Unidentified Genus Research Articles

Metagenomic signatures of transportation stress in the early life stages of cobia (Rachycentron canadum) to aid in mitigation strategies

Cobia (Rachycentron canadum) is a high-value marine aquaculture species. Knowledge of the microbial dynamics in various aquaculture operations is crucial for developing suitable management practices. The present study revealed the critical dysbiotic events in the whole larval and juvenile-gut microbiome of cobia, through an inevitable aquaculture operation, viz. live transportation. The results through both culture-dependent and independent techniques demonstrated the sensitivity of the cobia microbiome during early life, where live transport is inevitable. In detail, there was a significant change in the microbial composition and reduction in the cultivable load of all the life stages. Further, a significant reduction in functional metagenomics along with an increase in taxonomic metagenomics was recorded in the L21 stage. Significant reductions of the putative healthy microbiota, viz., Proteobacteria and Actinobacteria were remarkable in the whole larval microbiome. The analysis through linear discriminant analysis effect size revealed that the opportunistic fish pathogens, viz., Vibrio spp., Arcobacter spp., and Acinetobacter spp. were increased whereas, Pseudomonas spp. was decreased in larvae following transportation. The significant reduction in the taxonomic diversity measures was noteworthy in the juvenile-gut microbiome. Transportation promoted Serratia spp., Enterobacter spp., an unidentified genus in Flavobacteriaceae, Pseudoalteromonas spp., Alteromonas spp., and Enterovibrio spp., and inhibited Empedobacter spp. in the juvenile gut. Collectively, the results provide the prospective metagenomic signatures of health and stress in the early life stages of cobia and novel possible explanations for increased disease susceptibility post-transportation. The study warrants future research on the microbes which were found to be decreased following transportation, as potential probiotics to mitigate the stress in the marine aquaculture practices. The metagenomic signatures revealed through the study can be further applied for evaluating different husbandry practices to mitigate stress during live transportation.

A synbiotics, long chain polyunsaturated fatty acids, and milk fat globule membranes supplemented formula modulates microbiota maturation and neurodevelopment

The critical window of concurrent developmental paths of the nervous system and gut microbiota in infancy provides an opportunity for nutritional interventions with potential health benefits later in life. We compared the dynamics of gut microbiota maturation and explored its association with neurodevelopment at 12 months and 4 years of age in 170 full-term healthy infants fed a standard formula (SF) or a new formula (EF) based on standard formula supplemented with synbiotics, long chain polyunsaturated fatty acids (LC-PUFA) and bovine milk fat globule membranes (MFGM), including a breastfed reference group (BF). Using Dirichlet Multinomial Modelling, we characterized three microbial enterotypes (Mixed, anaerobic and aerobic profile; Bact, Bacteroides-dominant; Firm, Firmicutes-enriched) and identified a new enterotype dominated by an unidentified genus within Lachnospiraceae (U_Lach). Enterotypes were associated with age (Mixed with baseline, U_Lach with month 6, Bact and Firm with months 12 and 18). Trajectories or timely enterotype shifts in each infant were not random but strongly associated with type of feeding. Trajectories in SF shifted from initial Mixed to U_Lach, Bact or Firm at month. Microbiota maturation in EF split into a fast trajectory as in SF, and a slow trajectory with Mixed to U_Lach, Bact or Firm transitions at months 12 or 18, as in BF. EF infants with slow trajectories were more often in-home reared and born by vaginal delivery to mothers with pre-pregnancy lean BMI. At 12 months of age, language and expressive language scores were significantly higher in EF infants with fast trajectories than in BF. Neurodevelopmental outcomes were similar between EF infants with slow trajectories and BF at 12 months and 4 years of age. Feeding a synbiotics, LC-PUFA and MFGM supplemented formula in a specific infant environment promoted probiotic growth and retarded gut microbiota maturation with similar neurodevelopment outcomes to breastfed infants. NCT02094547.

Sex-dependent host-microbiome dynamics in zebrafish: Implications for toxicology and gastrointestinal physiology

The physiology of males and females can be vastly different, complicating interpretation of toxicological and physiological data. The objectives of this study were to elucidate the sex differences in the microbiome-gastrointestinal (GI) transcriptome of adult zebrafish. We compared microbial composition and diversity in both males and females fed the same diet and housed in the same environment. There were no sex-specific differences in weight gain nor gastrointestinal morphology based on histopathology. There was no difference in gut microbial diversity, richness (Shannon and Chao1 index) nor predicted functional composition of the microbiome between males and females. Prior to post-hoc correction, male zebrafish showed higher abundance for the bacterial families Erythrobacteraceae and Lamiaceae, both belonging to the phyla Actinobacteria and Proteobacteria. At the genus level, Lamia and Altererythrobacter were more dominant in males and an unidentified genus in Bacteroidetes was more abundant in females. There were 16 unique differentially expressed transcripts in the gastrointestinal tissue between male and female zebrafish (FDR corrected, p < 0.05). Relative to males, the mRNA expression for trim35–9, slc25a48, chchd3b, csad, and hsd17b3 were lower in female GI while cyp2k6, adra2c, and bckdk were higher in the female GI. Immune and lipid-related gene network expression differed between the sexes (i.e., cholesterol export and metabolism) as well as networks related to gastric motility, gastrointestinal system absorption and digestion. Such data provide clues as to putative differences in gastrointestinal physiology between male and female zebrafish. This study identifies host-transcriptome differences that can be considered when interpreting the microgenderome of zebrafish in studies investigating GI physiology and toxicology of fishes.

Evolution and predicted functions of the microbiota of the medium‐slow growing chicken during the first 4 weeks of chick development

AbstractChicken gut microbiota–host interactions play essential roles in the productivity and health of chickens. Deciphering the microbial composition and its functions are crucial for understanding the roles of gut microbiota within chickens. Although there are some research studies focusing on different chicken microbiota, none of them have considered medium‐slow growing chicken as a model host. Here, the microbial composition of the faeces of medium‐slow growing chicken, grown in an organic farming system, has been elucidated through 16S rRNA gene amplicon‐based metagenomics. We found a diverse microbiota that does not present major shifts during the first 4 weeks of the animal's life, although the abundance of only 2 OTUs (LactobacillusandBacteroides) increase during this time.Lactobacillusappear to govern the bacterial composition, followed distantly byClostridiales(mainlyFaecalibacterium,Ruminococcusand unidentified genera from the familiesPeptostreptococaceaeandRuminococcaceae) andBacteroidales(BacteroidesandParabacteroides). The roles of Redbro faeces microbiota have been revealed through in silico functional predictions. We found thatLactobacillusmembers may play relevant roles within its host and seem to highly influence the metabolism of fructose and mannose among other relevant functions.

Microbiome structure and response to watering in rhizosphere of Nitrosalsola vermiculata and surrounding bulk soil

The plant rhizosphere microbiomes were thought to help the plant stands adverse condition. The study aims at deciphering signatures of rhizosphere soil microbiomes of the medicinal plant Nitrosalsola vermiculata and those of the surrounding bulk soil as well as to detect influence of watering in restructuring soil microbes that can improve the plant’s ability to tolerate drought stress. Amplicon sequencing of partial 16S rRNA gene indicated that alpha diversity indices are higher in rhizosphere than in bulk soils, while no distinctive differences were observed due to the watering. Relative abundance of phylum Cyanobacteria and its descendent unidentified genus is the highest among phyla and genera of bulk soil. Relative abundance of phyla Euryarchaeota, Chloroflexi, Actinobacteria, Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria and Gemmatimonadetes as well as genera Bacillus, Ammoniphilus, Sphingomonas, Microvirga, Pontibacter, Adhaeribacter and Arthrobacter was significantly higher in rhizosphere soil. The latter taxa were reported to act as plant growth-promoting bacteria (PGPB) through symbiotic associations. We speculate that relative abundance and mutual dominance of these taxa in rhizosphere of N. vermiculata were due to the intensity and type of plant root exudates. Other factors include soil pH where microbes favoring high soil pH can show better growth in rhizosphere soil. Also, co-existence of phyla that promote sustainability of cohabiting phyla in the rhizosphere and have high synergism prevalence in biofilm formation can be one extra factor. Quorum sensing (QS) also mediates bacterial population density in a given environment and elicit specific plant responses. The low abundance of Cyanobacteria in rhizosphere soil can be due to the inhibitory effect of highly abundant members of Firmicutes, especially those of genus Bacillus. The latter conclusion was confirmed by the occurrence of high expression rate of comQ gene triggering QS in genus Bacillus. Highly abundant microbes whose abundance was not changed due to watering are phyla Firmicutes, Proteobacteria, Chloroflexi and Cyanobacteria and their descendent genera Bacillus, Ammoniphilus, Sphingomonas, Microvirga and unidentified genus of Cyanobacteria. We speculate that non-responsive taxa to watering were drought tolerant and can help plants stand adverse conditions of water scarce. In conclusion, insights on the factors involved in shaping microbiome signatures and those eliciting differential plant responses to drought stress are raised and warrant further investigations.

Alpine meadow degradation depresses soil nitrogen fixation by regulating plant functional groups and diazotrophic community composition

Biological nitrogen fixation (BNF), a function performed by diazotrophic microbes, plays an essential role in nitrogen (N) bioavailability in terrestrial ecosystems. However, little is known about the effects of meadow degradation on soil BNF and diazotrophic communities in alpine meadows. We investigated changes in soil BNF and their potential drivers in alpine meadows along a degradation gradient on the Tibetan Plateau (non-degraded, lightly degraded, moderately degraded, and severely degraded meadows) using real-time quantitative PCR and amplicon sequencing. Soil BNF rates decreased significantly along the meadow degradation gradient with a range of 17.34–79.84 nmol C2H4 g−1 dry soil d−1 across all sites. The highest BNF rate in the non-degraded meadow was 1.5–4.6-fold higher than that in the degraded meadows. The abundance and diversity of diazotrophs measured by nifH abundance and Shannon diversity was also decreased in the degraded meadows, accompanied by decreases in plant biomass, soil moisture, and nutrient content (C, N). Soil BNF rate was correlated with plant biomass, soil nutrient content, and diazotrophic abundance (including Nostoc, Scytonema, Rhodopseudomonas, and unidentified genera within the Rhizobiales and Proteobacteria). The community composition of diazotrophs differed markedly among sites with different levels of degradation, with both autotrophic (Cyanobacteria) and heterotrophic (Proteobacteria) diazotrophs contributing significantly to BNF. The plant functional groups, particularly the sedge family, were the primary drivers of soil BNF rates via mediating soil moisture, nutrient content (dissolved organic C and N), nifH gene abundance, and diazotrophic community composition. Our results reveal the main drivers of decreased BNF during alpine meadow degradation and emphasize the importance of plant functional groups in shaping the diazotrophic community and regulating the BNF rate. This information can be applied to the restoration of degraded meadow ecosystems.

Progression of diabetes is associated with changes in the ileal transcriptome and ileal-colon morphology in the UC Davis Type 2 Diabetes Mellitus rat.

Deterioration in glucose homeostasis has been associated with intestinal dysbiosis, but it is not known how metabolic dysregulation alters the gastrointestinal environment. We investigated how the progression of diabetes alters ileal and colonic epithelial mucosal structure, microbial abundance, and transcript expression in the University of California Davis Type 2 Diabetes Mellitus (UCD‐T2DM) rat model. Male UCD‐T2DM rats (age ~170 days) were included if <1‐month (n = 6, D1M) or 3‐month (n = 6, D3M) post‐onset of diabetes. Younger nondiabetic UCD‐T2DM rats were included as a nondiabetic comparison (n = 6, ND, age ~70 days). Ileum villi height/crypt depths and colon crypt depths were assessed by histology. Microbial abundance of colon content was measured with 16S rRNA sequencing. Ileum and colon transcriptional abundances were analyzed using RNA sequencing. Ileum villi height and crypt depth were greater in D3M rats compared to ND. Colon crypt depth was greatest in D3M rats compared to both ND and D1M rats. Colon abundances of Akkermansia and Muribaculaceae were lower in D3M rats relative to D1M, while Oscillospirales, Phascolarctobacterium, and an unidentified genus of Lachnospiraceae were higher. Only two transcripts were altered by diabetes advancement within the colon; however, 2039 ileal transcripts were altered. Only colonic abundances of Sptlc3, Enpp7, Slc7a15, and Kctd14 had more than twofold changes between D1M and D3M rats. The advancement of diabetes in the UCD‐T2DM rat results in a trophic effect on the mucosal epithelia and was associated with regulation of gastrointestinal tract RNA expression, which appears more pronounced in the ileum relative to the colon.

Microbiome profiles are associated with cognitive functioning in 45-month-old children

Prenatal, perinatal, and postnatal factors have been shown to shape neurobiological functioning and alter the risk for mental disorders later in life. The gut microbiome is established early in life, and interacts with the brain via the brain-immune-gut axis. However, little is known about how the microbiome relates to early-life cognitive functioning in children. The present study, where the fecal microbiome of 380 children was characterized using 16S rDNA and metagenomic sequencing aimed to investigate the association between the microbiota and cognitive functioning of children at the age of 45 months measured with the Wechsler Preschool and Primary Scale of Intelligence (WPPSI-III).Overall the microbiome profile showed a significant association with cognitive functioning. A strong correlation was found between cognitive functioning and the relative abundance of an unidentified genus of the family Enterobacteriaceae. Follow-up mediation analyses revealed significant mediation effects of the level of this genus on the association of maternal smoking during pregnancy and current cigarette smoking with cognitive function. Metagenomic sequencing of a subset of these samples indicated that the identified genus was most closely related to Enterobacter asburiae. Analysis of metabolic potential showed a nominally significant association of cognitive functioning with the microbial norspermidine biosynthesis pathway.Our results indicate that alteration of the gut microflora is associated with cognitive functioning in childhood. Furthermore, they suggest that the altered microflora might interact with other environmental factors such as maternal cigarette smoking. Interventions directed at altering the microbiome should be explored in terms of improving cognitive functioning in young children.

A Subtropical Nudibranch, Polycera hummi (Abbott 1952), Described for the First Time from Virginia

We collected an individual Polycera hummi, a subtropical nudibranch, in association with a green macroalga Ulva sp. from an intertidal oyster reef in Burtons Bay, Wachapreague, VA. The established range of P. hummi is based solely on a handful of records from Mississippi and Florida in the Gulf of Mexico and the Carolinas in the Atlantic Ocean. This finding marks the highest latitude that this species has been found, 350 km north of its previously established range from Mississippi to Beaufort, NC. We observed the individual actively navigate the Ulva thallus which had encrusting bryozoans (unidentified genus) and arborescent bryozoans (Bugula sp.)—likely prey species. We briefly summarize the current knowledge on this rarely encountered nudibranch, provide information on the collection site, including other sea slugs often encountered in this area, note its behavior and interactions with macroalgae and bryozoans, and suggest some fruitful avenues of future work on the evolutionary ecology of rare nudibranch species like P. hummi.

Bacterial Diversity in Rhipicephalus sanguineus (Acari: Ixodidae) from Two States in Nigeria

Abstract Rhipicephalus sanguineus (Latreille) is the most widely distributed tick species globally and plays a major role in tick-borne pathogen transmission among canine populations. The microbial community of this tick has not been characterized previously in Nigeria. Thus, in this study, the bacterial diversity in R. sanguineus collected from two states in Nigeria was explored using 16S rRNA high-throughput sequencing (IonS5TM XL sequencing platform). Three hundred genera (although 18 groups belong to unidentified genera) of bacteria belonging to 22 phyla were detected after pooling and sequencing, indicating a diverse bacterial community profile. At the phylum level, Actinobacteria (47.39%) was the most abundant phylum in the Benue state samples, followed by Proteobacteria (43.87%) and Firmicutes (8.21%), whereas Fusobacteria (38.14%) was the most abundant phylum in Plateau state samples, followed by Bacteroidetes (17.57%) and Firmicutes (17.54%). Proteobacteria accounts for 17% of samples from Plateau state. In general, Cetobacterium (35.86%) was the most abundant genus, followed by an unidentified genus under Corynebacteriaceae (29.94%) and Stenotrophomonas (19.52%). Coxiella spp., one common endosymbiont found in various tick species, was present in R. sanguineus. This study provides a baseline of knowledge of the bacterial microbiome of R. sanguineus in Nigeria. Nonpathogenic bacteria species were prevalent, and not much is known about their role. Thus, their composition, functional, and ecologic implications merit further investigation because this will aid in the subsequent management of ticks and tick-borne diseases.

Molecular Diversity and Distribution of Arbuscular Mycorrhizal Fungi at Different Elevations in Mt. Taibai of Qinling Mountain.

Arbuscular mycorrhizal fungi (AMFs) play a vital role in ecosystems, especially in ecosystem variability, diversity, and function. Understanding the AMF diversity, distribution, and their driver at different altitudinal gradients is a benefit for understanding the ecological function of AMF in mountain ecosystems. In this study, we explored the AMF molecular diversity and their distribution from 660 to 3,500 m a.s.l. in Mount Taibai of Qinling Mountains based on high-throughput sequencing technology. A total of 702 operational taxonomic units (OTUs) in 103 species of AMF are isolated from soil samples, which belong to 18 identified and 1 unidentified genus in 10 families. The fungi in the genus of Glomus is the most dominant, with the occurrence frequency of 100% and the relative abundance of 42.268% and 33.048% on the species and OTU level, respectively. The AMF colonization in root could be simulated by a cubic function with the change of altitudes with the peak and trough at a.s.l. 1,170 and 2,850 m, respectively. Further, AMF diversity indices including Sob, Shannon diversity, and Pielou evenness also showed the same cubic function change trends with increasing altitude at OTU and species levels. However, the average values of diversity indices at OTU level are always higher than these at the species level. Based on the OTU level, the highest and lowest values of Shannon and Pielou indices are observed at the altitudes of 1,400 and 2,800 m, respectively. The pattern of AMF community distribution in Mt. Taibai is driven by altitude with the characteristics of more abundance in the medium- to low-altitude than high-altitude areas. In general, abundant AMF molecular diversity and species exit in different elevations of Mt. Taibai, which indicate gradient changes with elevations.

Diversity and Composition of Gut Bacterial Community in Giant Panda with Anorexia.

The giant panda (GP) is the most precious animal in China. Gastrointestinal tract disease, especially associated with dysbiosis of gut microbiota, is the leading cause of death in GPs. Here, we performed 16S rRNA high-throughput sequencing to investigate the gut microbiota of GPs having symptoms of anorexia. Results showed that gut microbiota of GP with anorexia had lower richness (Chao1 index) than the healthy GP. However, no significant differences in alpha diversity were observed. There is a significance in the microbial structure between anorexia and healthy GPs. The abundance of phylum Firmicutes (99.23% ± 7.1%), unidentified genus Clostridiales (24.75% ± 2.5%), was significantly higher in the subadult anorexia group (P < 0.01), and that of the unidentified genus Clostridiales (4.53% ± 1.2%) was also significantly higher in the adult anorexia group (P < 0.01). Weissella and Streptococcus were found to be decreased in both anorexia groups. The decreased abundance of Weissella (0.02% ± 0.0%, 0.08% ± 0.0%) and Streptococcus (73.89% ± 4.3%, 91.15% ± 7.6%) and increase in Clostridium may cause symptoms of anorexia in giant pandas. The correlation analysis indicated that there is a symbiotic relationship among Streptococcus, Leuconostoc, Weissella, and Bacillus which are classified as probiotics (r > 0.6, P < 0.05). Importantly, a negative correlation has been found between Streptococcus and unidentified_Clostridium in two groups (r > 0.6, P < 0.05). Our results suggested that Streptococcus might be used as probiotics to control the growth of Clostridium causing the anorexia.

Co-exposure to inorganic arsenic and fluoride prominently disrupts gut microbiota equilibrium and induces adverse cardiovascular effects in offspring rats

Co-exposure to inorganic arsenic (iAs) and fluoride (F−) and their collective actions on cardiovascular systems have been recognized as a global public health concern. Emerging studies suggest an association between the perturbation of gut bacterial microbiota and adverse cardiovascular effects (CVEs), both of which are the consequence of iAs and F− exposure in human and experimental animals. The aim of this study was to fill the gap of understanding the relationship among co-exposure to iAs and F−, gut microbiota perturbation, and adverse CVEs. We systematically assessed cardiac morphology and functions (blood pressure, echocardiogram, and electrocardiogram), and generated gut microbiota profiles using 16S rRNA gene sequencing on rats exposed to iAs (50 mg/L NaAsO2), F− (100 mg/L NaF) or combined iAs and F− (50 mg/L NaAsO2 + 100 mg/L NaF), in utero and during early postnatal periods (postnatal day 90). Correlation analysis was then performed to examine relationship between significantly altered microbiota and cardiac performance indices. Our results showed that co-exposure to iAs and F− resulted in more prominent effects in CVEs and perturbation of gut microbiota profiles, compared to iAs or F− treatment alone. Furthermore, nine bacterial genera (Adlercreutzia, Clostridium sensu stricto 1, Coprococcus 3, Romboutsia, [Bacteroides] Pectinophilus group, Lachnospiraceae NC2004 group, Desulfovibrio, and two unidentified genera in Muribaculaceae and Ruminococcaceae family), which differed significantly in relative abundance between control and iAs and F− co-exposure group, were strongly correlated with the higher risk of CVEs (correlation coefficient = 0.70–0.88, p < 0.05). Collectively, these results suggest that co-exposure to iAs and F− poses a higher risk of CVEs, and the part of the mode of action is potentially through inducing gut microbiota disruption, and the strong correlations between them indicate a high potential for the development of novel microbiome-based biomarkers of iAs and/or F− associated CVEs.

An exercise intervention alters stool microbiota and metabolites among older, sedentary adults.

Background:Physiologic aging has been associated with gut dysbiosis. Although short exercise interventions have been linked to beneficial changes in gut microbiota in younger adults, limited data are available from older populations. We hypothesized that exercise would produce beneficial shifts in microbiota and short-chain fatty acid (SCFA) levels in older persons.Methods:Stool samples were collected before and at completion of a supervised 24-week cardiovascular and resistance exercise intervention among 50–75-year-old participants. SCFA levels were analyzed by gas chromatography and microbiome by 16S rRNA gene sequencing. Negative binomial regression models compared pre- and post-differences using false discovery rates for multiple comparison.Results:A total of 22 participants provided pre-intervention samples; 15 provided samples at study completion. At baseline, the majority of participants were men (95%), mean age 58.0 (8.8) years, mean body mass index 27.4 (6.4) kg/m2. After 24 weeks of exercise, at the genus level, exercise was associated with significant increases in Bifidobacterium (and other unidentified genera within Bifidobacteriaceae), Oscillospira, Anaerostipes, and decreased Prevotella and Oribacterium (p < 0.001). Stool butyrate increased with exercise [5.44 (95% confidence interval 1.54, 9.24) mmol/g, p = 0.02], though no significant differences in acetate or propionate (p ⩾ 0.09) were seen.Conclusion:Our pilot study suggested that an exercise intervention is associated with changes in the microbiome of older adults and a key bacterial metabolite, butyrate. Although some of these changes could potentially reverse age-related dysbiosis, future studies are required to determine the contribution of changes to the microbiome in the beneficial effect of exercise on overall health of older adults. Clinical Trials NCT02404792

Interrelationships of Polydolopidae (Mammalia: Marsupialia) from South America and Antarctica

AbstractPolydolopidae is a family of Palaeogene marsupials recorded from outcrops in southern South America and the Antarctic Peninsula. They are mostly represented by skull fragments or maxillary, dentary and molar remains. A taxonomic and systematic revision is carried out with the inclusion of a phylogenetic analysis encompassing almost every polydolopid species and five marsupial species found to be related to them in previous analyses (Bonapartherium hinakusijum, Epidolops ameghinoi, Microbiotherium tehuelchum, Prepidolops didelphoides and Roberthoffstetteria nationalgeographica). The Polydolopidae was recovered as a monophyletic group, even though no resolution about its sister-group can be found. The following genera are recovered: Antarctodolops, Amphidolops, Archaeodolops, Eudolops, Hypodolops gen. nov., Kramadolops, Pliodolops, Pseudolops and two unidentified genera (Gen. et sp. indet 1 and 2). One genus and three new species are recognized. The family appeared at the beginning of the Palaeocene and disappeared during the Early Oligocene. The extinction of the group could be related to climatic deterioration in the Early Oligocene, when temperature and the humidity dropped, provoking desertification in the region where Polydolopids evolved.

Long-term effects of mixed planting on arbuscular mycorrhizal fungal communities in the roots and soils of Juglans mandshurica plantations

BackgroundEstablishing mixed plantations is an effective way to improve soil fertility and increase forest productivity. Arbuscular mycorrhizal (AM) fungi are obligate symbiotic fungi that can promote mineral nutrient absorption and regulate intraspecific and interspecific competition in plants. However, the effects of mixed plantations on the community structure and abundance of AM fungi are still unclear. Illumina MiSeq sequencing was used to investigate the AM fungal community in the roots and soils of pure and mixed plantations (Juglans mandshurica × Larix gmelinii). The objective of this study is to compare the differential responses of the root and rhizosphere soil AM fungal communities of Juglans mandshurica to long-term mixed plantation management.ResultsGlomus and Paraglomus were the dominant genera in the root samples, accounting for more than 80% of the sequences. Compared with that in the pure plantation, the relative abundance of Glomus was higher in the mixed plantation. Glomus, Diversispora and Paraglomus accounted for more than 85% of the sequences in the soil samples. The relative abundances of Diversispora and an unidentified genus of Glomeromycetes were higher and lower in the pure plantation, respectively. The Root_P samples (the roots in the pure plantation) had the highest number of unique OTUs (operational taxonomic units), which belonged mainly to an unidentified genus of Glomeromycetes, Paraglomus, Glomus and Acaulospora. The number of unique OTUs detected in the soil was lower than that in the roots. In both the root and soil samples, the forest type did not have a significant effect on AM fungal diversity, but the Sobs value and the Shannon, Chao1 and Ace indices of AM fungi in the roots were significantly higher than those in the soil.ConclusionsMixed forest management had little effect on the AM fungal community of Juglans mandshurica roots and significantly changed the community composition of the soil AM fungi, but not the diversity.

In ovo Administration of Defined Lactic Acid Bacteria Previously Isolated From Adult Hens Induced Variations in the Cecae Microbiota Structure and Enterobacteriaceae Colonization on a Virulent Escherichia coli Horizontal Infection Model in Broiler Chickens

The effects of in ovo administration of a defined lactic acid microbiota (LAM), previously isolated from adult hens, in the cecae microbiota structure and Enterobacteriaceae colonization after exposure to virulent Escherichia coli during the hatching phase of broiler chickens were evaluated. Embryos inoculated with LAM showed a significant (P < 0.05) reduction of Enterobacteriaceae colonization at day-of-hatch (DOH) and day (d) 7. Furthermore, there was a significant increase in total lactic acid bacteria on DOH, body weight (BW) DOH, BW d7, and d0–d7 BW gain and reduced mortality d0–d7 was observed in the LAM group compared with that in phosphate-buffered saline (PBS) control. The bacterial composition at the family level revealed that the Enterobacteriaceae was numerically reduced, whereas the Ruminococcaceae was significantly increased in the LAM group when compared with that in the PBS control. Moreover, the bacterial genera Proteus and Butyricicoccus and unidentified bacterial genera of family Lachnospiraceae and Erysipelotrichaceae were significantly enriched in the LAM group. In contrast, the Clostridium of the family Peptostreptococcaceae and unidentified genus of family Enterobacteriaceae were significantly abundant in the PBS control group. In summary, in ovo administration of a defined LAM isolated from adult hens did not affect hatchability, improved body weight gain and reduced mortality at d7, induced variations in the cecae microbiota structure and reduced Enterobacteriaceae colonization on a virulent E. coli horizontal infection model in broiler chickens.

Analysis of bacterial community structure and diversity during mountain-agarwood formation

As an important substitute for agarwood, mountain-agarwood, belonging to the family Oleaceae, comes from the root, stem and thick branch of Syringa pinnatifolia, which has a wide range of application in Inner Mongolia, China. It has good clinical efficacy in the use of cardiovascular diseases. However, the formation speed of mountain-agarwood is extremely slow, and its cultivated seedlings have low resin content. Therefore, how to speed up the formation of mountain-agarwood and increase the resin content is a hot research topic in this field. In this work, 16 S rDNA amplicon sequencing method was used to systematically analyze the bacterial communities of different samples of mountain-agarwood. Our data revealed that the samples of mountain-agarwood had more obvious species diversity than the ones of non-mountain-agarwood, especially the wild mountain-agarwood samples. By analysis of bacterial community composition and species abundance, Sphingomonas, Modestobacter and unidentified Cyanobacteria genus were three dominant bacterial genera in all samples. In addition, there are two identified genera of dominant bacteria, namely Actinoplanes and Microbacterium in both wild and cultivated mountain-agarwood, by bacterial community composition and species richness analysis. Meanwhile, Roseomonas was the dominant bacterial genus in both wild and cultivated non-mountain-agarwood samples. Our work could provides basic data for exploring the mechanism of the mountain-agarwood formation, and help to exploit resource of endophytic bacteria reasonably.

Neonatal diet alters fecal microbiota and metabolome profiles at different ages in infants fed breast milk or formula

Neonatal diet has a large influence on child health and might modulate changes in fecal microbiota and metabolites. The aim is to investigate fecal microbiota and metabolites at different ages in infants who were breastfed (BF), received dairy-based milk formula (MF), or received soy-based formula (SF). Fecal samples were collected at 3 (n=16, 12, and 14, respectively), 6 (n=20, 19, and 15, respectively), 9 (n=12, 11, and 12, respectively), and 12 mo (n=14, 14, and 15, respectively) for BF, MF, and SF infants. Infants that breastfed until 9 mo and switched to formula were considered as no longer breastfeeding at 12 mo. Microbiota data were obtained using 16S ribosomal RNA sequencing. Untargeted metabolomics was conducted using a Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer. The data were analyzed using R (version 3.6.0) within the RStudio (version 1.1.463) platform. At 3, 6, and 9 mo of age BF infants had the lowest α-diversity, SF infants had the highest diversity, and MF was intermediate. Bifidobacterium was 2.6- to 5-fold lower in SF relative to BF infants through 1 y of life. An unidentified genus from Ruminococcaceae higher in the SF (2%) than in the MF (0.4%) and BF (0.08%) infants at 3 mo of age was observed. In BF infants higher levels of butyric acid, d-sphingosine, kynurenic acid, indole-3-lactic acid, indole-3-acetic acid, and betaine were observed than in MF and SF infants. At 3 mo Ruminococcaceae was positively correlated to azelaic, gentisic, isocitric, sebacic, and syringic acids. At 6 mo Oscillospira was negatively correlated with 3-hydroxybutyric-acid, hydroxy-hydrocinnamic acid, and betaine whereas Bifidobacterium was negatively associated with 5-hydroxytryptamine. At 12 mo of age, Lachnospiraceae was negatively associated with hydroxyphenyllactic acid. Infant diet has a large impact on the fecal microbiome and metabolome in the first year of life.This study was registered at clinicaltrials.gov as NCT00616395.

Diversity of Chironomidae (Insecta: Diptera) genera in Taleghan River, Alborz province, Iran.

Chironomidae is one of the most important elements of the aquatic benthos all over the world, which has its own ecological and biological importance in different aspects. The present study has been conducted to investigate the chironomid diversity in Taleghan River in two seasons, spring and summer 2016 for six sampling points (Asfaran, Varkesh, Mir, Jostan, Barikan and Gooran). The sampling procedure was done by applying a simple dredge in five replications for each sampling point. The results have showed that there was a great diversity of Chironomidae in Taleghan River which composed of four sub-families and 21 different genera; Chironominae (Chironomus, Robackia, Stenochironomus, Omisus, Cryptochironomus, Saetheria, Cryptotendipes, Microtendipes, Paratendipes, Constempellina and Neozavrelia),Orthocladiinae (Bryophaenocladius, Comptocladius, Echinocladius, Smittia, Botryocladius, Symbiocladius, Psectrocladius and Gymnometriocnemus), Tanypodinae (unidentified genera in Pentaneurini tribe) and Diamesinae (Potthastia and Diamesa). Ten genera have been reported for the first time in Iran. Diversity on abundance of each genus in different months and sampling points might be the result of the environmental conditions and water pollution.