The impact of human-facilitated selection on the gut microbiota of domesticated mammals

2019 ◽  
Vol 95 (9) ◽  
Author(s):  
Giulia Alessandri ◽  
Christian Milani ◽  
Leonardo Mancabelli ◽  
Marta Mangifesta ◽  
Gabriele Andrea Lugli ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Horizontal Transmission ◽  
Taxonomic Composition ◽  
Functional Adaptation ◽  
Rrna Gene ◽  
Feed Conversion ◽  
Shotgun Metagenomics ◽  
Domesticated Animals ◽  
And Behavior ◽  
The Impact

ABSTRACT Domestication is the process by which anthropogenic forces shape lifestyle and behavior of wild species to accommodate human needs. The impact of domestication on animal physiology and behavior has been extensively studied, whereas its effect on the gut microbiota is still largely unexplored. For this reason, 16S rRNA gene-based and internal transcribed spacer-mediated bifidobacterial profiling, together with shotgun metagenomics, was employed to investigate the taxonomic composition and metabolic repertoire of 146 mammalian fecal samples, corresponding to 12 domesticated–feral dyads. Our results revealed that changes induced by domestication have extensively shaped the taxonomic composition of the mammalian gut microbiota. In this context, the selection of microbial taxa linked to a more efficient feed conversion into body mass and putative horizontal transmission of certain bacterial genera from humans were observed in the fecal microbiota of domesticated animals when compared to their feral relatives and to humans. In addition, profiling of the metabolic arsenal through metagenomics highlighted extensive functional adaptation of the fecal microbial community of domesticated mammals to changes induced by domestication. Remarkably, domesticated animals showed, when compared to their feral relatives, increased abundance of specific glycosyl hydrolases, possibly due to the higher intake of complex plant carbohydrates typical of commercial animal feeds.

scholarly journals Multi-omics Approaches To Decipher the Impact of Diet and Host Physiology on the Mammalian Gut Microbiome

2020 ◽  
Vol 86 (23) ◽  
Author(s):  
Christian Milani ◽  
Giulia Alessandri ◽  
Leonardo Mancabelli ◽  
Marta Mangifesta ◽  
Gabriele Andrea Lugli ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Host Species ◽  
Taxonomic Composition ◽  
Tree Of Life ◽  
Metabolic Potential ◽  
Shotgun Metagenomics ◽  
Fecal Samples ◽  
Functional Features ◽  
Host Physiology ◽  
The Impact

ABSTRACT In recent years, various studies have demonstrated that the gut microbiota influences host metabolism. However, these studies were focused primarily on a single or a limited range of host species, thus preventing a full exploration of possible taxonomic and functional adaptations by gut microbiota members as a result of host-microbe coevolution events. In the current study, the microbial taxonomic profiles of 250 fecal samples, corresponding to 77 host species that cover the mammalian branch of the tree of life, were reconstructed by 16S rRNA gene-based sequence analysis. Moreover, shotgun metagenomics was employed to investigate the metabolic potential of the fecal microbiomes of 24 mammals, and subsequent statistical analyses were performed to assess the impact of host diet and corresponding physiology of the digestive system on gut microbiota composition and functionality. Functional data were confirmed and extended through metatranscriptome assessment of gut microbial populations of eight animals, thus providing insights into the transcriptional response of gut microbiota to specific dietary lifestyles. Therefore, the analyses performed in this study support the notion that the metabolic features of the mammalian gut microbiota have adapted to maximize energy extraction from the host’s diet. IMPORTANCE Diet and host physiology have been recognized as main factors affecting both taxonomic composition and functional features of the mammalian gut microbiota. However, very few studies have investigated the bacterial biodiversity of mammals by using large sample numbers that correspond to multiple mammalian species, thus resulting in an incomplete understanding of the functional aspects of their microbiome. Therefore, we investigated the bacterial taxonomic composition of 250 fecal samples belonging to 77 host species distributed along the tree of life in order to assess how diet and host physiology impact the intestinal microbial community by selecting specific microbial players. Conversely, the application of shotgun metagenomics and metatranscriptomics approaches to a group of selected fecal samples allowed us to shed light on both metabolic features and transcriptional responses of the intestinal bacterial community based on different diets.

scholarly journals Effects of Psychotropics on the Microbiome in Patients With Depression and Anxiety: Considerations in a Naturalistic Clinical Setting

2020 ◽  
Author(s):  
Yoshihiro Tomizawa ◽  
Shunya Kurokawa ◽  
Daiki Ishii ◽  
Katsuma Miyaho ◽  
Chiharu Ishii ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Depressive Disorders ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Shannon Index ◽  
Rrna Gene ◽  
Depression And Anxiety ◽  
The Impact ◽  
Whole Tree

Abstract Background The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication. Method We longitudinally investigated the relationship between patients’ prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at 3 time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions. Results We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity whole-tree diversity decreased in patients on antipsychotics compared with patients without (P = .027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and phylogenic diversity whole tree (estimate = −0.00254, SE = 0.000595, P < .0001; estimate = −0.02644, SE = 0.00833, P = .002, respectively). Conclusion Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients’ types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.

scholarly journals Dietary Proteins Relevant to Human Consumption Impact the Development of Obesity and Type 2 Diabetes in Association with Major Changes in the Gut Microbiota in a Mouse Model (OR27-03-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Noëmie Daniel ◽  
Béatrice Choi ◽  
Vanessa Houde ◽  
Thibault Varin ◽  
Cecile Vors ◽  
...  
Keyword(s):  
Animal Models ◽  
Gut Microbiota ◽  
Insulin Signaling ◽  
Body Weight Gain ◽  
Bacterial Species ◽  
Human Consumption ◽  
Oral Glucose ◽  
Rrna Gene ◽  
Dietary Proteins ◽  
The Impact

Abstract Objectives Animal models fed a high-fat high-sucrose (HFHS) diet are commonly used to study obesity and cardiometabolic diseases. While much attention is paid to the impact of fat and carbohydrates sources, very little consideration is given to the composition of dietary proteins. Indeed, casein is often the only source of protein in rodent's diet. This study aimed to evaluate the impact of a dietary protein mix that is more relevant to typical intakes of proteins in humans and its influences on body weight gain, metabolic health and gut microbiota. Methods Our new diet contained a mix of 10 protein sources based on NHANES data that were incorporated into low-fat low-sucrose (LFLS) and HFHS diets. C57BL/6J mice were fed these diets or control diets containing identical amounts of casein as the only source of protein for 12 weeks. Feces were collected for gut microbiota investigation, an oral glucose tolerance test was performed and tissues were harvested for analysis of insulin signaling and mTOR/S6K1 activation. Results 16S rRNA gene sequencing of fecal samples showed that both LFLS and HFHS mice fed the protein mix had increased gut microbiota diversity, and significant changes in the relative abundance of several bacterial species (higher Adlercreutzia or Tyzzerella, lower Bacteroides or Akkermansia) as compared to mice fed casein only. Importantly, inclusion of the protein mix amplified the effects of the HFHS diet on the development of obesity, glucose intolerance and hyperinsulinemia as compared to casein-fed animals, whereas no difference was observed in the context of LFLS feeding. Evaluation of insulin signaling in the liver also revealed that the protein mix potentiated the effect of HFHS feeding on the mTORC1/S6K1 pathway, increasing inhibitory phosphorylation of IRS-1 on Ser1101 and leading to further impairment of Akt activation by insulin. Conclusions Our results reveal that compared to pure casein, feeding a protein mixture causes major changes in the gut microbiota profile and greater impact on HFHS-induced obesity and associated metabolic impairments. This study illustrates the importance of considering a diverse source of dietary proteins when using laboratory animal models to more reliably reproduce the development of metabolic syndrome in humans, and to enhance the clinical relevance of nutritional and therapeutic interventions. Funding Sources N/A.

scholarly journals Impact of a Moderately Hypocaloric Mediterranean Diet on the Gut Microbiota Composition of Italian Obese Patients

Nutrients ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2707 ◽  
Author(s):  
Silvia Pisanu ◽  
Vanessa Palmas ◽  
Veronica Madau ◽  
Emanuela Casula ◽  
Andrea Deledda ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Mediterranean Diet ◽  
Illumina Miseq ◽  
Nutritional Intervention ◽  
Rrna Gene ◽  
Obese Patients ◽  
Dietary Interventions ◽  
The Impact ◽  
The 16S Rrna Gene ◽  
Gut Microbiota Composition

Although it is known that the gut microbiota (GM) can be modulated by diet, the efficacy of specific dietary interventions in determining its composition and diversity in obese patients remains to be ascertained. The present work aims to evaluate the impact of a moderately hypocaloric Mediterranean diet on the GM of obese and overweight patients (OB). The GM of 23 OB patients (F/M = 20/3) was compared before (T0) and after 3 months (T3) of nutritional intervention (NI). Fecal samples were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. At baseline, GM characterization confirmed typical obesity-associated dysbiosis. After 3 months of NI, patients presented a statistically significant reduction in body weight and fat mass, along with changes in the relative abundance of many microbial patterns. In fact, an increase in the abundance of several Bacteroidetes taxa (i.e., Sphingobacteriaceae, Sphingobacterium, Bacteroides spp., Prevotella stercorea) and a depletion of many Firmicutes taxa (i.e., Lachnospiraceae members, Ruminococcaceae and Ruminococcus, Veillonellaceae, Catenibacterium, Megamonas) were observed. In addition, the phylum Proteobacteria showed an increased abundance, while the genus Sutterella, within the same phylum, decreased after the intervention. Metabolic pathways, predicted by bioinformatic analyses, showed a decrease in membrane transport and cell motility after NI. The present study extends our knowledge of the GM profiles in OB, highlighting the potential benefit of moderate caloric restriction in counteracting the gut dysbiosis.

scholarly journals In Vitro Fecal Fermentation Patterns of Arabinoxylan from Rice Bran on Gut Microbiota in Normal Weight and Overweight/Obese Subjects

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1560-1560
Author(s):  
Inah Gu ◽  
Wing Shun Lam ◽  
Daya Marasini ◽  
Cindi Brownmiller ◽  
Brett Savary ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Rice Bran ◽  
Block Design ◽  
16S Rrna Gene Sequencing ◽  
Short Chain Fatty Acids ◽  
Normal Weight ◽  
Rrna Gene ◽  
Gut Health ◽  
The Impact

Abstract Objectives Arabinoxylan is a non-starch polysaccharide and rich in wheat, rice and many other cereal grains. Diets high in fiber help promoting gut health in obesity. The objective of this study was to investigate the impact of arabinoxylan from rice bran on the gut microbiota and short chain fatty acids (SCFA) in normal weight (NW) and overweight/obese (OO) subjects through in vitro fecal fermentation. Methods Arabinoxylan was extracted from rice bran fiber. For in vitro fecal fermentation, each fecal sample from NW (n = 6, 3 males and 3 females) and OO (n = 7, 3 males and 4 females) was diluted into anaerobic medium with three treatments: control (no substrates), fructooligosaccharides (FOS, a well-known prebiotic), and arabinoxylan. Samples were incubated at 37˚C and aliquots were taken at 0, 4, 8, 12 and 24 h. SCFA content from samples at all timepoints was analyzed using HPLC. Samples at 0 and 24 h were used for gut microbiota analysis through 16S rRNA gene sequencing. Statistical analyses were performed for the randomized complete block design, where the weight classes are confounded with blocks (subjects). Friedman test was used to determine the difference at 5% level of significance. Results As a result, arabinoxylan treatment significantly increased total SCFA concentration in both NW and OO subjects than control (P < 0.05), comparable to FOS treatment. Between weight classes under arabinoxylan treatment, OO group showed a significantly higher total SCFA content than NW group (P < 0.05). Arabinoxylan changed gut microbial population at the genus level, stimulating Bifidobacterium, Collinsella and Blautia and decreasing Clostridium XIVa and b, Dorea and Oscillibacter (P < 0.05). In addition, different microbiome population was shown in weight classes with three treatments, showing higher Bacteroides in NW and higher Prevotella in OO. Conclusions These results showed that arabinoxylan from rice bran modified gut microbiota in both weight classes, increasing total SCFA content. This study suggests that arabinoxylan from rice bran may have a potential impact on microbial gut health in obesity with prebiotic activities. Funding Sources University of Arkansas.

scholarly journals Inbreeding Alters the Gut Microbiota of the Banna Minipig

Animals ◽  
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.

scholarly journals Gut Microbiota Analysis Results Are Highly Dependent on the 16S rRNA Gene Target Region, Whereas the Impact of DNA Extraction Is Minor

2017 ◽  
Vol 28 (1) ◽  
pp. 19-30 ◽  
Author(s):  
Anniina Rintala ◽  
Sami Pietilä ◽  
Eveliina Munukka ◽  
Erkki Eerola ◽  
Juha-Pekka Pursiheimo ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Dna Extraction ◽  
Rrna Gene ◽  
Gene Target ◽  
Target Region ◽  
Microbiota Analysis ◽  
The Impact ◽  
The 16S Rrna Gene

scholarly journals Impact of a Moderately Hypocaloric Mediterranean Diet on the Gut Microbiota Composition of Italian Obese Patients

2020 ◽  
Author(s):  
Silvia Pisanu ◽  
Vanessa Palmas ◽  
Veronica Madau ◽  
Emanuela Casula ◽  
Andrea Deledda ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Mediterranean Diet ◽  
Illumina Miseq ◽  
Nutritional Intervention ◽  
The Body ◽  
Rrna Gene ◽  
Obese Patients ◽  
Dietary Interventions ◽  
The Impact ◽  
Gut Microbiota Composition

Although it is known that the gut microbiota (GM) can be modulated by diet, the efficacy of specific dietary interventions in determining its composition and diversity in obese patients remains to be ascertained. The present work aims to evaluate the impact of a moderately hypocaloric Mediterranean diet on the GM of obese and overweight patients (OB). The GM of 23 OB patients (F/M= 20/3) was compared before (T0) and after 3 months (T3) of the nutritional intervention (NI). Fecal samples were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. At baseline, the GM characterization confirmed the typical obesity-associated dysbiosis. After 3 months of NI, patients presented a statistically significant reduction of the body weight and fat mass, along with changes in the relative abundance of many microbial patterns. In fact, we observed an increased abundance in several Bacteroidetes taxa (i.e. Sphingobacteriaceae, Sphingobacterium, Bacteroides spp., Prevotella stercorea) and depletion of many Firmicutes taxa (i.e. Lachnospiraceae members, Ruminococcaceae and Ruminococcus, Veillonellaceae, Catenibacterium, Megamonas). In addition, the phylum Proteobacteria showed an increased abundance, while the genus Sutterella, within the same phylum, decreased after the intervention. Metabolic pathways, predicted by bioinformatic analyses, showed a decrease in membrane transport and cell motility after NI. The present study extends our knowledge of the GM profiles in OB, highlighting the potential benefit of a moderate caloric restriction in counteracting the gut dysbiosis.

scholarly journals Altered Gut Microbiota Taxonomic Compositions of Patients With Sepsis in a Pediatric Intensive Care Unit

2021 ◽  
Vol 9 ◽  
Author(s):  
Jing Liu ◽  
Mingbang Wang ◽  
Weiming Chen ◽  
Jian Ma ◽  
Yi Peng ◽  
...  
Keyword(s):  
Intensive Care ◽  
Gut Microbiota ◽  
Pathogenic Bacteria ◽  
Pediatric Intensive Care ◽  
16S Rrna Gene Sequencing ◽  
Taxonomic Composition ◽  
Rrna Gene ◽  
Healthy Children ◽  
Commensal Flora ◽  
Opportunistic Pathogenic

Background: The gut is thought to play an important role in the pathogenesis of sepsis. Changes in the gut microbiota are closely related to the occurrence and development of human diseases, but few studies have focused on taxonomic composition of gut microbiota in septic patients. Knowledge of changes in the gut microbiota is a key issue in intensive care. Clinicians must understand how an altered gut microbiota affects the susceptibility and prognosis of septic patients.Measurements and Main Results: In the single-center case control study, 20 septic patients and 20 healthy children were recruited. The taxonomic composition of gut microbiota was determined via 16S rRNA gene sequencing. Gut microbiota diversity in children with sepsis was significantly reduced compared with that in healthy children. The taxonomic composition of gut microbiota can effectively distinguish children with sepsis from healthy children. Thirteen taxa of gut microbiota were significantly increased in the guts of children with sepsis compared with those of healthy children. The increased abundances of Enterococcaceae, Enterococcus, and Enterococcus durans in gut of septic patients were significantly positively correlated with blood inflammation indicators CRP and WBC. The abundances of seven bacteria were significantly decreased in the guts of septic children compared with those of healthy children. The decreased abundance of Bifidobacteriales in gut of septic patients is significantly negatively correlated with blood inflammation index WBC. A machine-learning classifier was built for distinguishing sepsis and achieved the AUC value of 81.25%. It shows that the composition of gut microbiota has certain potential for diagnosis of sepsis.Conclusions: Gut microbiota alterations in septic patients exhibit proliferation of opportunistic pathogenic bacteria, the massive reduction of the commensal flora, and the significant decrease in the diversity of the gut microbiota. Dysbiosis may also account for some changes in the inflammation indexes.

scholarly journals Using fecal immunochemical tubes for the analysis of gut microbiome has potential to improve colorectal cancer screening

2021 ◽  
Author(s):  
Kertu Liis Krigul ◽  
Oliver Aasmets ◽  
Kreete Lull ◽  
Tonis Org ◽  
Elin Org
Keyword(s):  
Colorectal Cancer ◽  
Cancer Screening ◽  
Gut Microbiota ◽  
Colorectal Cancer Screening ◽  
Public Health Problem ◽  
Fecal Occult Blood ◽  
Rrna Gene ◽  
Screening Programs ◽  
Fresh Frozen ◽  
The Impact

Background: Colorectal cancer (CRC) is an important and challenging public health problem which successful treatment depends on the early detection of the disease. Recently, colorectal cancer specific microbiome signatures have been proposed as an additional marker for CRC detection. A desirable aim would be the possibility to analyze microbiome from the fecal samples collected during CRC screening programs into FIT tubes for fecal occult blood testing. Methods: We investigated the impact of Fecal Immunohistochemical Test (FIT) and stabilization buffer on the microbial community structure in stool samples from 30 volunteers and compared their communities to fresh-frozen samples highlighting also the previously published cancer-specific communities. Altogether 214 samples were analyzed including positive and negative controls using 16S rRNA gene sequencing. Results: The variation between individuals is greater than differences introduced by collection strategy. The vast majority of the genera are stable up to 7 days. None of the changes observed between fresh frozen samples and FIT tubes are related to previously shown colorectal cancer specific bacteria. Conclusions: Overall, our results show that FIT tubes can be used for profiling the gut microbiota in colorectal cancer screening programs as the community is similar to fresh frozen samples and stable at least for 7 days. Impact: Sample material from FIT tubes could be used in addition to fecal immunochemical tests for future investigations into the role of gut microbiota in colorectal cancer screening programs circumventing the need to collect additional samples and possibly improving the sensitivity of FIT.

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