGNs with a molecular weight (Mw) higher than 100 kDa are not degraded by human fecal microbiota, but low Mw CGNs with an Mw around ~4.5 kDa (KCOs) could be degraded by seven of eight human fecal microbiota samples. KCO degrading B. xylanisolvens was isolated from fecal samples, and PCR-DGGE profiling with band sequencing suggested that B. xylanisolvens was the key KCO degrader in the human gut. Two putative κ-carrageenase genes were identified in the genome sequence of B. xylanisolvens. However, their function on KCO degrading was not verified in vitro. And the sulfate group from KCO is not removed after in vitro degradation by human fecal microbiota, as shown by ESI-MS analysis. The effects of KCO and KCO degrading bacteria on the inflammatory response were investigated in germ-free mice. Increased numbers of P-P38-, CD3a-, and CD79a-positive cells were found in the colon and rectum in mice fed with KCO plus KCO degrading bacteria than in mice fed with only KCO or only B. xylanisolvens and E. coli, as shown by RNA-Seq analysis, HE staining, and IHC. Conclusion: Our data suggested that the presence of KCO degrading bacteria promote the pro-inflammatory effects of CGNs.

scholarly journals The effects of fermentation products of prebiotic fibres on gut barrier and immune functions in vitro

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5288 ◽  
Author(s):  
Van T. Pham ◽  
Nicole Seifert ◽  
Nathalie Richard ◽  
Daniel Raederstorff ◽  
Robert Steinert ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Barrier ◽  
Mucus Production ◽  
Fermentation Products ◽  
Barrier Integrity ◽  
Positive Effects ◽  
Dietary Fibres ◽  
Chicory Root ◽  
Luminex Technology

The beneficial effects of prebiotic fibres on human health have been related to their capacities to alter the gut microbiota and modify the growth of beneficial microorganisms. It is long appreciated that bacterial metabolites affect the host’s physiology. The inner lining of the intestinal tract is the first level of interaction between the host and bacteria and their metabolites. Therefore, we set out to test the effects of five common dietary fibres (oat β-glucan 28%; oat β-glucan 94%; dried chicory root containing inulin 75%; xylo-oligosaccharide; inulin 90%) and maltodextrin, after fermentation by human gut microbiota in vitro, on measures of gut barrier integrity using a Caco-2/HT29-MTX co-culture as well as mucus production and immune parameters using HT29-MTX and HT29 cell models, respectively. Our data show that all fibres, fermentation products increased the tightness of the gut barrier with oat β-glucan 28% having the largest effect. Fermentation supernatants were tested also in models of the compromised gut barrier (leaky gut). After the addition of ethanol as basolateral stressor, only fermentation supernatant of oat β-glucan 28%, oat β-glucan 94% and maltodextrin improved the gut barrier integrity, while oat β-glucan 28% and dried chicory root containing inulin 75% significantly improved the gut barrier integrity after addition of rhamnolipids as apical stressor. Using the Luminex Technology, we demonstrated an important role of oat β-glucan fermentation products in modulating cytokine and chemokine productions. Furthermore, treating the goblet cells with effluent from xylo-oligosaccharide fermentation significantly increased mucus production. In summary, our data emphasize the potential positive effects of fermentation supernatant of dietary fibres on gut-related physiological outcomes and show that prebiotic fibres may have promising potential to induce specific gut health benefits.

scholarly journals Division of labor in honey bee gut microbiota for plant polysaccharide digestion

2019 ◽  
Vol 116 (51) ◽  
pp. 25909-25916 ◽  
Author(s):  
Hao Zheng ◽  
Julie Perreau ◽  
J. Elijah Powell ◽  
Benfeng Han ◽  
Zijing Zhang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Honey Bee ◽  
Short Chain Fatty Acids ◽  
Gene Expressions ◽  
Plant Polysaccharide ◽  
Genes Encoding ◽  
Host Nutrition ◽  
Different Strains

Bees acquire carbohydrates from nectar and lipids; and amino acids from pollen, which also contains polysaccharides including cellulose, hemicellulose, and pectin. These potential energy sources could be degraded and fermented through microbial enzymatic activity, resulting in short chain fatty acids available to hosts. However, the contributions of individual microbiota members to polysaccharide digestion have remained unclear. Through analysis of bacterial isolate genomes and a metagenome of the honey bee gut microbiota, we identify thatBifidobacteriumandGilliamellaare the principal degraders of hemicellulose and pectin. BothBifidobacteriumandGilliamellashow extensive strain-level diversity in gene repertoires linked to polysaccharide digestion. Strains from honey bees possess more such genes than strains from bumble bees. InBifidobacterium, genes encoding carbohydrate-active enzymes are colocated within loci devoted to polysaccharide utilization, as inBacteroidesfrom the human gut. Carbohydrate-active enzyme-encoding gene expressions are up-regulated in response to particular hemicelluloses both in vitro and in vivo. Metabolomic analyses document that bees experimentally colonized by different strains generate distinctive gut metabolomic profiles, with enrichment for specific monosaccharides, corresponding to predictions from genomic data. The other 3 core gut species clusters (Snodgrassellaand 2Lactobacillusclusters) possess few or no genes for polysaccharide digestion. Together, these findings indicate that strain composition within individual hosts determines the metabolic capabilities and potentially affects host nutrition. Furthermore, the niche specialization revealed by our study may promote overall community stability in the gut microbiomes of bees.

Investigation of in vitro methods for screening fungal probiotics

1991 ◽  
Vol 1991 ◽  
pp. 111-111
Author(s):  
C.J. Newbold ◽  
P.P. Frumholtz ◽  
R.J. Wallace
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rapid Method ◽  
Probiotic Properties ◽  
Growth Promoters ◽  
Short Term ◽  
Fermentation Products ◽  
In Vitro Methods ◽  
Selection Of

Fungal probiotics are gaining increasing acceptance as growth promoters that act via the rumen fermentation. Products have been described based on Saccharomyces cerevisiae and Aspergillus oryzac (Williams and Newbold, 1990). However not all species of Aspergillus or strains of S. cerevisiae exhibit probiotic properties (Tapia and llerrera-Saldana, 1989; Newbold, 1990). The selection of fungi with probiotic properties would be greatly facilitated by the development of a rapid method for assessing their efficacy. In the present study the effects of one of these products (Amaferm, based on Aspergillus oryzae; AO) on short term incubations invitro were compared with results obtained previously in longer-term in vitro fermentations (Rusitec) and with in vivo measurements.

scholarly journals Antidiabetic Function of Lactobacillus fermentum MF423-Fermented Rice Bran and Its Effect on Gut Microbiota Structure in Type 2 Diabetic Mice

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaojuan Ai ◽  
Cuiling Wu ◽  
Tingting Yin ◽  
Olena Zhur ◽  
Congling Liu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Rice Bran ◽  
High Throughput Sequencing ◽  
Short Chain Fatty Acids ◽  
Lactobacillus Fermentum ◽  
Fermentation Products ◽  
Type 2 Diabetic

Rice bran is an industrial byproduct that exerts several bioactivities despite its limited bioavailability. In this study, rice bran fermented with Lactobacillus fermentum MF423 (FLRB) had enhanced antidiabetic effects both in vitro and in vivo. FLRB could increase glucose consumption and decrease lipid accumulation in insulin resistant HepG2 cells. Eight weeks of FLRB treatment significantly reduced the levels of blood glucose and lipids and elevated antioxidant activity in type 2 diabetic mellitus (T2DM) mice. H&E staining revealed alleviation of overt lesions in the livers of FLRB-treated mice. Moreover, high-throughput sequencing showed notable variation in the composition of gut microbiota in FLRB-treated mice, especially for short-chain fatty acids (SCFAs)-producing bacteria such as Dubosiella and Lactobacillus. In conclusion, our results suggested that rice bran fermentation products can modulate the intestinal microbiota and improve T2DM-related biochemical abnormalities, so they can be applied as potential probiotics or dietary supplements.

scholarly journals Multi-omics study of keystone species in the cystic fibrosis lung microbiome

2020 ◽  
Author(s):  
Cynthia Silveira ◽  
Ana Georgina Cobian-Guemes ◽  
Carla Uranga ◽  
Jonathon Baker ◽  
Anna Edlund ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Microbial Community ◽  
Lung Function ◽  
Respiratory Health ◽  
Keystone Species ◽  
Fermentation Products ◽  
Community Function ◽  
Degrading Bacteria

Abstract Background: Ecological networking and in vitro studies have predicted that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes by sustaining the growth of canonical CF pathogens. Here, a multi-omics approach was deployed to test this hypothesis in vivo and in real time during a transition in antibiotic therapy of a CF patient with a hypervariable lung function phenotype . Results: Quantitative meta-omics and community culturing demonstrated that the use of a non-traditional clindamycin therapy targeting gram-positives and gram-negative anaerobes re-structured the entire CF microbial community. During rapid lung function loss, when the patient was off antibiotics, the microbial community was dominated by anaerobic mucus-degrading Streptococcus sp., Veilonella sp., and Prevotella sp. that produced fermentation gas and led to the accumulation of fermentation products in sputum. The rise of anaerobes was followed within 6 days by an increase in Pseudomonas aeruginosa transcripts encoding the acquisition of fermentation products from anaerobes and the production of virulence factors. The initiation of clindamycin treatment reduced the fermentation and the abundance of anaerobes. Clindamycin also lowered the abundance and transcription of P. aeruginosa, which is resistant to this antibiotic. The treatment stabilized the patient’s lung function and improved respiratory health for two months, lengthening by a factor of four the between-hospitalization time for this patient. Conclusions: The results presented here show that killing anaerobes, the weakest link in the community in terms of antibiotic resistance, effectively limited the growth of classic CF pathogen by disrupting community cross-feeding. The role that anaerobic, mucus-degrading bacteria played in structuring the CF microbiome corroborates in vivo their position as keystone bacteria, with high impact on community function despite lower relative abundances.

scholarly journals Metabolic Basis for Mutualism between Gut Bacteria and Its Impact on theDrosophila melanogasterHost

2018 ◽  
Vol 85 (2) ◽  
Author(s):  
Andrew J. Sommer ◽  
Peter D. Newell
Keyword(s):  
Gut Microbiota ◽  
Bacterial Species ◽  
Waste Products ◽  
Fermentation Products ◽  
Content Type ◽  
Starting Point ◽  
Host Physiology ◽  
The Impact

ABSTRACTInteractions between species shape the formation and function of microbial communities. In the gut microbiota of animals, cross-feeding of metabolites between microbes can enhance colonization and influence host physiology. We examined a mutually beneficial interaction between two bacteria isolated from the gut microbiota ofDrosophila, i.e.,Acetobacter fabarumandLactobacillus brevis. After developing anin vitrococulture assay, we utilized a genetic screen to identifyA. fabarumgenes required for enhanced growth withL. brevis. The screen, and subsequent genetic analyses, showed that the gene encoding pyruvate phosphate dikinase (ppdK) is required forA. fabarumto benefit fully from coculture. By testing strains with mutations in a range of metabolic genes, we provide evidence thatA. fabarumcan utilize multiple fermentation products ofL. brevis. Mutualism between the bacteriain vivoaffects gnotobioticDrosophila melanogaster; flies associated withA. fabarumandL. brevisshowed >1,000-fold increases in bacterial cell density and significantly lower triglyceride storage than monocolonized flies. Mutation ofppdKdecreasedA. fabarumdensity in flies cocolonized withL. brevis, consistent with the model in whichAcetobacteremploys gluconeogenesis to assimilateLactobacillusfermentation products as a source of carbonin vivo. We propose that cross-feeding between these groups is a common feature of microbiota inDrosophila.IMPORTANCEThe digestive tracts of animals are home to a community of microorganisms, the gut microbiota, which affects the growth, development, and health of the host. Interactions among microbes in this inner ecosystem can influence which species colonize the gut and can lead to changes in host physiology. We investigated a mutually beneficial interaction between two bacterial species from the gut microbiota of fruit flies. By coculturing the bacteriain vitro, we were able to identify a metabolic gene required for the bacteria to grow better together than they do separately. Our data suggest that one species consumes the waste products of the other, leading to greater productivity of the microbial community and modifying the nutrients available to the host. This study provides a starting point for investigating how these and other bacteria mutually benefit by sharing metabolites and for determining the impact of mutualism on host health.

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