**2. Conclusion**

and next-generation-sequencing (NGS) technologies in the last decade has pushed the gut

The infant microbiota is highly dynamic and susceptible to antibiotics [58]. The disruption of microbiota at such stage could have significant ill effects throughout life by interfering with the metabolic and immune system [59]. The infant microbiota development is linked to various factors such as the host genetic makeup, nutrition, and environment [60–62]. The microbiota of a new born baby, even without antibiotic treatment, harbors a diverse resistance gene in their resistome [63, 64]. However, antibiotic treatments increase the abundance of pathogenic *Enterobacteriaceae* and lower healthy microbiota such as *Bifidobacteriaceae*, *Bacilli*, and *Lactobacillales* spp. [59, 65–67]. It is believed that the *Lactobacillus* and *Bifidobacterium* spp. are originated from maternal microbiome which is an essential component for the development of infant gut microbiome [62, 68]. The treatment of *L. acidophilus* and *Bifidobacterium* as probiotics in low birthweight infants increases the daily weight gain and recedes morbidity [69, 70], possibly by promoting the healthy gut microbiome and intestinal epithelial layer [58, 71]. The two modes of delivery, vaginally and C-section, can also distinctly affect an infant's microbiota in the first year after delivery. Vaginally delivered infants harbor comparatively higher resemblance to mother's microbiota [72]. Microbes such as *Bacteroides* and *Bifidobacterium* are less frequent in C-section-delivered infants; however, an increased frequency of bacteria is associated to oral and skin [73]. Studies have also found that the microbiota of a 2-month infant and their mother shares distinction in resistome which includes broad-spectrum beta-lactam antibiotics to be found only in the infants [74]. In fact, comparison between infant and their mother to an unrelated infant showed no significant difference [74]. It is proposed that the host genetic makeup and the environmental factors could play a role in the shaping resistome [74]. Infant microbiota shapes into an adult-like by increasing the alpha diversity while reducing the beta diversity which continues until the age of 3 [60]. Maturation of the infant microbiota is also driven by the feeding habit. The addition of solid food does not induce the maturation of microbiota significantly. However, cessation of breastfeeding enriches the gut microbiota to adult-like [72]. Infants with breastfeeding are enriched by *Bifidobacterium and Lactobacillus* even at the age of 1 while infants who no longer breastfeed are enriched with *Roseburia*, *Clostridium*, and *Anaerostipes,* which are prevalent in adults. Functionally, polysaccharide-degrading genes are enriched only after the cessation of breastfeeding [72]. The microbiota also acquires significant essential amino acids, irons, and vitamins genes after 4 months, which are essential for normal brain development [9, 75]. Functional metagenomics from healthy infants and children isolated three novel ARGs and also demonstrated that the ARG in gut resistome is

microbiota research into full swing [20].

significantly higher than previously estimated [64, 76].

Large-scale metagenomic study of 252 fecal metagenomes samples identified 50 antibiotic classes [42]. Tetracycline resistance gene, tetQ, is the most abundant resistance gene in fecal samples of Chinese, Danish, and Spanish individuals. In fact, tetracycline resistance genes

*1.4.2. The adult gut resistome*

*1.4.1. The infants' gut resistome*

8 Metagenomics for Gut Microbes

Gut microbiome is an essential "organ" without which the host would be deprived of various benefits derived from the numerous gut microbes. The benefits range from food metabolism to the mental health of the host. Hence, it requires attention as much as any other organ in our body. Various studies have, however, noticed the dynamic nature in the compositing and diversity of the gut microbiome making it one of the most dynamic "organs" in us. In addition, the wide application of antibiotic treatment for human as well as animals has enriched the gut ARGs. Hence, strict polices has to be implemented in order to maintain a moderate antibiotics usage. In addition, the surge in ARGs is a clear indication that the research on antibiotic alternative is a necessity for the coming future.
