Mediation Analysis as a Means of Identifying Dietary Components That Differentially Affect the Fecal Microbiota of Infants Weaned by Modified Baby-Led and Traditional Approaches

ABSTRACT The introduction of “solids” (i.e., complementary foods) to the milk-only diet in early infancy affects the development of the gut microbiota. The aim of this study was to determine whether a “baby-led” approach to complementary feeding that encourages the early introduction of an adult-type diet results in alterations of the gut microbiota composition compared to traditional spoon-feeding. The Baby-Led Introduction to SolidS (BLISS) study randomized 206 infants to BLISS (a modified version of baby-led weaning [BLW], the introduction of solids at 6 months of age, followed by self-feeding of family foods) or control (traditional spoon-feeding of purées) groups. Fecal microbiotas and 3-day weighed-diet records were analyzed for a subset of 74 infants at 7 and 12 months of age. The composition of the microbiota was determined by sequencing of 16S rRNA genes amplified by PCR from bulk DNA extracted from feces. Diet records were used to estimate food and dietary fiber intake. Alpha diversity (number of operational taxonomic units [OTUs]) was significantly lower in BLISS infants at 12 months of age (difference [95% confidence interval {CI}] of 31 OTUs [3.4 to 58.5]; P = 0.028), and while there were no significant differences between control and BLISS infants in relative abundances of Bifidobacteriaceae, Enterobacteriaceae, Veillonellaceae, Bacteroidaceae, Erysipelotrichaceae, Lachnospiraceae, or Ruminococcaceae at 7 or 12 months of age, OTUs representing the genus Roseburia were less prevalent in BLISS microbiotas at 12 months. Mediation models demonstrated that the intake of “fruit and vegetables” and “dietary fiber” explained 29% and 25%, respectively, of the relationship between group (BLISS versus control) and alpha diversity. IMPORTANCE The introduction of solid foods (complementary feeding or weaning) to infants leads to more-complex compositions of microbial communities (microbiota or microbiome) in the gut. In baby-led weaning (BLW), infants are given only finger foods that they can pick up and feed themselves—there is no parental spoon-feeding of puréed baby foods—and infants are encouraged to eat family meals. BLW is a new approach to infant feeding that is increasing in popularity in the United States, New Zealand, the United Kingdom, and Canada. We used mediation modeling, commonly used in health research but not in microbiota studies until now, to identify particular dietary components that affected the development of the infant gut microbiota.

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Revealing microbial species diversity using sequence capture by hybridization

Microbial Genomics ◽

10.1099/mgen.0.000714 ◽

2021 ◽

Vol 7 (12) ◽

Author(s):

Sophie Marre ◽

Cyrielle Gasc ◽

Camille Forest ◽

Yacine Lebbaoui ◽

Pascale Mosoni ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rdna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Taxonomic Resolution ◽

Human Gut ◽

Content Type ◽

Innovative Strategy ◽

Human Gut Microbiota ◽

Rare Biosphere

Targeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative strategy using gene capture by hybridization. From three OTU sequences detected upon polyphenol supplementation and belonging to the rare biosphere of the human gut microbiota, we revealed 59 nearly full-length 16S rRNA genes, highlighting high bacterial diversity hidden behind OTUs while evidencing novel taxa. Inside each OTU, revealed 16S rDNA sequences could be highly distant from each other with similarities down to 85 %. We identified one new family belonging to the order Clostridiales , 39 new genera and 52 novel species. Related bacteria potentially involved in polyphenol degradation have also been identified through genome mining and our results suggest that the human gut microbiota could be much more diverse than previously thought.

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Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats

Applied and Environmental Microbiology ◽

10.1128/aem.00203-15 ◽

2015 ◽

Vol 81 (10) ◽

pp. 3502-3509 ◽

Cited By ~ 47

Author(s):

Jinzhen Jiao ◽

Jinyu Huang ◽

Chuanshe Zhou ◽

Zhiliang Tan

Keyword(s):

Bacterial Diversity ◽

Bacterial Colonization ◽

Alpha Diversity ◽

Shannon Index ◽

16S Rrna Genes ◽

Rrna Genes ◽

Age Group ◽

Content Type ◽

Age Related ◽

Rumen Development

ABSTRACTUnderstanding of the colonization process of epithelial bacteria attached to the rumen tissue during rumen development is very limited. Ruminal epithelial bacterial colonization is of great significance for the relationship between the microbiota and the host and can influence the early development and health of the host. MiSeq sequencing of 16S rRNA genes and quantitative real-time PCR (qPCR) were applied to characterize ruminal epithelial bacterial diversity during rumen development in this study. Seventeen goat kids were selected to reflect the no-rumination (0 and 7 days), transition (28 and 42 days), and rumination (70 days) phases of animal development. Alpha diversity indices (operational taxonomic unit [OTU] numbers, Chao estimate, and Shannon index) increased (P< 0.01) with age, and principal coordinate analysis (PCoA) revealed that the samples clustered together according to age group. Phylogenetic analysis revealed thatProteobacteria,Firmicutes, andBacteroideteswere detected as the dominant phyla regardless of the age group, and the abundance ofProteobacteriadeclined quadratically with age (P< 0.001), while the abundances ofBacteroidetes(P= 0.088) andFirmicutes(P= 0.009) increased with age. At the genus level,Escherichia(80.79%) dominated at day zero, whilePrevotella,Butyrivibrio, andCampylobactersurged (linearly;P< 0.01) in abundance at 42 and 70 days. qPCR showed that the total copy number of epithelial bacteria increased linearly (P= 0.013) with age. In addition, the abundances of the generaButyrivibrio,Campylobacter, andDesulfobulbuswere positively correlated with rumen weight, rumen papilla length, ruminal ammonia and total volatile fatty acid concentrations, and activities of carboxymethylcellulase (CMCase) and xylanase. Taking the data together, colonization by ruminal epithelial bacteria is age related (achieved at 2 months) and might participate in the anatomic and functional development of the rumen.

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Berberine Blocks the Relapse of Clostridium difficile Infection in C57BL/6 Mice after Standard Vancomycin Treatment

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.04794-14 ◽

2015 ◽

Vol 59 (7) ◽

pp. 3726-3735 ◽

Cited By ~ 22

Author(s):

Zhi Lv ◽

Guoli Peng ◽

Weihua Liu ◽

Hufeng Xu ◽

JianRong Su

Keyword(s):

Clostridium Difficile ◽

Mouse Model ◽

Gut Microbiota ◽

Inflammatory Responses ◽

Relative Weight ◽

16S Rrna Genes ◽

Rrna Genes ◽

Therapeutic Effects ◽

Content Type ◽

Vancomycin Treatment

ABSTRACTVancomycin is a preferred antibiotic for treatingClostridium difficileinfection (CDI) and has been associated with a rate of recurrence of CDI of as high as 20% in treated patients. Recent studies have suggested that berberine, an alternative medical therapy for gastroenteritis and diarrhea, exhibits several beneficial effects, including induction of anti-inflammatory responses and restoration of the intestinal barrier function. This study investigated the therapeutic effects of berberine on preventing CDI relapse and restoring the gut microbiota in a mouse model. Berberine was administered through gavage to C57BL/6 mice with established CDI-induced intestinal injury and colitis. The disease activity index (DAI), mean relative weight, histopathology scores, and levels of toxins A and B in fecal samples were measured. An Illumina sequencing-based analysis of 16S rRNA genes was used to determine the overall structural change in the microbiota in the mouse ileocecum. Berberine administration significantly promoted the restoration of the intestinal microbiota by inhibiting the expansion of members of the familyEnterobacteriaceaeand counteracting the side effects of vancomycin treatment. Therapy consisting of vancomycin and berberine combined prevented weight loss, improved the DAI and the histopathology scores, and effectively decreased the mortality rate. Berberine prevented CDIs from relapsing and significantly improved survival in the mouse model of CDI. Our data indicate that a combination of berberine and vancomycin is more effective than vancomycin alone for treating CDI. One of the possible mechanisms by which berberine prevents a CDI relapse is through modulation of the gut microbiota. Although this conclusion was generated in the case of the mouse model, use of the combination of vancomycin and berberine and represent a novel therapeutic approach targeting CDI.

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Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches

Applied and Environmental Microbiology ◽

10.1128/aem.03700-15 ◽

2015 ◽

Vol 82 (4) ◽

pp. 1256-1263 ◽

Cited By ~ 32

Author(s):

Aram Mikaelyan ◽

Claire L. Thompson ◽

Markus J. Hofer ◽

Andreas Brune

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

16S Rrna Genes ◽

Rrna Genes ◽

Experimental Proof ◽

Content Type ◽

Germ Free ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

Axenic Conditions

ABSTRACTThe gut microbiota of termites plays important roles in the symbiotic digestion of lignocellulose. However, the factors shaping the microbial community structure remain poorly understood. Because termites cannot be raised under axenic conditions, we established the closely related cockroachShelfordella lateralisas a germ-free model to study microbial community assembly and host-microbe interactions. In this study, we determined the composition of the bacterial assemblages in cockroaches inoculated with the gut microbiota of termites and mice using pyrosequencing analysis of their 16S rRNA genes. Although the composition of the xenobiotic communities was influenced by the lineages present in the foreign inocula, their structure resembled that of conventional cockroaches. Bacterial taxa abundant in conventional cockroaches but rare in the foreign inocula, such asDysgonomonasandParabacteroidesspp., were selectively enriched in the xenobiotic communities. Donor-specific taxa, such as endomicrobia or spirochete lineages restricted to the gut microbiota of termites, however, either were unable to colonize germ-free cockroaches or formed only small populations. The exposure of xenobiotic cockroaches to conventional adults restored their normal microbiota, which indicated that autochthonous lineages outcompete foreign ones. Our results provide experimental proof that the assembly of a complex gut microbiota in insects is deterministic.

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Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host

Applied and Environmental Microbiology ◽

10.1128/aem.01226-14 ◽

2014 ◽

Vol 80 (17) ◽

pp. 5254-5264 ◽

Cited By ~ 264

Author(s):

Ji-Hyun Yun ◽

Seong Woon Roh ◽

Tae Woong Whon ◽

Mi-Ja Jung ◽

Min-Soo Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Developmental Stage ◽

Bacterial Diversity ◽

Bacterial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Content Type ◽

Operational Taxonomic Units ◽

Insect Order ◽

Insect Gut

ABSTRACTInsects are the most abundant animals on Earth, and the microbiota within their guts play important roles by engaging in beneficial and pathological interactions with these hosts. In this study, we comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes. In total, 174,374 sequence reads were obtained, identifying 9,301 bacterial operational taxonomic units (OTUs) at the 3% distance level from all samples, with an average of 84.3 (±97.7) OTUs per sample. The insect gut microbiota were dominated byProteobacteria(62.1% of the total reads, including 14.1%Wolbachiasequences) andFirmicutes(20.7%). Significant differences were found in the relative abundances of anaerobes in insects and were classified according to the criteria of host environmental habitat, diet, developmental stage, and phylogeny. Gut bacterial diversity was significantly higher in omnivorous insects than in stenophagous (carnivorous and herbivorous) insects. This insect-order-spanning investigation of the gut microbiota provides insights into the relationships between insects and their gut bacterial communities.

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Comparison of the Microbial Community Structures of Untreated Wastewaters from Different Geographic Locales

Applied and Environmental Microbiology ◽

10.1128/aem.03448-12 ◽

2013 ◽

Vol 79 (9) ◽

pp. 2906-2913 ◽

Cited By ~ 94

Author(s):

Orin C. Shanks ◽

Ryan J. Newton ◽

Catherine A. Kelty ◽

Susan M. Huse ◽

Mitchell L. Sogin ◽

...

Keyword(s):

United States ◽

Microbial Communities ◽

Dna Sequences ◽

The United States ◽

16S Rrna Genes ◽

Rrna Genes ◽

Content Type ◽

Untreated Sewage ◽

Wide Range ◽

Taxonomic Groups

ABSTRACTMicrobial sewage communities consist of a combination of human fecal microorganisms and nonfecal microorganisms, which may be residents of urban sewer infrastructure or flowthrough originating from gray water or rainwater inputs. Together, these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high-quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups withinFirmicutes,Bacteroidetes,Actinobacteria, andProteobacteria. DNA sequences were also classified into fecal, sewage infrastructure (i.e., nonfecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal in origin, while 81.4% were consistently associated with the sewage infrastructure. The composition of feces-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States.

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Sputum Microbiome Composition in Patients With Squamous Cell Lung Carcinoma

10.21203/rs.3.rs-902707/v1 ◽

2021 ◽

Author(s):

E. D. Baranova ◽

V. G. Druzhinin ◽

L. V. Matskova ◽

P. S. Demenkov ◽

V. P . Volobaev ◽

...

Keyword(s):

Squamous Cell ◽

Inflammatory Responses ◽

Alpha Diversity ◽

Taxonomic Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Cell Lung Carcinoma ◽

Microbiome Composition ◽

Β Diversity ◽

Genome Damage

Abstract Recent findings indicate that the microbiome can have a significant impact on the development of lung cancer by inducing inflammatory responses, causing dysbiosis and generating genome damage. The aim of this study was to search for bacterial markers of squamous cell carcinoma (LUSC). In the study, the taxonomic composition of the sputum microbiome of 40 men with untreated LUSC was compared with 40 healthy controls. Next Generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. There was no differences in alpha diversity between the LUSC and control groups. Meanwhile, differences in the structure of bacterial communities (β diversity) among patients and controls differed significantly in sputum samples (pseudo-F = 1.65; p = 0.026). Only Streptococcus, Bacillus, Gemella and Haemophilus were found to be significantly increased in patients with LUSC compared to the control subjects, while 19 bacterial genera were significantly reduced, indicating a decrease in beta diversity in the microbiome of patients with LUSC. From our study, Streptococcus (Streptococcus agalactiae) emerges as the most likely LUSC biomarker, but more research is needed to confirm this assumption.

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Taxonomic composition and biodiversity of the gut microbiome from patients with irritable bowel syndrome, ulcerative colitis, and asthma

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj21.100 ◽

2022 ◽

Vol 25 (8) ◽

pp. 864-873

Author(s):

A. Y. Tikunov ◽

A. N. Shvalov ◽

V. V. Morozov ◽

I. V. Babkin ◽

G. V. Seledtsova ◽

...

Keyword(s):

Ulcerative Colitis ◽

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Gut Microbiome ◽

Taxonomic Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Taxonomic Structure ◽

Opportunistic Bacteria ◽

Irritable Bowel

To date, the association of an imbalance of the intestinal microbiota with various human diseases, including both diseases of the gastrointestinal tract and disorders of the immune system, has been shown. However, despite the huge amount of accumulated data, many key questions still remain unanswered. Given limited data on the composition of the gut microbiota in patients with ulcerative colitis (UC) and irritable bowel syndrome (IBS) from different parts of Siberia, as well as the lack of data on the gut microbiota of patients with bronchial asthma (BA), the aim of the study was to assess the biodiversity of the gut microbiota of patients with IBS, UC and BA in comparison with those of healthy volunteers (HV). In this study, a comparative assessment of the biodiversity and taxonomic structure of gut microbiome was conducted based on the sequencing of 16S rRNA genes obtained from fecal samples of patients with IBS, UC, BA and volunteers. Sequences of the Firmicutes and Bacteroidetes types dominated in all samples studied. The third most common in all samples were sequences of the Proteobacteria type, which contains pathogenic and opportunistic bacteria. Sequences of the Actinobacteria type were, on average, the fourth most common. The results showed the presence of dysbiosis in the samples from patients compared to the sample from HVs. The ratio of Firmicutes/Bacteroidetes was lower in the IBS and UC samples than in HV and higher the BA samples. In the samples from patients with intestinal diseases (IBS and UC), an increase in the proportion of sequences of the Bacteroidetes type and a decrease in the proportion of sequences of the Clostridia class, as well as the Ruminococcaceae, but not Erysipelotrichaceae family, were found. The IBS, UC, and BA samples had signif icantly more Proteobacteria sequences, including Methylobacterium, Sphingomonas, Parasutterella, Halomonas, Vibrio, as well as Escherichia spp. and Shigella spp. In the gut microbiota of adults with BA, a decrease in the proportion of Roseburia, Lachnospira, Veillonella sequences was detected, but the share of Faecalibacterium and Lactobacillus sequences was the same as in healthy individuals. A signif icant increase in the proportion of Halomonas and Vibrio sequences in the gut microbiota in patients with BA has been described for the f irst time.

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Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.058651-0 ◽

2014 ◽

Vol 64 (Pt_5) ◽

pp. 1501-1506 ◽

Cited By ~ 32

Author(s):

Bacem Mnasri ◽

Tian Yan Liu ◽

Sabrine Saidi ◽

Wen Feng Chen ◽

Wen Xin Chen ◽

...

Keyword(s):

Type Species ◽

Root Nodules ◽

16S Rrna Genes ◽

Rrna Genes ◽

The Novel ◽

Content Type ◽

Link Type ◽

Physiological Properties ◽

Microbial Strains ◽

Type Strains

Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum , are further studied here. Their 16S rRNA genes showed 98.5–99 % similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA–DNA relatedness between strain 23C2T and the type strains of R. loessense , R. mongolense , R. gallicum and R. yanglingense ranged from 58.1 to 61.5 %. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52 %. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T ( = CCBAU 101087T = HAMBI3541T) was designated as the type strain.

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Application of a Euryarchaeota-Specific Helicase from Thermococcus kodakarensis for Noise Reduction in PCR

Applied and Environmental Microbiology ◽

10.1128/aem.04116-15 ◽

2016 ◽

Vol 82 (10) ◽

pp. 3022-3031 ◽

Cited By ~ 8

Author(s):

Ayako Fujiwara ◽

Katsuhiro Kawato ◽

Saori Kato ◽

Kiyoshi Yasukawa ◽

Ryota Hidese ◽

...

Keyword(s):

Noise Reduction ◽

Dna Polymerase ◽

Biological Activities ◽

Genetic Diagnosis ◽

Gc Content ◽

Dna Amplification ◽

16S Rrna Genes ◽

Rrna Genes ◽

Content Type ◽

Thermococcus Kodakarensis

ABSTRACTDNA/RNA helicases, which are enzymes for eliminating hydrogen bonds between bases of DNA/DNA, DNA/RNA, and RNA/RNA using the energy of ATP hydrolysis, contribute to various biological activities. In the present study, theEuryarchaeota-specific helicase EshA (TK0566) from the hyperthermophilic archaeonThermococcus kodakarensis(Tk-EshA) was obtained as a recombinant form, and its enzymatic properties were examined.Tk-EshA exhibited maximal ATPase activity in the presence of RNA at 80°C. Unwinding activity was evaluated with various double-stranded DNAs (forked, 5′ overhung, 3′ overhung, and blunt end) at 50°C.Tk-EshA unwound forked and 3′ overhung DNAs. These activities were expected to unwind the structured template and to peel off misannealed primers whenTk-EshA was added to a PCR mixture. To examine the effect ofTk-EshA on PCR, various target DNAs were selected, and DNA synthesis was investigated. When 16S rRNA genes were used as a template, several misamplified products (noise DNAs) were detected in the absence ofTk-EshA. In contrast, noise DNAs were eliminated in the presence ofTk-EshA. Noise reduction byTk-EshA was also confirmed whenTaqDNA polymerase (a family A DNA polymerase, PolI type) and KOD DNA polymerase (a family B DNA polymerase, α type) were used for PCR. Misamplified bands were also eliminated duringtoxAgene amplification fromPseudomonas aeruginosaDNA, which possesses a high GC content (69%).Tk-EshA addition was more effective than increasing the annealing temperature to reduce misamplified DNAs duringtoxAamplification.Tk-EshA is a useful tool to reduce noise DNAs for accurate PCR.IMPORTANCEPCR is a technique that is useful for genetic diagnosis, genetic engineering, and detection of pathogenic microorganisms. However, troubles with nonspecific DNA amplification often occur from primer misannealing. In order to achieve a specific DNA amplification by eliminating noise DNAs derived from primer misannealing, a thermostableEuryarchaeota-specific helicase (Tk-EshA) was included in the PCR mixture. The addition ofTk-EshA has reduced noise DNAs in PCR.

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